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Surovy MZ, Dutta S, Mahmud NU, Gupta DR, Farhana T, Paul SK, Win J, Dunlap C, Oliva R, Rahman M, Sharpe AG, Islam T. Biological control potential of worrisome wheat blast disease by the seed endophytic bacilli. Front Microbiol 2024; 15:1336515. [PMID: 38529179 PMCID: PMC10961374 DOI: 10.3389/fmicb.2024.1336515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
Crop production often faces challenges from plant diseases, and biological control emerges as an effective, environmentally friendly, cost-effective, and sustainable alternative to chemical control. Wheat blast disease caused by fungal pathogen Magnaporthe oryzae Triticum (MoT), is a potential catastrophic threat to global food security. This study aimed to identify potential bacterial isolates from rice and wheat seeds with inhibitory effects against MoT. In dual culture and seedling assays, three bacterial isolates (BTS-3, BTS-4, and BTLK6A) demonstrated effective suppression of MoT growth and reduced wheat blast severity when artificially inoculated at the seedling stage. Genome phylogeny identified these isolates as Bacillus subtilis (BTS-3) and B. velezensis (BTS-4 and BTLK6A). Whole-genome analysis revealed the presence of genes responsible for controlling MoT through antimicrobial defense, antioxidant defense, cell wall degradation, and induced systemic resistance (ISR). Taken together, our results suggest that the suppression of wheat blast disease by seed endophytic B. subtilis (BTS-3) and B. velezensis (BTS-4 and BTLK6A) is liked with antibiosis and induced systemic resistance to wheat plants. A further field validation is needed before recommending these endophytic bacteria for biological control of wheat blast.
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Affiliation(s)
- Musrat Zahan Surovy
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Sudipta Dutta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Nur Uddin Mahmud
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Tarin Farhana
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Sanjay Kumar Paul
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Joe Win
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Christopher Dunlap
- Crop Bioprotection Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture (USDA), Peoria, IL, United States
| | | | - Mahfuzur Rahman
- W.V.U. Extension Service, West Virginia University, Morgantown, WV, United States
| | | | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
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Chaudhary R, Higgins EE, Eynck C, Sharpe AG, Parkin IAP. Mapping QTL for vernalization requirement identified adaptive divergence of the candidate gene Flowering Locus C in polyploid Camelina sativa. Plant Genome 2023; 16:e20397. [PMID: 37885362 DOI: 10.1002/tpg2.20397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
Vernalization requirement is an integral component of flowering in winter-type plants. The availability of winter ecotypes among Camelina species facilitated the mapping of quantitative trait loci (QTL) for vernalization requirement in Camelina sativa. An inter and intraspecific crossing scheme between related Camelina species, where one spring and two different sources of winter-type habit were used, resulted in the development of two segregating populations. Linkage maps generated with sequence-based markers identified three QTLs associated with vernalization requirement in C. sativa; two from the interspecific (chromosomes 13 and 20) and one from the intraspecific cross (chromosome 8). Notably, the three loci were mapped to different homologous regions of the hexaploid C. sativa genome. All three QTLs were found in proximity to Flowering Locus C (FLC), variants of which have been reported to affect the vernalization requirement in plants. Temporal transcriptome analysis for winter-type Camelina alyssum demonstrated reduction in expression of FLC on chromosomes 13 and 20 during cold treatment, which would trigger flowering, since FLC would be expected to suppress floral initiation. FLC on chromosome 8 also showed reduced expression in the C. sativa ssp. pilosa winter parent upon cold treatment, but was expressed at very high levels across all time points in the spring-type C. sativa. The chromosome 8 copy carried a deletion in the spring-type line, which could impact its functionality. Contrary to previous reports, all three FLC loci can contribute to controlling the vernalization response in C. sativa and provide opportunities for manipulating this requirement in the crop.
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Affiliation(s)
- Raju Chaudhary
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
- Global Institute for Food Security, Saskatoon, Saskatchewan, Canada
| | - Erin E Higgins
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Christina Eynck
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security, Saskatoon, Saskatchewan, Canada
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Islam T, Fatema, Hoque MN, Gupta DR, Mahmud NU, Sakif TI, Sharpe AG. Improvement of growth, yield and associated bacteriome of rice by the application of probiotic Paraburkholderia and Delftia. Front Microbiol 2023; 14:1212505. [PMID: 37520368 PMCID: PMC10375411 DOI: 10.3389/fmicb.2023.1212505] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Plant probiotic bacteria enhance growth and yield of crop plants when applied at the appropriate time and dose. Two rice probiotic bacteria, Paraburkholderia fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 promote growth and yield of plants. However, no information is available on application of these two bacteria on growth, yield, and diversity and population of bacteriome in roots and rhizosphere soils of the treated rice plants. This study aimed to assess the effect of BRRh-4 and BTL-M2 application on growth, yield and bacteriome in roots and rhizosphere soil of rice under varying doses of N, P and K fertilizers. Application of BRRh-4 and BTL-M2 strains significantly (p < 0.05) increased seed germination, growth and yield of rice compared to an untreated control. Interestingly, the grain yield of rice by these bacteria with 50% less of the recommended doses of N, P, and K fertilizers were statistically similar to or better than the rice plants treated with 100% doses of these fertilizers. Targeted amplicon (16S rRNA) sequence-based analysis revealed significant differences (PERMANOVA, p = 0.00035) in alpha-diversity between the root (R) and rhizosphere soil (S) samples, showing higher diversity in the microbial ecosystem of root samples. Additionally, the bacteriome diversity in the root of rice plants that received both probiotic bacteria and chemical fertilizers were significantly higher (PERMANOVA, p = 0.0312) compared to the rice plants treated with fertilizers only. Out of 185 bacterial genera detected, Prevotella, an anaerobic and Gram-negative bacterium, was found to be the predominant genus in both rhizosphere soil and root metagenomes. However, the relative abundance of Prevotella remained two-fold higher in the rhizosphere soil metagenome (52.02%) than in the root metagenome (25.04%). The other predominant bacterial genera detected in the rice root metagenome were Bacillus (11.07%), Planctomyces (4.06%), Faecalibacterium (3.91%), Deinococcus (2.97%), Bacteroides (2.61%), and Chryseobacterium (2.30%). On the other hand, rhizosphere soil metagenome had Bacteroides (12.38%), Faecalibacterium (9.50%), Vibrio (5.94%), Roseomonas (3.40%), and Delftia (3.02%). Interestingly, we found the presence and/or abundance of specific genera of bacteria in rice associated with the application of a specific probiotic bacterium. Taken together, our results indicate that improvement of growth and yield of rice by P. fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 is likely linked with modulation of diversity, structures, and signature of bacteriome in roots and rhizosphere soils. This study for the first time demonstrated that application of plant growth promoting bacteria significantly improve growth, yield and increase the diversity of bacterial community in rice.
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Affiliation(s)
- Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Fatema
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, BSMRAU, Gazipur, Bangladesh
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nur Uddin Mahmud
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Tahsin Islam Sakif
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, United States
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
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Jiang Y, N'Diaye A, Koh CS, Quilichini TD, Shunmugam ASK, Kirzinger MW, Konkin D, Bekkaoui Y, Sari E, Pasha A, Esteban E, Provart NJ, Higgins JD, Rozwadowski K, Sharpe AG, Pozniak CJ, Kagale S. The coordinated regulation of early meiotic stages is dominated by non-coding RNAs and stage-specific transcription in wheat. Plant J 2023; 114:209-224. [PMID: 36710629 DOI: 10.1111/tpj.16125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Reproductive success hinges on precisely coordinated meiosis, yet our understanding of how structural rearrangements of chromatin and phase transitions during meiosis are transcriptionally regulated is limited. In crop plants, detailed analysis of the meiotic transcriptome could identify regulatory genes and epigenetic regulators that can be targeted to increase recombination rates and broaden genetic variation, as well as provide a resource for comparison among eukaryotes of different taxa to answer outstanding questions about meiosis. We conducted a meiotic stage-specific analysis of messenger RNA (mRNA), small non-coding RNA (sncRNA), and long intervening/intergenic non-coding RNA (lincRNA) in wheat (Triticum aestivum L.) and revealed novel mechanisms of meiotic transcriptional regulation and meiosis-specific transcripts. Amidst general repression of mRNA expression, significant enrichment of ncRNAs was identified during prophase I relative to vegetative cells. The core meiotic transcriptome was comprised of 9309 meiosis-specific transcripts, 48 134 previously unannotated meiotic transcripts, and many known and novel ncRNAs differentially expressed at specific stages. The abundant meiotic sncRNAs controlled the reprogramming of central metabolic pathways by targeting genes involved in photosynthesis, glycolysis, hormone biosynthesis, and cellular homeostasis, and lincRNAs enhanced the expression of nearby genes. Alternative splicing was not evident in this polyploid species, but isoforms were switched at phase transitions. The novel, stage-specific regulatory controls uncovered here challenge the conventional understanding of this crucial biological process and provide a new resource of requisite knowledge for those aiming to directly modulate meiosis to improve crop plants. The wheat meiosis transcriptome dataset can be queried for genes of interest using an eFP browser located at https://bar.utoronto.ca/efp_wheat/cgi-bin/efpWeb.cgi?dataSource=Wheat_Meiosis.
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Affiliation(s)
- Yunfei Jiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Amidou N'Diaye
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Chu Shin Koh
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Rd., Saskatoon, SK, S7N 4L8, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Arun S K Shunmugam
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Morgan W Kirzinger
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yasmina Bekkaoui
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Ehsan Sari
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Adrian Building, University Road, Leicester, Leicestershire, LE1 7RH, UK
| | - Kevin Rozwadowski
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Pl., Saskatoon, SK, S7N 0X2, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Rd., Saskatoon, SK, S7N 4L8, Canada
| | - Curtis J Pozniak
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
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5
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Chaudhary R, Koh CS, Perumal S, Jin L, Higgins EE, Kagale S, Smith MA, Sharpe AG, Parkin IAP. Sequencing of Camelina neglecta, a diploid progenitor of the hexaploid oilseed Camelina sativa. Plant Biotechnol J 2023; 21:521-535. [PMID: 36398722 PMCID: PMC9946149 DOI: 10.1111/pbi.13968] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/26/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Camelina neglecta is a diploid species from the genus Camelina, which includes the versatile oilseed Camelina sativa. These species are closely related to Arabidopsis thaliana and the economically important Brassica crop species, making this genus a useful platform to dissect traits of agronomic importance while providing a tool to study the evolution of polyploids. A highly contiguous chromosome-level genome sequence of C. neglecta with an N50 size of 29.1 Mb was generated utilizing Pacific Biosciences (PacBio, Menlo Park, CA) long-read sequencing followed by chromosome conformation phasing. Comparison of the genome with that of C. sativa shows remarkable coincidence with subgenome 1 of the hexaploid, with only one major chromosomal rearrangement separating the two. Synonymous substitution rate analysis of the predicted 34 061 genes suggested subgenome 1 of C. sativa directly descended from C. neglecta around 1.2 mya. Higher functional divergence of genes in the hexaploid as evidenced by the greater number of unique orthogroups, and differential composition of resistant gene analogs, might suggest an immediate adaptation strategy after genome merger. The absence of genome bias in gene fractionation among the subgenomes of C. sativa in comparison with C. neglecta, and the complete lack of fractionation of meiosis-specific genes attests to the neopolyploid status of C. sativa. The assembled genome will provide a tool to further study genome evolution processes in the Camelina genus and potentially allow for the identification and exploitation of novel variation for Camelina crop improvement.
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Affiliation(s)
- Raju Chaudhary
- Agriculture and Agri‐Food CanadaSaskatoonSKCanada
- Global Institute for Food SecuritySaskatoonSKCanada
| | - Chu Shin Koh
- Global Institute for Food SecuritySaskatoonSKCanada
| | | | - Lingling Jin
- Department of Computer ScienceUniversity of SaskatchewanSaskatoonSKCanada
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Islam T, Afroz N, Koh C, Hoque MN, Rahman MJ, Gupta DR, Mahmud NU, Nahid AA, Islam R, Bhowmik PK, Sharpe AG. Whole-genome sequencing of a year-round fruiting jackfruit ( Artocarpus heterophyllus Lam.) reveals high levels of single nucleotide variation. Front Plant Sci 2022; 13:1044420. [PMID: 36605965 PMCID: PMC9809283 DOI: 10.3389/fpls.2022.1044420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Jackfruit (Artocarpus heterophyllus Lam.) is the national fruit of Bangladesh and produces fruit in the summer season only. However, jackfruit is not commercially grown in Bangladesh because of an extremely high variation in fruit quality, short seasonal fruiting (June-August) and susceptibility to abiotic stresses. Conversely, a year-round high yielding (ca. 4-fold higher than the seasonal variety) jackfruit variety, BARI Kanthal-3 developed by the Bangladesh Agricultural Research Institute (BARI) derived from a wild accession found in Ramgarh of Chattogram Hiltracts of Bangladesh, provides fruits from September to June. This study aimed to generate a draft whole-genome sequence (WGS) of BARI Kanthal-3 to obtain molecular insights including genes associated with year-round fruiting trait of this important unique variety. The estimated genome size of BARI Kanthal-3 was 1.04-gigabase-pair (Gbp) with a heterozygosity rate of 1.62%. De novo assembly yielded a scaffolded 817.7 Mb genome while a reference-guided approach, yielded 843 Mb of genome sequence. The estimated GC content was 34.10%. Variant analysis revealed that BARI Kanthal-3 included 5.7 M (35%) and 10.4 M (65%) simple and heterozygous single nucleotide polymorphisms (SNPs), and about 90% of all these polymorphisms are in inter-genic regions. Through BUSCO assessment, 97.2% of the core genes were represented in the assembly with 1.3% and 1.5% either fragmented or missing, respectively. By comparing identified orthologous gene groups in BARI Kanthal-3 with five closely and one distantly related species of 10,092 common orthogroups were found across the genomes of the six species. The phylogenetic analysis of the shared orthogroups showed that A. heterophyllus was the closest species to BARI Kanthal-3 and orthogroups related to flowering time were found to be more highly prevalent in BARI Kanthal-3 compared to the other Arctocarpus spp. The findings of this study will help better understanding the evolution, domestication, phylogenetic relationships, year-round fruiting of this highly nutritious fruit crop as well as providing a resource for molecular breeding.
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Affiliation(s)
- Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nadia Afroz
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - ChuShin Koh
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Md. Jillur Rahman
- Pomology Division, Horticultural Research Center, Bangladesh Agricultural Research Institute, Gazipur, Bangladesh
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nur Uddin Mahmud
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Abdullah Al Nahid
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Rashedul Islam
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Pankaj K. Bhowmik
- Cell Technologies and Trait Development, National Research Council of Canada, Saskatoon, SK, Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
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Ubbens J, Feldmann MJ, Stavness I, Sharpe AG. Quantitative evaluation of nonlinear methods for population structure visualization and inference. G3 Genes|Genomes|Genetics 2022; 12:6651067. [PMID: 35900169 PMCID: PMC9434256 DOI: 10.1093/g3journal/jkac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/20/2022] [Indexed: 11/20/2022]
Abstract
Population structure (also called genetic structure and population stratification) is the presence of a systematic difference in allele frequencies between subpopulations in a population as a result of nonrandom mating between individuals. It can be informative of genetic ancestry, and in the context of medical genetics, it is an important confounding variable in genome-wide association studies. Recently, many nonlinear dimensionality reduction techniques have been proposed for the population structure visualization task. However, an objective comparison of these techniques has so far been missing from the literature. In this article, we discuss the previously proposed nonlinear techniques and some of their potential weaknesses. We then propose a novel quantitative evaluation methodology for comparing these nonlinear techniques, based on populations for which pedigree is known a priori either through artificial selection or simulation. Based on this evaluation metric, we find graph-based algorithms such as t-SNE and UMAP to be superior to principal component analysis, while neural network-based methods fall behind.
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Affiliation(s)
- Jordan Ubbens
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SKS7N 0W9, Canada
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California , Davis, CA95616, USA
| | - Ian Stavness
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SKS7N 0W9, Canada
- Department of Computer Science, University of Saskatchewan , Saskatoon, SKS7N 0W9, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SKS7N 0W9, Canada
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8
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Buchwaldt L, Garg H, Puri KD, Durkin J, Adam J, Harrington M, Liabeuf D, Davies A, Hegedus DD, Sharpe AG, Gali KK. Sources of genomic diversity in the self-fertile plant pathogen, Sclerotinia sclerotiorum, and consequences for resistance breeding. PLoS One 2022; 17:e0262891. [PMID: 35130285 PMCID: PMC8820597 DOI: 10.1371/journal.pone.0262891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/09/2022] [Indexed: 11/18/2022] Open
Abstract
The ascomycete, Sclerotinia sclerotiorum, has a broad host range and causes yield loss in dicotyledonous crops world wide. Genomic diversity was determined in a population of 127 isolates obtained from individual canola (Brassica napus) fields in western Canada. Genotyping with 39 simple sequence repeat (SSR) markers revealed each isolate was a unique haplotype. Analysis of molecular variance showed 97% was due to isolate and 3% due to geographical location. Testing of mycelium compatibility among 133 isolates identified clones of mutually compatible isolates with 86–95% similar SSR haplotype, whereas incompatible isolates were highly diverse. In the Province of Manitoba, 61% of isolates were compatible forming clones and stings of pairwise compatible isolates not described before. In contrast, only 35% of isolates were compatible in Alberta without forming clones and strings, while 39% were compatible in Saskatchewan with a single clone, but no strings. These difference can be explained by wetter growing seasons and more susceptible crop species in Manitoba favouring frequent mycelium interaction and more life cycles over time, which might also explain similar differences observed in other geographical areas and host crops. Analysis of linkage disequilibrium rejected random recombination, consistent with a self-fertile fungus, restricted outcrossing due to mycelium incompatibility, and only a single annual opportunity for genomic recombination during meiosis in the ascospore stage between non-sister chromatids in the rare event nuclei from different isolates come together. More probable sources of genomic diversity is slippage during DNA replication and point mutation affecting single nucleotides that accumulate and likely increase mycelium incompatibility in a population over time. A phylogenetic tree based on SSR haplotype grouped isolates into 17 sub-populations. Aggressiveness was tested by inoculating one isolate from each sub-population onto B. napus lines with quantitative resistance. Analysis of variance was significant for isolate, line, and isolate by line interaction. These isolates represent the genomic and pathogenic diversity in western Canada, and are suitable for resistance screening in canola breeding programs.
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Affiliation(s)
- Lone Buchwaldt
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Canada
- * E-mail:
| | - Harsh Garg
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Canada
| | - Krishna D. Puri
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Canada
| | - Jonathan Durkin
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Canada
| | - Jennifer Adam
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Canada
| | - Myrtle Harrington
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Canada
| | - Debora Liabeuf
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Canada
| | - Alan Davies
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Canada
| | - Dwayne D. Hegedus
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
| | - Krishna Kishore Gali
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, Canada
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9
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Ubbens J, Parkin I, Eynck C, Stavness I, Sharpe AG. Deep neural networks for genomic prediction do not estimate marker effects. Plant Genome 2021; 14:e20147. [PMID: 34596363 DOI: 10.1002/tpg2.20147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Genomic prediction is a promising technology for advancing both plant and animal breeding, with many different prediction models evaluated in the literature. It has been suggested that the ability of powerful nonlinear models, such as deep neural networks, to capture complex epistatic effects between markers offers advantages for genomic prediction. However, these methods tend not to outperform classical linear methods, leaving it an open question why this capacity to model nonlinear effects does not seem to result in better predictive capability. In this work, we propose the theory that, because of a previously described principle called shortcut learning, deep neural networks tend to base their predictions on overall genetic relatedness rather than on the effects of particular markers such as epistatic effects. Using several datasets of crop plants [lentil (Lens culinaris Medik.), wheat (Triticum aestivum L.), and Brassica carinata A. Braun], we demonstrate the network's indifference to the values of the markers by showing that the same network, provided with only the locations of matches between markers for two individuals, is able to perform prediction to the same level of accuracy.
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Affiliation(s)
- Jordan Ubbens
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada
| | - Isobel Parkin
- Agriculture and Agri-Food Canada, Saskatoon, SK, S7N 0X2, Canada
| | - Christina Eynck
- Agriculture and Agri-Food Canada, Saskatoon, SK, S7N 0X2, Canada
| | - Ian Stavness
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada
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10
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Gao P, Quilichini TD, Zhai C, Qin L, Nilsen KT, Li Q, Sharpe AG, Kochian LV, Zou J, Reddy AS, Wei Y, Pozniak C, Patterson N, Gillmor CS, Datla R, Xiang D. Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species. Plant Biotechnol J 2021; 19:1624-1643. [PMID: 33706417 PMCID: PMC8384600 DOI: 10.1111/pbi.13579] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 05/07/2023]
Abstract
Among polyploid species with complex genomic architecture, variations in the regulation of alternative splicing (AS) provide opportunities for transcriptional and proteomic plasticity and the potential for generating trait diversities. However, the evolution of AS and its influence on grain development in diploid grass and valuable polyploid wheat crops are poorly understood. To address this knowledge gap, we developed a pipeline for the analysis of alternatively spliced transcript isoforms, which takes the high sequence similarity among polyploid wheat subgenomes into account. Through analysis of synteny and detection of collinearity of homoeologous subgenomes, conserved and specific AS events across five wheat and grass species were identified. A global analysis of the regulation of AS in diploid grass and polyploid wheat grains revealed diversity in AS events not only between the endosperm, pericarp and embryo overdevelopment, but also between subgenomes. Analysis of AS in homoeologous triads of polyploid wheats revealed evolutionary divergence between gene-level and transcript-level regulation of embryogenesis. Evolutionary age analysis indicated that the generation of novel transcript isoforms has occurred in young genes at a more rapid rate than in ancient genes. These findings, together with the development of comprehensive AS resources for wheat and grass species, advance understanding of the evolution of regulatory features of AS during embryogenesis and grain development in wheat.
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Affiliation(s)
- Peng Gao
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Teagen D. Quilichini
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
| | - Chun Zhai
- Agriculture and Agri‐Food CanadaSaskatoon Research and Development CentreSaskatoonSKCanada
| | - Li Qin
- College of Art & ScienceUniversity of SaskatchewanSaskatoonSKCanada
| | - Kirby T. Nilsen
- Agriculture and Agri‐Food CanadaBrandon Research and Development CentreBrandonMBCanada
| | - Qiang Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Andrew G. Sharpe
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Leon V. Kochian
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Jitao Zou
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
| | - Anireddy S.N. Reddy
- Department of Biology and Program in Cell and Molecular BiologyColorado State UniversityFort CollinsCOUSA
| | - Yangdou Wei
- College of Art & ScienceUniversity of SaskatchewanSaskatoonSKCanada
| | - Curtis Pozniak
- Crop Development CentreUniversity of SaskatchewanSaskatoonSKCanada
| | - Nii Patterson
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
| | - C. Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)Unidad de Genómica AvanzadaCentro de Investigación y Estudios Avanzados del IPN (CINVESTAV‐IPN)IrapuatoGuanajuatoMexico
| | - Raju Datla
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Daoquan Xiang
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
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11
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Mascher M, Wicker T, Jenkins J, Plott C, Lux T, Koh CS, Ens J, Gundlach H, Boston LB, Tulpová Z, Holden S, Hernández-Pinzón I, Scholz U, Mayer KFX, Spannagl M, Pozniak CJ, Sharpe AG, Šimková H, Moscou MJ, Grimwood J, Schmutz J, Stein N. Long-read sequence assembly: a technical evaluation in barley. Plant Cell 2021; 33:1888-1906. [PMID: 33710295 PMCID: PMC8290290 DOI: 10.1093/plcell/koab077] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/28/2021] [Indexed: 05/19/2023]
Abstract
Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even five-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland 06466, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig 04103, Germany
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zürich 8008, Switzerland
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | | | - Thomas Lux
- PGSB–Plant Genome and Systems Biology, Helmholtz Center Munich–German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Chu Shin Koh
- Global Institute for Food Security, University of Saskatchewan, Saskatoon SK S7N 4L8, Canada
| | - Jennifer Ens
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon SK S7N 5A8, Canada
| | - Heidrun Gundlach
- PGSB–Plant Genome and Systems Biology, Helmholtz Center Munich–German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Lori B Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Zuzana Tulpová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Samuel Holden
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
| | | | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland 06466, Germany
| | - Klaus F X Mayer
- PGSB–Plant Genome and Systems Biology, Helmholtz Center Munich–German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Manuel Spannagl
- PGSB–Plant Genome and Systems Biology, Helmholtz Center Munich–German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Curtis J Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon SK S7N 5A8, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon SK S7N 4L8, Canada
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland 06466, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen 37073, Germany
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12
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Perumal S, Koh CS, Jin L, Buchwaldt M, Higgins EE, Zheng C, Sankoff D, Robinson SJ, Kagale S, Navabi ZK, Tang L, Horner KN, He Z, Bancroft I, Chalhoub B, Sharpe AG, Parkin IAP. A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome. Nat Plants 2020; 6:929-941. [PMID: 32782408 PMCID: PMC7419231 DOI: 10.1038/s41477-020-0735-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/28/2020] [Indexed: 05/19/2023]
Abstract
It is only recently, with the advent of long-read sequencing technologies, that we are beginning to uncover previously uncharted regions of complex and inherently recursive plant genomes. To comprehensively study and exploit the genome of the neglected oilseed Brassica nigra, we generated two high-quality nanopore de novo genome assemblies. The N50 contig lengths for the two assemblies were 17.1 Mb (12 contigs), one of the best among 324 sequenced plant genomes, and 0.29 Mb (424 contigs), respectively, reflecting recent improvements in the technology. Comparison with a de novo short-read assembly corroborated genome integrity and quantified sequence-related error rates (0.2%). The contiguity and coverage allowed unprecedented access to low-complexity regions of the genome. Pericentromeric regions and coincidence of hypomethylation enabled localization of active centromeres and identified centromere-associated ALE family retro-elements that appear to have proliferated through relatively recent nested transposition events (<1 Ma). Genomic distances calculated based on synteny relationships were used to define a post-triplication Brassica-specific ancestral genome, and to calculate the extensive rearrangements that define the evolutionary distance separating B. nigra from its diploid relatives.
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Affiliation(s)
- Sampath Perumal
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Chu Shin Koh
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lingling Jin
- Department of Computing Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Miles Buchwaldt
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Erin E Higgins
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Sateesh Kagale
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Zahra-Katy Navabi
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lily Tang
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Kyla N Horner
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Zhesi He
- Department of Biology, University of York, York, UK
| | - Ian Bancroft
- Department of Biology, University of York, York, UK
| | - Boulos Chalhoub
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Andrew G Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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13
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Bokore FE, Knox RE, Cuthbert RD, Pozniak CJ, McCallum BD, N’Diaye A, DePauw RM, Campbell HL, Munro C, Singh A, Hiebert CW, McCartney CA, Sharpe AG, Singh AK, Spaner D, Fowler DB, Ruan Y, Berraies S, Meyer B. Mapping quantitative trait loci associated with leaf rust resistance in five spring wheat populations using single nucleotide polymorphism markers. PLoS One 2020; 15:e0230855. [PMID: 32267842 PMCID: PMC7141615 DOI: 10.1371/journal.pone.0230855] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/10/2020] [Indexed: 01/27/2023] Open
Abstract
Growing resistant wheat (Triticum aestivum L) varieties is an important strategy for the control of leaf rust, caused by Puccinia triticina Eriks. This study sought to identify the chromosomal location and effects of leaf rust resistance loci in five Canadian spring wheat cultivars. The parents and doubled haploid lines of crosses Carberry/AC Cadillac, Carberry/Vesper, Vesper/Lillian, Vesper/Stettler and Stettler/Red Fife were assessed for leaf rust severity and infection response in field nurseries in Canada near Swift Current, SK from 2013 to 2015, Morden, MB from 2015 to 2017 and Brandon, MB in 2016, and in New Zealand near Lincoln in 2014. The populations were genotyped with the 90K Infinium iSelect assay and quantitative trait loci (QTL) analysis was performed. A high density consensus map generated based on 14 doubled haploid populations and integrating SNP and SSR markers was used to compare QTL identified in different populations. AC Cadillac contributed QTL on chromosomes 2A, 3B and 7B (2 loci), Carberry on 1A, 2B (2 loci), 2D, 4B (2 loci), 5A, 6A, 7A and 7D, Lillian on 4A and 7D, Stettler on 2D and 6B, Vesper on 1B, 1D, 2A, 6B and 7B (2 loci), and Red Fife on 7A and 7B. Lillian contributed to a novel locus QLr.spa-4A, and similarly Carberry at QLr.spa-5A. The discovery of novel leaf rust resistance QTL QLr.spa-4A and QLr.spa-5A, and several others in contemporary Canada Western Red Spring wheat varieties is a tremendous addition to our present knowledge of resistance gene deployment in breeding. Carberry demonstrated substantial stacking of genes which could be supplemented with the genes identified in other cultivars with the expectation of increasing efficacy of resistance to leaf rust and longevity with little risk of linkage drag.
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Affiliation(s)
- Firdissa E Bokore
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - Ron E. Knox
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
- * E-mail: (REK); (RDC); (CJP)
| | - Richard D. Cuthbert
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
- * E-mail: (REK); (RDC); (CJP)
| | - Curtis J. Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
- * E-mail: (REK); (RDC); (CJP)
| | - Brent D. McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - Amidou N’Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | | | - Heather L. Campbell
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - Catherine Munro
- Plant and Food Research, Canterbury Agriculture and Science Centre, Lincoln, New Zealand
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Colin W. Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - Curt A. McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Dean Spaner
- Department of Agricultural, Food and Nutritional Science, 4–10N Agriculture-Forestry Centre, University of Alberta, Edmonton, Canada
| | - D. B. Fowler
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - Samia Berraies
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - Brad Meyer
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
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14
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Cram D, Kulkarni M, Buchwaldt M, Rajagopalan N, Bhowmik P, Rozwadowski K, Parkin IAP, Sharpe AG, Kagale S. WheatCRISPR: a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat. BMC Plant Biol 2019; 19:474. [PMID: 31694550 PMCID: PMC6836449 DOI: 10.1186/s12870-019-2097-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/23/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND CRISPR/Cas9 gene editing has become a revolutionary technique for crop improvement as it can facilitate fast and efficient genetic changes without the retention of transgene components in the final plant line. Lack of robust bioinformatics tools to facilitate the design of highly specific functional guide RNAs (gRNAs) and prediction of off-target sites in wheat is currently an obstacle to effective application of CRISPR technology to wheat improvement. DESCRIPTION We have developed a web-based bioinformatics tool to design specific gRNAs for genome editing and transcriptional regulation of gene expression in wheat. A collaborative study between the Broad Institute and Microsoft Research used large-scale empirical evidence to devise algorithms (Doech et al., 2016, Nature Biotechnology 34, 184-191) for predicting the on-target activity and off-target potential of CRISPR/SpCas9 (Streptococcus pyogenes Cas9). We applied these prediction models to determine on-target specificity and potential off-target activity for individual gRNAs targeting specific loci in the wheat genome. The genome-wide gRNA mappings and the corresponding Doench scores predictive of the on-target and off-target activities were used to create a gRNA database which was used as a data source for the web application termed WheatCRISPR. CONCLUSION The WheatCRISPR tool allows researchers to browse all possible gRNAs targeting a gene or sequence of interest and select effective gRNAs based on their predicted high on-target and low off-target activity scores, as well as other characteristics such as position within the targeted gene. It is publicly available at https://crispr.bioinfo.nrc.ca/WheatCrispr/ .
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Affiliation(s)
- Dustin Cram
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Manoj Kulkarni
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Miles Buchwaldt
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | | | - Pankaj Bhowmik
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Kevin Rozwadowski
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Isobel A. P. Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Andrew G. Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
- Global Institute for Food Security, University of Saskatchewan, 110 Gymnasium Place, Saskatoon, SK S7N 4J8 Canada
| | - Sateesh Kagale
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
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15
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Bokore FE, Cuthbert RD, Knox RE, Singh A, Campbell HL, Pozniak CJ, N'Diaye A, Sharpe AG, Ruan Y. Mapping quantitative trait loci associated with common bunt resistance in a spring wheat (Triticum aestivum L.) variety Lillian. Theor Appl Genet 2019; 132:3023-3033. [PMID: 31410494 PMCID: PMC6791905 DOI: 10.1007/s00122-019-03403-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/18/2019] [Indexed: 05/20/2023]
Abstract
Based on their consistency over environments, two QTL identified in Lillian on chromosomes 5A and 7A could be useful targets for marker assisted breeding of common bunt resistance. Common bunt of wheat (Triticum aestivum L.) caused by Tilletia tritici and T. laevis is an economically important disease because of losses in grain yield and reduced grain quality. Resistance can be quantitative, under the control of multiple small effect genes. The Canada Western Red Spring wheat variety Lillian is moderately resistant to common bunt races found on the Canadian prairies. This study was conducted to identify and map quantitative trait loci (QTL) conferring resistance against common bunt in Lillian. A doubled haploid population comprising 280 lines was developed from F1 plants of the cross of Lillian by Vesper. The lines were inoculated at seeding with the two races L16 (T. laevis) and T19 (T. tritici), grown in field near Swift Current, SK, in 2014, 2015 and 2016 and assessed for disease incidence. The lines were genotyped with the 90 K iSelect SNP genotyping assay, and a high-density genetic map was constructed. Quantitative trait locus analysis was performed with MapQTL.6® software. Two relatively stable common bunt resistance QTL, detected in two of the 3 years, were identified on chromosomes 5A and 7A from Lillian. In addition, three less stable QTL, appearing in one out of 3 years, were identified: one was contributed by Lillian on chromosome 3D and two were contributed by Vesper on chromosomes 1D and 2A. Epistatic interaction was identified for the bunt incidence between 3D and 7A resulting in greater bunt resistance. Future bunt resistance breeding will benefit from combining these QTL through gene pyramiding.
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Affiliation(s)
- Firdissa E Bokore
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Richard D Cuthbert
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada.
| | - Ron E Knox
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada.
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Heather L Campbell
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Curtis J Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Amidou N'Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Andrew G Sharpe
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
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16
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Shunmugam ASK, Bollina V, Dukowic-Schulze S, Bhowmik PK, Ambrose C, Higgins JD, Pozniak C, Sharpe AG, Rozwadowski K, Kagale S. Correction to: MeioCapture: an efficient method for staging and isolation of meiocytes in the prophase I sub-stages of meiosis in wheat. BMC Plant Biol 2019; 19:178. [PMID: 31046681 PMCID: PMC6498528 DOI: 10.1186/s12870-019-1780-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Following publication of the original article [1], a reader spotted an incorrect citation of the reference 14 [2] in the 'Background'. The male meiocyte isolation work described in this article [2] was carried out in rice and not in Brassica as originally stated in the 'Background' [1]. Thus, the following amendment to the Background section should be noted.
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Affiliation(s)
| | | | | | | | - Chris Ambrose
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Andrew G Sharpe
- National Research Council Canada, Saskatoon, SK, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
| | | | - Sateesh Kagale
- National Research Council Canada, Saskatoon, SK, Canada.
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17
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Handa H, Kanamori H, Tanaka T, Murata K, Kobayashi F, Robinson SJ, Koh CS, Pozniak CJ, Sharpe AG, Paux E, Wu J, Nasuda S. Structural features of two major nucleolar organizer regions (NORs), Nor-B1 and Nor-B2, and chromosome-specific rRNA gene expression in wheat. Plant J 2018; 96:1148-1159. [PMID: 30238531 DOI: 10.1111/tpj.14094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/09/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
The reference genome sequence of wheat 'Chinese Spring' (CS) is now available (IWGSC RefSeq v1.0), but the core sequences defining the nucleolar organizer regions (NORs) have not been characterized. We estimated that the total copy number of the rDNA units in the wheat genome is 11 160, of which 30.5%, 60.9% and 8.6% are located on Nor-B1 (1B), Nor-B2 (6B) and other NORs, respectively. The total length of the NORs is estimated to be 100 Mb, corresponding to approximately 10% of the unassembled portion of the genome not represented in RefSeq v1.0. Four subtypes (S1-S4) of the rDNA units were identified based on differences within the 3' external transcribed spacer regions in Nor-B1 and Nor-B2, and quantitative PCR indicated locus-specific variation in rDNA subtype contents. Expression analyses of rDNA subtypes revealed that S1 was predominantly expressed and S2 weakly expressed, in contrast to the relative abundance of rDNA subtypes in the wheat genome. These results suggest a regulation mechanism of differential rDNA expression based on sequence differences. S3 expression increased in the ditelosomic lines Dt1BL and Dt6BL, suggesting that S3 is subjected to chromosome-mediated silencing. Structural differences were detected in the regions surrounding the NOR among homoeologous chromosomes of groups 1 and 6. The adjacent regions distal to the major NORs were expanded compared with their homoeologous counterparts, and the gene density of these expanded regions was relatively low. We provide evidence that these regions are likely to be important for autoregulation of the associated major NORs as well as silencing of minor NORs.
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Affiliation(s)
- Hirokazu Handa
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | - Tsuyoshi Tanaka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | - Kazuki Murata
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | - Stephen J Robinson
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, S7N 0X2, Canada
| | - Chu S Koh
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Curtis J Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Etienne Paux
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Jianzhong Wu
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | - Shuhei Nasuda
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
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18
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Shunmugam ASK, Bollina V, Dukowic-Schulze S, Bhowmik PK, Ambrose C, Higgins JD, Pozniak C, Sharpe AG, Rozwadowski K, Kagale S. MeioCapture: an efficient method for staging and isolation of meiocytes in the prophase I sub-stages of meiosis in wheat. BMC Plant Biol 2018; 18:293. [PMID: 30463507 PMCID: PMC6249822 DOI: 10.1186/s12870-018-1514-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/31/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Molecular analysis of meiosis has been hindered by difficulties in isolating high purity subpopulations of sporogenous cells representing the succeeding stages of meiosis. Isolation of purified male meiocytes from defined meiotic stages is crucial in discovering meiosis specific genes and associated regulatory networks. RESULTS We describe an optimized method termed MeioCapture for simultaneous isolation of uncontaminated male meiocytes from wheat (Triticum spp.), specifically from the pre-meiotic G2 and the five sub-stages of meiotic prophase I. The MeioCapture protocol builds on the traditional anther squash technique and the capillary collection method, and involves extrusion of intact sporogenous archesporial columns (SACs) containing meiocytes. This improved method exploits the natural meiotic synchrony between anthers of the same floret, the correlation between the length of anthers and meiotic stage, and the occurrence of meiocytes in intact SACs largely free of somatic cells. The main advantage of MeioCapture, compared to previous methods, is that it allows simultaneous collection of meiocytes from different sub-stages of prophase I at a very high level of purity, through correlation of stages with anther sizes. A detailed description is provided for all steps, including the collection of tissue, isolation and size sorting of anthers, extrusion of intact SACs, and staging of meiocytes. Precautions for individual steps throughout the procedure are also provided to facilitate efficient isolation of pure meiocytes. The proof-of-concept was successfully established in wheat, and a light microscopic atlas of meiosis, encompassing all stages from pre-meiosis to telophase II, was developed. CONCLUSION The MeioCapture method provides an essential technique to study the molecular basis of chromosome pairing and exchange of genetic information in wheat, leading to strategies for manipulating meiotic recombination frequencies. The method also provides a foundation for similar studies in other crop species.
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Affiliation(s)
| | | | | | | | - Chris Ambrose
- Department of Biology, University of Saskatchewan, Saskatoon, SK Canada
| | - James D. Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Andrew G. Sharpe
- National Research Council Canada, Saskatoon, SK Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
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19
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Lin X, N’Diaye A, Walkowiak S, Nilsen KT, Cory AT, Haile J, Kutcher HR, Ammar K, Loladze A, Huerta-Espino J, Clarke JM, Ruan Y, Knox R, Fobert P, Sharpe AG, Pozniak CJ. Genetic analysis of resistance to stripe rust in durum wheat (Triticum turgidum L. var. durum). PLoS One 2018; 13:e0203283. [PMID: 30231049 PMCID: PMC6145575 DOI: 10.1371/journal.pone.0203283] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 08/19/2018] [Indexed: 12/18/2022] Open
Abstract
Stripe rust, caused by the fungal pathogen Puccinia striiformis Westend. f. sp. tritici Eriks, is an important disease of bread wheat (Triticum aestivum L.) worldwide and there is an indication that it may also become a serious disease of durum wheat (T. turgidum L. var. durum). Therefore, we investigated the genetic architecture underlying resistance to stripe rust in adapted durum wheat germplasm. Wheat infection assays were conducted under controlled conditions in Canada and under field conditions in Mexico. Disease assessments were performed on a population of 155 doubled haploid (DH) lines derived from the cross of Kofa (susceptible) and W9262-260D3 (moderately resistant) and on a breeding panel that consisted of 92 diverse cultivars and breeding lines. Both populations were genotyped using the 90K single-nucleotide polymorphism (SNP) iSelect assay. In the DH population, QTL for stripe rust resistance were identified on chromosome 7B (LOD 6.87-11.47) and chromosome 5B (LOD 3.88-9.17). The QTL for stripe rust resistance on chromosome 7B was supported in the breeding panel. Both QTL were anchored to the genome sequence of wild emmer wheat, which identified gene candidates involved in disease resistance. Exome capture sequencing identified variation in the candidate genes between Kofa and W9262-260D3. These genetic insights will be useful in durum breeding to enhance resistance to stripe rust.
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Affiliation(s)
- Xue Lin
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Amidou N’Diaye
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirby T. Nilsen
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Aron T. Cory
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jemanesh Haile
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hadley R. Kutcher
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Mexico D.F., Mexico
| | - Alexander Loladze
- International Maize and Wheat Improvement Center (CIMMYT), Mexico D.F., Mexico
| | - Julio Huerta-Espino
- INIFAP, Campo Experimental Valle de México, Chapingo, Edo. de México, México
| | - John M. Clarke
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Ron Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | | | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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20
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Ramírez-González RH, Borrill P, Lang D, Harrington SA, Brinton J, Venturini L, Davey M, Jacobs J, van Ex F, Pasha A, Khedikar Y, Robinson SJ, Cory AT, Florio T, Concia L, Juery C, Schoonbeek H, Steuernagel B, Xiang D, Ridout CJ, Chalhoub B, Mayer KFX, Benhamed M, Latrasse D, Bendahmane A, Wulff BBH, Appels R, Tiwari V, Datla R, Choulet F, Pozniak CJ, Provart NJ, Sharpe AG, Paux E, Spannagl M, Bräutigam A, Uauy C. The transcriptional landscape of polyploid wheat. Science 2018; 361:eaar6089. [PMID: 30115782 DOI: 10.1126/science.aar6089] [Citation(s) in RCA: 497] [Impact Index Per Article: 82.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 07/11/2018] [Indexed: 12/14/2022]
Abstract
The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world's major crops. Here we combine extensive gene expression datasets to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varies between tissues, with ~30% of wheat homoeologs showing nonbalanced expression. We found expression asymmetries along wheat chromosomes, with homoeologs showing the largest inter-tissue, inter-cultivar, and coding sequence variation, most often located in high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps toward neo- or subfunctionalization of wheat homoeologs. Coexpression networks reveal extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in wheat.
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21
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Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N, Pozniak CJ, Stein N, Choulet F, Distelfeld A, Eversole K, Poland J, Rogers J, Ronen G, Sharpe AG, Pozniak C, Ronen G, Stein N, Barad O, Baruch K, Choulet F, Keeble-Gagnère G, Mascher M, Sharpe AG, Ben-Zvi G, Josselin AA, Stein N, Mascher M, Himmelbach A, Choulet F, Keeble-Gagnère G, Mascher M, Rogers J, Balfourier F, Gutierrez-Gonzalez J, Hayden M, Josselin AA, Koh C, Muehlbauer G, Pasam RK, Paux E, Pozniak CJ, Rigault P, Sharpe AG, Tibbits J, Tiwari V, Choulet F, Keeble-Gagnère G, Mascher M, Josselin AA, Rogers J, Spannagl M, Choulet F, Lang D, Gundlach H, Haberer G, Keeble-Gagnère G, Mayer KFX, Ormanbekova D, Paux E, Prade V, Šimková H, Wicker T, Choulet F, Spannagl M, Swarbreck D, Rimbert H, Felder M, Guilhot N, Gundlach H, Haberer G, Kaithakottil G, Keilwagen J, Lang D, Leroy P, Lux T, Mayer KFX, Twardziok S, Venturini L, Appels R, Rimbert H, Choulet F, Juhász A, Keeble-Gagnère G, Choulet F, Spannagl M, Lang D, Abrouk M, Haberer G, Keeble-Gagnère G, Mayer KFX, Wicker T, Choulet F, Wicker T, Gundlach H, Lang D, Spannagl M, Lang D, Spannagl M, Appels R, Fischer I, Uauy C, Borrill P, Ramirez-Gonzalez RH, Appels R, Arnaud D, Chalabi S, Chalhoub B, Choulet F, Cory A, Datla R, Davey MW, Hayden M, Jacobs J, Lang D, Robinson SJ, Spannagl M, Steuernagel B, Tibbits J, Tiwari V, van Ex F, Wulff BBH, Pozniak CJ, Robinson SJ, Sharpe AG, Cory A, Benhamed M, Paux E, Bendahmane A, Concia L, Latrasse D, Rogers J, Jacobs J, Alaux M, Appels R, Bartoš J, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, Letellier T, Olsen OA, Šimková H, Singh K, Valárik M, van der Vossen E, Vautrin S, Weining S, Korol A, Frenkel Z, Fahima T, Glikson V, Raats D, Rogers J, Tiwari V, Gill B, Paux E, Poland J, Doležel J, Číhalíková J, Šimková H, Toegelová H, Vrána J, Sourdille P, Darrier B, Appels R, Spannagl M, Lang D, Fischer I, Ormanbekova D, Prade V, Barabaschi D, Cattivelli L, Hernandez P, Galvez S, Budak H, Steuernagel B, Jones JDG, Witek K, Wulff BBH, Yu G, Small I, Melonek J, Zhou R, Juhász A, Belova T, Appels R, Olsen OA, Kanyuka K, King R, Nilsen K, Walkowiak S, Pozniak CJ, Cuthbert R, Datla R, Knox R, Wiebe K, Xiang D, Rohde A, Golds T, Doležel J, Čížková J, Tibbits J, Budak H, Akpinar BA, Biyiklioglu S, Muehlbauer G, Poland J, Gao L, Gutierrez-Gonzalez J, N'Daiye A, Doležel J, Šimková H, Číhalíková J, Kubaláková M, Šafář J, Vrána J, Berges H, Bellec A, Vautrin S, Alaux M, Alfama F, Adam-Blondon AF, Flores R, Guerche C, Letellier T, Loaec M, Quesneville H, Pozniak CJ, Sharpe AG, Walkowiak S, Budak H, Condie J, Ens J, Koh C, Maclachlan R, Tan Y, Wicker T, Choulet F, Paux E, Alberti A, Aury JM, Balfourier F, Barbe V, Couloux A, Cruaud C, Labadie K, Mangenot S, Wincker P, Gill B, Kaur G, Luo M, Sehgal S, Singh K, Chhuneja P, Gupta OP, Jindal S, Kaur P, Malik P, Sharma P, Yadav B, Singh NK, Khurana J, Chaudhary C, Khurana P, Kumar V, Mahato A, Mathur S, Sevanthi A, Sharma N, Tomar RS, Rogers J, Jacobs J, Alaux M, Bellec A, Berges H, Doležel J, Feuillet C, Frenkel Z, Gill B, Korol A, van der Vossen E, Vautrin S, Gill B, Kaur G, Luo M, Sehgal S, Bartoš J, Holušová K, Plíhal O, Clark MD, Heavens D, Kettleborough G, Wright J, Valárik M, Abrouk M, Balcárková B, Holušová K, Hu Y, Luo M, Salina E, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A, Sergeeva E, Handa H, Kanamori H, Katagiri S, Kobayashi F, Nasuda S, Tanaka T, Wu J, Appels R, Hayden M, Keeble-Gagnère G, Rigault P, Tibbits J, Olsen OA, Belova T, Cattonaro F, Jiumeng M, Kugler K, Mayer KFX, Pfeifer M, Sandve S, Xun X, Zhan B, Šimková H, Abrouk M, Batley J, Bayer PE, Edwards D, Hayashi S, Toegelová H, Tulpová Z, Visendi P, Weining S, Cui L, Du X, Feng K, Nie X, Tong W, Wang L, Borrill P, Gundlach H, Galvez S, Kaithakottil G, Lang D, Lux T, Mascher M, Ormanbekova D, Prade V, Ramirez-Gonzalez RH, Spannagl M, Stein N, Uauy C, Venturini L, Stein N, Appels R, Eversole K, Rogers J, Borrill P, Cattivelli L, Choulet F, Hernandez P, Kanyuka K, Lang D, Mascher M, Nilsen K, Paux E, Pozniak CJ, Ramirez-Gonzalez RH, Šimková H, Small I, Spannagl M, Swarbreck D, Uauy C. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 2018; 361:361/6403/eaar7191. [PMID: 30115783 DOI: 10.1126/science.aar7191] [Citation(s) in RCA: 1459] [Impact Index Per Article: 243.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 07/11/2018] [Indexed: 12/14/2022]
Abstract
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
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Affiliation(s)
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, MD 20816, USA. .,Eversole Associates, 5207 Wyoming Road, Bethesda, MD 20816, USA
| | - Catherine Feuillet
- Bayer CropScience, Crop Science Division, Research and Development, Innovation Centre, 3500 Paramount Parkway, Morrisville, NC 27560, USA
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | | | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, MD 20816, USA. .,Eversole Associates, 5207 Wyoming Road, Bethesda, MD 20816, USA
| | - Jesse Poland
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - Gil Ronen
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Andrew G Sharpe
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | | | - Curtis Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Gil Ronen
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Omer Barad
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Kobi Baruch
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Andrew G Sharpe
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Gil Ben-Zvi
- NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel
| | - Ambre-Aurore Josselin
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - François Balfourier
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Juan Gutierrez-Gonzalez
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Matthew Hayden
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Ambre-Aurore Josselin
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - ChuShin Koh
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Gary Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Raj K Pasam
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Philippe Rigault
- GYDLE, Suite 220, 1135 Grande Allée, Ouest, Québec, QC G1S 1E7, Canada
| | - Andrew G Sharpe
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Josquin Tibbits
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Vijay Tiwari
- Plant Science and Landscape Architecture, University of Maryland, 4291 Fieldhouse Road, 2102 Plant Sciences Building, College Park, MD 20742, USA
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ambre-Aurore Josselin
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | | | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Georg Haberer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Klaus F X Mayer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Danara Ormanbekova
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,Department of Agricultural Sciences, University of Bologna, Viale Fanin, 44 40127 Bologna, Italy
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Verena Prade
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Hélène Rimbert
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Marius Felder
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Nicolas Guilhot
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Heidrun Gundlach
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Georg Haberer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Jens Keilwagen
- Julius Kühn-Institut, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Philippe Leroy
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Thomas Lux
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Klaus F X Mayer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Sven Twardziok
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Luca Venturini
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Hélène Rimbert
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Angéla Juhász
- Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia.,Agricultural Institute, MTA Centre for Agricultural Research, Applied Genomics Department, 2 Brunszvik Street, Martonvásár H 2462, Hungary
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Georg Haberer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Klaus F X Mayer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Heidrun Gundlach
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Iris Fischer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Cristobal Uauy
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Philippa Borrill
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Dominique Arnaud
- Institut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Smahane Chalabi
- Institut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Boulos Chalhoub
- Monsanto SAS, 28000 Boissay, France.,Institut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Aron Cory
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Raju Datla
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Mark W Davey
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Matthew Hayden
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - John Jacobs
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Stephen J Robinson
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Josquin Tibbits
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Vijay Tiwari
- Plant Science and Landscape Architecture, University of Maryland, 4291 Fieldhouse Road, 2102 Plant Sciences Building, College Park, MD 20742, USA
| | - Fred van Ex
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Brande B H Wulff
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Stephen J Robinson
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Andrew G Sharpe
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Aron Cory
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | | | - Moussa Benhamed
- Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Abdelhafid Bendahmane
- Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France
| | - Lorenzo Concia
- Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France
| | - David Latrasse
- Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France
| | | | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - John Jacobs
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Arnaud Bellec
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Hélène Berges
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Catherine Feuillet
- Bayer CropScience, Crop Science Division, Research and Development, Innovation Centre, 3500 Paramount Parkway, Morrisville, NC 27560, USA
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Abraham Korol
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | | | - Odd-Arne Olsen
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Kuldeep Singh
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | | | - Sonia Vautrin
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | | | - Abraham Korol
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Tzion Fahima
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | | | - Dina Raats
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | | | - Vijay Tiwari
- Plant Science and Landscape Architecture, University of Maryland, 4291 Fieldhouse Road, 2102 Plant Sciences Building, College Park, MD 20742, USA
| | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Jesse Poland
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jarmila Číhalíková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | | | | | - Benoit Darrier
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Iris Fischer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Danara Ormanbekova
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,Department of Agricultural Sciences, University of Bologna, Viale Fanin, 44 40127 Bologna, Italy
| | - Verena Prade
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Delfina Barabaschi
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d'Arda, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d'Arda, Italy
| | | | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS-CSIC), Consejo Superior de Investigaciones Científicas, Alameda del Obispo s/n, 14004 Córdoba, Spain
| | - Sergio Galvez
- Universidad de Málaga, Lenguajes y Ciencias de la Computación, Campus de Teatinos, 29071 Málaga, Spain
| | - Hikmet Budak
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | | | | | | | - Kamil Witek
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Brande B H Wulff
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Guotai Yu
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Ian Small
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Joanna Melonek
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Ruonan Zhou
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | | | - Angéla Juhász
- Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia.,Agricultural Institute, MTA Centre for Agricultural Research, Applied Genomics Department, 2 Brunszvik Street, Martonvásár H 2462, Hungary
| | - Tatiana Belova
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Odd-Arne Olsen
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | | | - Kostya Kanyuka
- Rothamsted Research, Biointeractions and Crop Protection, West Common, Harpenden AL5 2JQ, UK
| | - Robert King
- Rothamsted Research, Computational and Analytical Sciences, West Common, Harpenden AL5 2JQ, UK
| | | | - Kirby Nilsen
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Sean Walkowiak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Richard Cuthbert
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Box 1030, Swift Current, SK S9H 3X2, Canada
| | - Raju Datla
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Ron Knox
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Box 1030, Swift Current, SK S9H 3X2, Canada
| | - Krysta Wiebe
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Daoquan Xiang
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | | | - Antje Rohde
- Bayer CropScience, Breeding and Trait Development, Technologiepark 38, 9052 Gent, Belgium
| | - Timothy Golds
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Josquin Tibbits
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | | | - Hikmet Budak
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Bala Ani Akpinar
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Sezgi Biyiklioglu
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | | | - Gary Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Jesse Poland
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Liangliang Gao
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Juan Gutierrez-Gonzalez
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Amidou N'Daiye
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jarmila Číhalíková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | | | - Hélène Berges
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Arnaud Bellec
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Sonia Vautrin
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | | | - Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | | | | | - Raphael Flores
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Claire Guerche
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | | | - Mikaël Loaec
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | | | | | | | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Andrew G Sharpe
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.,University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | | | - Hikmet Budak
- Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Janet Condie
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Jennifer Ens
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - ChuShin Koh
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada
| | - Ron Maclachlan
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Yifang Tan
- National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | | | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Adriana Alberti
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Jean-Marc Aury
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - François Balfourier
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Valérie Barbe
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Arnaud Couloux
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Karine Labadie
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Sophie Mangenot
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France
| | - Patrick Wincker
- CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France.,CNRS, UMR 8030, CP5706, 91057 Evry, France.,Université d'Evry, UMR 8030, CP5706, 91057 Evry, France
| | | | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Gaganpreet Kaur
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | - Sunish Sehgal
- Agronomy Horticulture and Plant Science, South Dakota State University, 2108 Jackrabbit Drive, Brookings, SD 57006, USA
| | | | - Kuldeep Singh
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Parveen Chhuneja
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Om Prakash Gupta
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Suruchi Jindal
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Parampreet Kaur
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Palvi Malik
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Priti Sharma
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | - Bharat Yadav
- Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India
| | | | - Nagendra K Singh
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - JitendraP Khurana
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Chanderkant Chaudhary
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Paramjit Khurana
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Vinod Kumar
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Ajay Mahato
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Saloni Mathur
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Amitha Sevanthi
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Naveen Sharma
- University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India
| | - Ram Sewak Tomar
- ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | | | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - John Jacobs
- Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium
| | - Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Arnaud Bellec
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Hélène Berges
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Catherine Feuillet
- Bayer CropScience, Crop Science Division, Research and Development, Innovation Centre, 3500 Paramount Parkway, Morrisville, NC 27560, USA
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Abraham Korol
- University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
| | | | - Sonia Vautrin
- INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | | | - Bikram Gill
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Gaganpreet Kaur
- Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | - Sunish Sehgal
- Agronomy Horticulture and Plant Science, South Dakota State University, 2108 Jackrabbit Drive, Brookings, SD 57006, USA
| | | | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Ondřej Plíhal
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | | | - Matthew D Clark
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK.,Department of Lifesciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Darren Heavens
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | | | - Jon Wright
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | | | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Barbora Balcárková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Yuqin Hu
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | | | - Elena Salina
- The Federal Research Center Institute of Cytology and Genetics, SB RAS, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Nikolai Ravin
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia.,Faculty of Biology, Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia
| | - Konstantin Skryabin
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia.,Faculty of Biology, Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia
| | - Alexey Beletsky
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia
| | - Vitaly Kadnikov
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia
| | - Andrey Mardanov
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia
| | - Michail Nesterov
- The Federal Research Center Institute of Cytology and Genetics, SB RAS, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Andrey Rakitin
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia
| | - Ekaterina Sergeeva
- The Federal Research Center Institute of Cytology and Genetics, SB RAS, pr. Lavrentyeva 10, Novosibirsk 630090, Russia
| | | | - Hirokazu Handa
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Satoshi Katagiri
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tsuyoshi Tanaka
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jianzhong Wu
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | | | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Matthew Hayden
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Gabriel Keeble-Gagnère
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | - Philippe Rigault
- GYDLE, Suite 220, 1135 Grande Allée, Ouest, Québec, QC G1S 1E7, Canada
| | - Josquin Tibbits
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia
| | | | - Odd-Arne Olsen
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | - Tatiana Belova
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | | | - Min Jiumeng
- BGI-Shenzhen, BGI Genomics, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Karl Kugler
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Klaus F X Mayer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Matthias Pfeifer
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Simen Sandve
- Faculty of Bioscience, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | - Xu Xun
- BGI-Shenzhen, BGI Genomics, Yantian District, Shenzhen 518083, Guangdong, China
| | - Bujie Zhan
- Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway
| | | | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Satomi Hayashi
- Queensland University of Technology, Earth, Environmental and Biological Sciences, Brisbane, QLD 4001, Australia
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Zuzana Tulpová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Paul Visendi
- University of Greenwich, Natural Resources Institute, Central Avenue, Chatham, Kent ME4 4TB, UK
| | | | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Licao Cui
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Xianghong Du
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Kewei Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Wei Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | - Le Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China
| | | | - Philippa Borrill
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Heidrun Gundlach
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Sergio Galvez
- Universidad de Málaga, Lenguajes y Ciencias de la Computación, Campus de Teatinos, 29071 Málaga, Spain
| | | | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Thomas Lux
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Danara Ormanbekova
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,Department of Agricultural Sciences, University of Bologna, Viale Fanin, 44 40127 Bologna, Italy
| | - Verena Prade
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Cristobal Uauy
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Luca Venturini
- Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK
| | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. .,The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. .,Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, MD 20816, USA. .,Eversole Associates, 5207 Wyoming Road, Bethesda, MD 20816, USA
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK
| | - Philippa Borrill
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d'Arda, Italy
| | - Frédéric Choulet
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS-CSIC), Consejo Superior de Investigaciones Científicas, Alameda del Obispo s/n, 14004 Córdoba, Spain
| | - Kostya Kanyuka
- Rothamsted Research, Biointeractions and Crop Protection, West Common, Harpenden AL5 2JQ, UK
| | - Daniel Lang
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Kirby Nilsen
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Etienne Paux
- GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Curtis J Pozniak
- University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | | | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Ian Small
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Manuel Spannagl
- Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
| | | | - Cristobal Uauy
- John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK
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22
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Brar GS, Ali S, Qutob D, Ambrose S, Lou K, Maclachlan R, Pozniak CJ, Fu YB, Sharpe AG, Kutcher HR. Genome re-sequencing and simple sequence repeat markers reveal the existence of divergent lineages in the Canadian Puccinia striiformis
f. sp. tritici
population with extensive DNA methylation. Environ Microbiol 2018; 20:1498-1515. [DOI: 10.1111/1462-2920.14067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Gurcharn S. Brar
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Sajid Ali
- Institute of Biotechnology and Genetic Engineering; University of Agriculture; Peshawar Pakistan
| | - Dinah Qutob
- Aquatic and Crop Resource Development; National Research Council of Canada, 110 Gymnasium Place; Saskatoon SK S7N 0W9 Canada
| | - Stephen Ambrose
- Aquatic and Crop Resource Development; National Research Council of Canada, 110 Gymnasium Place; Saskatoon SK S7N 0W9 Canada
| | - Kun Lou
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Ron Maclachlan
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Curtis J. Pozniak
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Yong-Bi Fu
- Plant Gene Resources of Canada, Agriculture & Agri-Food Canada- Saskatoon Research and Development Centre, 107 Science Place; Saskatoon SK S7N 0X2 Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, 110 Gymnasium Place; Saskatoon SK S7N 0W9 Canada
| | - Hadley R. Kutcher
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
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23
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Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, Jordan KW, Golan G, Deek J, Ben-Zvi B, Ben-Zvi G, Himmelbach A, MacLachlan RP, Sharpe AG, Fritz A, Ben-David R, Budak H, Fahima T, Korol A, Faris JD, Hernandez A, Mikel MA, Levy AA, Steffenson B, Maccaferri M, Tuberosa R, Cattivelli L, Faccioli P, Ceriotti A, Kashkush K, Pourkheirandish M, Komatsuda T, Eilam T, Sela H, Sharon A, Ohad N, Chamovitz DA, Mayer KFX, Stein N, Ronen G, Peleg Z, Pozniak CJ, Akhunov ED, Distelfeld A. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 2018; 357:93-97. [PMID: 28684525 DOI: 10.1126/science.aan0032] [Citation(s) in RCA: 465] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/08/2017] [Indexed: 01/07/2023]
Abstract
Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in Brittle Rachis 1 (TtBtr1) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties.
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Affiliation(s)
- Raz Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Moran Nave
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | | | - Sven O Twardziok
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | - Heidrun Gundlach
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | - Iago Hale
- University of New Hampshire, Durham, NH, USA
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Manuel Spannagl
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany
| | | | | | - Guy Golan
- The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jasline Deek
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Batsheva Ben-Zvi
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany
| | | | - Andrew G Sharpe
- University of Saskatchewan, Saskatoon, Canada.,Global Institute for Food Security, Saskatoon, SK, Canada
| | | | - Roi Ben-David
- Agricultural Research Organization (ARO), Bet Dagan, Israel
| | | | | | | | - Justin D Faris
- U.S. Department of Agriculture (USDA)-Agricultural Research Service, Fargo, ND, USA
| | | | | | | | | | | | | | - Luigi Cattivelli
- Council of Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Primetta Faccioli
- Council of Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Aldo Ceriotti
- CNR-National Research Council, Institute of Agricultural Biology and Biotechnology, Milano, Italy
| | | | | | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Tamar Eilam
- The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - Hanan Sela
- The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.,The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | - Nir Ohad
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Daniel A Chamovitz
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Klaus F X Mayer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany
| | | | - Zvi Peleg
- The Hebrew University of Jerusalem, Rehovot, Israel
| | | | | | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.,The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
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24
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Bokore FE, Cuthbert RD, Knox RE, Randhawa HS, Hiebert CW, DePauw RM, Singh AK, Singh A, Sharpe AG, N'Diaye A, Pozniak CJ, McCartney C, Ruan Y, Berraies S, Meyer B, Munro C, Hay A, Ammar K, Huerta-Espino J, Bhavani S. Quantitative trait loci for resistance to stripe rust of wheat revealed using global field nurseries and opportunities for stacking resistance genes. Theor Appl Genet 2017; 130:2617-2635. [PMID: 28913655 DOI: 10.1007/s00122-017-2980-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/30/2017] [Indexed: 05/19/2023]
Abstract
Quantitative trait loci controlling stripe rust resistance were identified in adapted Canadian spring wheat cultivars providing opportunity for breeders to stack loci using marker-assisted breeding. Stripe rust or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is a devastating disease of common wheat (Triticum aestivum L.) in many regions of the world. The objectives of this research were to identify and map quantitative trait loci (QTL) associated with stripe rust resistance in adapted Canadian spring wheat cultivars that are effective globally, and investigate opportunities for stacking resistance. Doubled haploid (DH) populations from the crosses Vesper/Lillian, Vesper/Stettler, Carberry/Vesper, Stettler/Red Fife and Carberry/AC Cadillac were phenotyped for stripe rust severity and infection response in field nurseries in Canada (Lethbridge and Swift Current), New Zealand (Lincoln), Mexico (Toluca) and Kenya (Njoro), and genotyped with SNP markers. Six QTL for stripe rust resistance in the population of Vesper/Lillian, five in Vesper/Stettler, seven in Stettler/Red Fife, four in Carberry/Vesper and nine in Carberry/AC Cadillac were identified. Lillian contributed stripe rust resistance QTL on chromosomes 4B, 5A, 6B and 7D, AC Cadillac on 2A, 2B, 3B and 5B, Carberry on 1A, 1B, 4A, 4B, 7A and 7D, Stettler on 1A, 2A, 3D, 4A, 5B and 6A, Red Fife on 2D, 3B and 4B, and Vesper on 1B, 2B and 7A. QTL on 1A, 1B, 2A, 2B, 3B, 4A, 4B, 5B, 7A and 7D were observed in multiple parents. The populations are compelling sources of recombination of many stripe rust resistance QTL for stacking disease resistance. Gene pyramiding should be possible with little chance of linkage drag of detrimental genes as the source parents were mostly adapted cultivars widely grown in Canada.
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Affiliation(s)
- Firdissa E Bokore
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada.
| | - Richard D Cuthbert
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada.
| | - Ron E Knox
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Harpinder S Randhawa
- Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Colin W Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Ron M DePauw
- Advancing Wheat Technologies, 870 Field Drive, Swift Current, SK, S9H 4N5, Canada
| | - Asheesh K Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Andrew G Sharpe
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Amidou N'Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Curtis J Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Curt McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Samia Berraies
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Brad Meyer
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Catherine Munro
- Plant and Food Research Canterbury Agriculture and Science Centre, Gerald St, Lincoln, 7608, New Zealand
| | - Andy Hay
- Plant and Food Research Canterbury Agriculture and Science Centre, Gerald St, Lincoln, 7608, New Zealand
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Apdo., Postal 6-6-41, 06600, Mexico, DF, Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de México INIFAP, Apdo., Postal 10, 56230, Chapingo, Edo. de México, Mexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
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25
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Kassa MT, You FM, Hiebert CW, Pozniak CJ, Fobert PR, Sharpe AG, Menzies JG, Humphreys DG, Rezac Harrison N, Fellers JP, McCallum BD, McCartney CA. Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr16. BMC Plant Biol 2017; 17:45. [PMID: 28202046 PMCID: PMC5311853 DOI: 10.1186/s12870-017-0993-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/31/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Lr16 is a widely deployed leaf rust resistance gene in wheat (Triticum aestivum L.) that is highly effective against the North American Puccinia triticina population when pyramided with the gene Lr34. Lr16 is a seedling leaf rust resistance gene conditioning an incompatible interaction with a distinct necrotic ring surrounding the uredinium. Lr16 was previously mapped to the telomeric region of the short arm of wheat chromosome 2B. The goals of this study were to develop numerous single nucleotide polymorphism (SNP) markers for the Lr16 region and identify diagnostic gene-specific SNP marker assays for marker-assisted selection (MAS). RESULTS Forty-three SNP markers were developed and mapped on chromosome 2BS tightly linked with the resistance gene Lr16 across four mapping populations representing a total of 1528 gametes. Kompetitive Allele Specific PCR (KASP) assays were designed for all identified SNPs. Resistance gene analogs (RGAs) linked with the Lr16 locus were identified and RGA-based SNP markers were developed. The diagnostic potential of the SNPs co-segregating with Lr16 was evaluated in a diverse set of 133 cultivars and breeding lines. Six SNP markers were consistent with the Lr16 phenotype and are accurately predictive of Lr16 for all wheat lines/cultivars in the panel. CONCLUSIONS Lr16 was mapped relative to SNP markers in four populations. Six SNP markers exhibited high quality clustering in the KASP assay and are suitable for MAS of Lr16 in wheat breeding programs.
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Affiliation(s)
- Mulualem T. Kassa
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB R6M 1Y5 Canada
- National Research Council, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Frank M. You
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB R6M 1Y5 Canada
| | - Colin W. Hiebert
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB R6M 1Y5 Canada
| | - Curtis J. Pozniak
- University of Saskatchewan, Crop Development Centre, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Pierre R. Fobert
- National Research Council, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Andrew G. Sharpe
- National Research Council, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
- University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8 Canada
| | - James G. Menzies
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB R6M 1Y5 Canada
| | - D. Gavin Humphreys
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 1341 Baseline Road, Ottawa, ON K1A 0C5 Canada
| | | | - John P. Fellers
- USDA–ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506 USA
| | - Brent D. McCallum
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB R6M 1Y5 Canada
| | - Curt A. McCartney
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB R6M 1Y5 Canada
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26
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Kagale S, Nixon J, Khedikar Y, Pasha A, Provart NJ, Clarke WE, Bollina V, Robinson SJ, Coutu C, Hegedus DD, Sharpe AG, Parkin IAP. The developmental transcriptome atlas of the biofuel crop Camelina sativa. Plant J 2016; 88:879-894. [PMID: 27513981 DOI: 10.1111/tpj.13302] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 08/01/2016] [Accepted: 08/04/2016] [Indexed: 05/17/2023]
Abstract
Camelina sativa is currently being embraced as a viable industrial bio-platform crop due to a number of desirable agronomic attributes and the unique fatty acid profile of the seed oil that has applications for food, feed and biofuel. The recent completion of the reference genome sequence of C. sativa identified a young hexaploid genome. To complement this work, we have generated a genome-wide developmental transcriptome map by RNA sequencing of 12 different tissues covering major developmental stages during the life cycle of C. sativa. We have generated a digital atlas of this comprehensive transcriptome resource that enables interactive visualization of expression data through a searchable database of electronic fluorescent pictographs (eFP browser). An analysis of this dataset supported expression of 88% of the annotated genes in C. sativa and provided a global overview of the complex architecture of temporal and spatial gene expression patterns active during development. Conventional differential gene expression analysis combined with weighted gene expression network analysis uncovered similarities as well as differences in gene expression patterns between different tissues and identified tissue-specific genes and network modules. A high-quality census of transcription factors, analysis of alternative splicing and tissue-specific genome dominance provided insight into the transcriptional dynamics and sub-genome interplay among the well-preserved triplicated repertoire of homeologous loci. The comprehensive transcriptome atlas in combination with the reference genome sequence provides a powerful resource for genomics research which can be leveraged to identify functional associations between genes and understand the regulatory networks underlying developmental processes.
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Affiliation(s)
- Sateesh Kagale
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada
| | - John Nixon
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Yogendra Khedikar
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Wayne E Clarke
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Venkatesh Bollina
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Stephen J Robinson
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Dwayne D Hegedus
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
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27
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Gruber MY, Xia J, Yu M, Steppuhn H, Wall K, Messer D, Sharpe AG, Acharya SN, Wishart DS, Johnson D, Miller DR, Taheri A. Transcript analysis in two alfalfa salt tolerance selected breeding populations relative to a non-tolerant population. Genome 2016; 60:104-127. [PMID: 28045337 DOI: 10.1139/gen-2016-0111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while expression remained unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population was observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa.
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Affiliation(s)
- M Y Gruber
- a Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7J 0X2, Canada.,b Department of Computing Science, University of Alberta, 2-21 Athabasca Hall, Edmonton, AB T6G 2R3, Canada
| | - J Xia
- b Department of Computing Science, University of Alberta, 2-21 Athabasca Hall, Edmonton, AB T6G 2R3, Canada
| | - M Yu
- a Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7J 0X2, Canada
| | - H Steppuhn
- c Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, SK S9H 3X2, Canada
| | - K Wall
- c Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, SK S9H 3X2, Canada
| | - D Messer
- c Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, SK S9H 3X2, Canada
| | - A G Sharpe
- d National Research Council, 110 Gymnasium Pl., Saskatoon, SK S7N 0W9, Canada
| | - S N Acharya
- e AAFC Lethbridge Research Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue S., Lethbridge, AB T1J 4B1, Canada
| | - D S Wishart
- b Department of Computing Science, University of Alberta, 2-21 Athabasca Hall, Edmonton, AB T6G 2R3, Canada.,f Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2R3, Canada
| | - D Johnson
- g Alforex Seeds, an affiliate of Dow AgroSciences, N4505 CTH M, West Salem, WI 54669, USA
| | - D R Miller
- g Alforex Seeds, an affiliate of Dow AgroSciences, N4505 CTH M, West Salem, WI 54669, USA
| | - A Taheri
- a Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7J 0X2, Canada
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28
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Clarke WE, Higgins EE, Plieske J, Wieseke R, Sidebottom C, Khedikar Y, Batley J, Edwards D, Meng J, Li R, Lawley CT, Pauquet J, Laga B, Cheung W, Iniguez-Luy F, Dyrszka E, Rae S, Stich B, Snowdon RJ, Sharpe AG, Ganal MW, Parkin IAP. A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome. Theor Appl Genet 2016; 129:1887-99. [PMID: 27364915 PMCID: PMC5025514 DOI: 10.1007/s00122-016-2746-7] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/18/2016] [Indexed: 05/18/2023]
Abstract
The Brassica napus Illumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploid B. napus and its progenitor diploid genomes. A high-density single nucleotide polymorphism (SNP) Illumina Infinium array, containing 52,157 markers, was developed for the allotetraploid Brassica napus. A stringent selection process employing the short probe sequence for each SNP assay was used to limit the majority of the selected markers to those represented a minimum number of times across the highly replicated genome. As a result approximately 60 % of the SNP assays display genome-specificity, resolving as three clearly separated clusters (AA, AB, and BB) when tested with a diverse range of B. napus material. This genome specificity was supported by the analysis of the diploid ancestors of B. napus, whereby 26,504 and 29,720 markers were scorable in B. oleracea and B. rapa, respectively. Forty-four percent of the assayed loci on the array were genetically mapped in a single doubled-haploid B. napus population allowing alignment of their physical and genetic coordinates. Although strong conservation of the two positions was shown, at least 3 % of the loci were genetically mapped to a homoeologous position compared to their presumed physical position in the respective genome, underlying the importance of genetic corroboration of locus identity. In addition, the alignments identified multiple rearrangements between the diploid and tetraploid Brassica genomes. Although mostly attributed to genome assembly errors, some are likely evidence of rearrangements that occurred since the hybridisation of the progenitor genomes in the B. napus nucleus. Based on estimates for linkage disequilibrium decay, the array is a valuable tool for genetic fine mapping and genome-wide association studies in B. napus and its progenitor genomes.
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Affiliation(s)
- Wayne E Clarke
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Erin E Higgins
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Joerg Plieske
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany
| | - Ralf Wieseke
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany
| | - Christine Sidebottom
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9, Canada
| | - Yogendra Khedikar
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Jacqueline Batley
- School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Dave Edwards
- School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruiyuan Li
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Jérôme Pauquet
- BIOGEMMA 6, chemin des Panedautes, 31700, Mondonville, France
- SYNGENTA France SAS, 346, route des Pasquiers, 84260, Sarrians, France
| | | | - Wing Cheung
- DNA Landmarks Inc, 84 Rue Richelieu, St-Jean-sur-Richelieu, QC, J3B 6X3, Canada
| | - Federico Iniguez-Luy
- Genomics and Bioinformatics Unit, Agri Aquaculture Nutritional Genomic Center (CGNA), Conicyt-Regional, Gore La Araucania, R10C1001, Temuco, Chile
| | - Emmanuelle Dyrszka
- Syngenta France SAS, 12 Chemin de l'hobit, B.P. 27, 31790, Saint-Sauveur, France
| | | | - Benjamin Stich
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, S7N 0W9, Canada
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, 06466, Gatersleben, Germany
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
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Kassa MT, Haas S, Schliephake E, Lewis C, You FM, Pozniak CJ, Krämer I, Perovic D, Sharpe AG, Fobert PR, Koch M, Wise IL, Fenwick P, Berry S, Simmonds J, Hourcade D, Senellart P, Duchalais L, Robert O, Förster J, Thomas JB, Friedt W, Ordon F, Uauy C, McCartney CA. A saturated SNP linkage map for the orange wheat blossom midge resistance gene Sm1. Theor Appl Genet 2016; 129:1507-1517. [PMID: 27160855 DOI: 10.1007/s00122-016-2720-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/22/2016] [Indexed: 06/05/2023]
Abstract
SNP markers were developed for the OWBM resistance gene Sm1 that will be useful for MAS. The wheat Sm1 region is collinear with an inverted syntenic interval in B. distachyon. Orange wheat blossom midge (OWBM, Sitodiplosis mosellana Géhin) is an important insect pest of wheat (Triticum aestivum) in many growing regions. Sm1 is the only described OWBM resistance gene and is the foundation of managing OWBM through host genetics. Sm1 was previously mapped to wheat chromosome arm 2BS relative to simple sequence repeat (SSR) markers and the dominant, sequence characterized amplified region (SCAR) marker WM1. The objectives of this research were to saturate the Sm1 region with markers, develop improved markers for marker-assisted selection (MAS), and examine the synteny between wheat, Brachypodium distachyon, and rice (Oryza sativa) in the Sm1 region. The present study mapped Sm1 in four populations relative to single nucleotide polymorphisms (SNPs), SSRs, Diversity Array Technology (DArT) markers, single strand conformation polymorphisms (SSCPs), and the SCAR WM1. Numerous high quality SNP assays were designed that mapped near Sm1. BLAST delineated the syntenic intervals in B. distachyon and rice using gene-based SNPs as query sequences. The Sm1 region in wheat was inverted relative to B. distachyon and rice, which suggests a chromosomal rearrangement within the Triticeae lineage. Seven SNPs were tested on a collection of wheat lines known to carry Sm1 and not to carry Sm1. Sm1-flanking SNPs were identified that were useful for predicting the presence or absence of Sm1 based upon haplotype. These SNPs will be a major improvement for MAS of Sm1 in wheat breeding programs.
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Affiliation(s)
- Mulualem T Kassa
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
- National Research Council, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Sabrina Haas
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Edgar Schliephake
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Clare Lewis
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Frank M You
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Curtis J Pozniak
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Ilona Krämer
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Dragan Perovic
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Andrew G Sharpe
- National Research Council, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Pierre R Fobert
- National Research Council, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Michael Koch
- Deutsche Saatveredelung AG (DSV), Lippstadt, Nordrhein-Westfalen, Germany
| | - Ian L Wise
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | | | | | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Delphine Hourcade
- Arvalis, Institut du Végétal. 6 chemin de la Côte Vieille, 31450, Baziege, France
| | | | - Laure Duchalais
- RAGT 2n, Rout e d'Epincy, 28150, Louville la Chenard, France
| | - Olivier Robert
- Bioplante Florimond Desprez, BP41, 59242, Cappelle en Pévèle, France
| | | | - Julian B Thomas
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Wolfgang Friedt
- Department of Plant Breeding, Research Center for BioSystems, Land Use and Nutrition (IFZ), Giessen University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Frank Ordon
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Curt A McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada.
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Gujaria-Verma N, Ramsay L, Sharpe AG, Sanderson LA, Debouck DG, Tar'an B, Bett KE. Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping. BMC Genomics 2016; 17:239. [PMID: 26979462 PMCID: PMC4793507 DOI: 10.1186/s12864-016-2499-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 02/18/2016] [Indexed: 11/10/2022] Open
Abstract
Background Common bean (Phaseolus vulgaris) is an important grain legume and there has been a recent resurgence in interest in its relative, tepary bean (P. acutifolius), owing to this species’ ability to better withstand abiotic stresses. Genomic resources are scarce for this minor crop species and a better knowledge of the genome-level relationship between these two species would facilitate improvement in both. High-throughput genotyping has facilitated large-scale single nucleotide polymorphism (SNP) identification leading to the development of molecular markers with associated sequence information that can be used to place them in the context of a full genome assembly. Results Transcript-based SNPs were identified from six common bean and two tepary bean accessions and a subset were used to generate a 768-SNP Illumina GoldenGate assay for each species. The tepary bean assay was used to assess diversity in wild and cultivated tepary bean and to generate the first gene-based map of the tepary bean genome. Genotypic analyses of the diversity panel showed a clear separation between domesticated and cultivated tepary beans, two distinct groups within the domesticated types, and P. parvifolius was confirmed to be distinct. The genetic map of tepary bean was compared to the common bean genome assembly to demonstrate high levels of collinearity between the two species with differences limited to a few intra-chromosomal rearrangements. Conclusions The development of the first set of genomic resources specifically for tepary bean has allowed for greater insight into the structure of this species and its relationship to its agriculturally more prominent relative, common bean. These resources will be helpful in the development of efficient breeding strategies for both species and will facilitate the introgression of agriculturally important traits from one crop into the other. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2499-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Neha Gujaria-Verma
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada
| | - Larissa Ramsay
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Lacey-Anne Sanderson
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada
| | - Daniel G Debouck
- Genetic Resources Program, International Center for Tropical Agriculture, Km 17 recta a Palmira, AA6713, Cali, Colombia
| | - Bunyamin Tar'an
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada.
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Abstract
The development of genotyping-by-sequencing (GBS) to rapidly detect nucleotide variation at the whole genome level, in many individuals simultaneously, has provided a transformative genetic profiling technique. GBS can be carried out in species with or without reference genome sequences yields huge amounts of potentially informative data. One limitation with the approach is the paucity of tools to transform the raw data into a format that can be easily interrogated at the genetic level. In this chapter we describe bioinformatics tools developed to address this shortfall together with experimental design considerations to fully leverage the power of GBS for genetic analysis.
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Affiliation(s)
- Sateesh Kagale
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada, S7N 0W9
| | - Chushin Koh
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada, S7N 0W9
| | - Wayne E Clarke
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - Venkatesh Bollina
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada, S7N 0W9.
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32
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Jordan KW, Wang S, Lun Y, Gardiner LJ, MacLachlan R, Hucl P, Wiebe K, Wong D, Forrest KL, Sharpe AG, Sidebottom CH, Hall N, Toomajian C, Close T, Dubcovsky J, Akhunova A, Talbert L, Bansal UK, Bariana HS, Hayden MJ, Pozniak C, Jeddeloh JA, Hall A, Akhunov E. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol 2015; 16:48. [PMID: 25886949 PMCID: PMC4389885 DOI: 10.1186/s13059-015-0606-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/04/2015] [Indexed: 12/21/2022] Open
Abstract
Background Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. Results A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. Conclusions Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0606-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine W Jordan
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Shichen Wang
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Yanni Lun
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
| | - Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Ron MacLachlan
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Pierre Hucl
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Krysta Wiebe
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Debbie Wong
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | - Kerrie L Forrest
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | | | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0 W9, Canada.
| | | | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | | | - Timothy Close
- Department Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA.
| | - Jorge Dubcovsky
- Department Plant Sciences, University of California, Davis, CA, 95616, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Alina Akhunova
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
| | - Luther Talbert
- Department Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
| | - Urmil K Bansal
- Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Harbans S Bariana
- Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Matthew J Hayden
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | - Curtis Pozniak
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | | | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Eduard Akhunov
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
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Sindhu A, Ramsay L, Sanderson LA, Stonehouse R, Li R, Condie J, Shunmugam ASK, Liu Y, Jha AB, Diapari M, Burstin J, Aubert G, Tar’an B, Bett KE, Warkentin TD, Sharpe AG. Gene-based SNP discovery and genetic mapping in pea. Theor Appl Genet 2014; 127:2225-41. [PMID: 25119872 PMCID: PMC4180032 DOI: 10.1007/s00122-014-2375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 07/29/2014] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE Gene-based SNPs were identified and mapped in pea using five recombinant inbred line populations segregating for traits of agronomic importance. Pea (Pisum sativum L.) is one of the world's oldest domesticated crops and has been a model system in plant biology and genetics since the work of Gregor Mendel. Pea is the second most widely grown pulse crop in the world following common bean. The importance of pea as a food crop is growing due to its combination of moderate protein concentration, slowly digestible starch, high dietary fiber concentration, and its richness in micronutrients; however, pea has lagged behind other major crops in harnessing recent advances in molecular biology, genomics and bioinformatics, partly due to its large genome size with a large proportion of repetitive sequence, and to the relatively limited investment in research in this crop globally. The objective of this research was the development of a genome-wide transcriptome-based pea single-nucleotide polymorphism (SNP) marker platform using next-generation sequencing technology. A total of 1,536 polymorphic SNP loci selected from over 20,000 non-redundant SNPs identified using deep transcriptome sequencing of eight diverse Pisum accessions were used for genotyping in five RIL populations using an Illumina GoldenGate assay. The first high-density pea SNP map defining all seven linkage groups was generated by integrating with previously published anchor markers. Syntenic relationships of this map with the model legume Medicago truncatula and lentil (Lens culinaris Medik.) maps were established. The genic SNP map establishes a foundation for future molecular breeding efforts by enabling both the identification and tracking of introgression of genomic regions harbouring QTLs related to agronomic and seed quality traits.
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Affiliation(s)
- Anoop Sindhu
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Larissa Ramsay
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
- Present Address: Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Lacey-Anne Sanderson
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Robert Stonehouse
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Rong Li
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Janet Condie
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Arun S. K. Shunmugam
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Yong Liu
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Ambuj B. Jha
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Marwan Diapari
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Judith Burstin
- UMR1347 Agroecology, INRA, 17 rue de Sully, 21065 Dijon Cedex, France
| | - Gregoire Aubert
- UMR1347 Agroecology, INRA, 17 rue de Sully, 21065 Dijon Cedex, France
| | - Bunyamin Tar’an
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Kirstin E. Bett
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Thomas D. Warkentin
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Andrew G. Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
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Brown AF, Yousef GG, Chebrolu KK, Byrd RW, Everhart KW, Thomas A, Reid RW, Parkin IAP, Sharpe AG, Oliver R, Guzman I, Jackson EW. High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets. Theor Appl Genet 2014; 127:2051-64. [PMID: 25119868 DOI: 10.1007/s00122-014-2360-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/13/2014] [Indexed: 05/19/2023]
Abstract
A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae. A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.
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Affiliation(s)
- Allan F Brown
- Department of Horticultural Science, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA,
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Deokar AA, Ramsay L, Sharpe AG, Diapari M, Sindhu A, Bett K, Warkentin TD, Tar'an B. Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly. BMC Genomics 2014; 15:708. [PMID: 25150411 PMCID: PMC4158123 DOI: 10.1186/1471-2164-15-708] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/31/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In the whole genome sequencing, genetic map provides an essential framework for accurate and efficient genome assembly and validation. The main objectives of this study were to develop a high-density genetic map using RAD-Seq (Restriction-site Associated DNA Sequencing) genotyping-by-sequencing (RAD-Seq GBS) and Illumina GoldenGate assays, and to examine the alignment of the current map with the kabuli chickpea genome assembly. RESULTS Genic single nucleotide polymorphisms (SNPs) totaling 51,632 SNPs were identified by 454 transcriptome sequencing of Cicer arietinum and Cicer reticulatum genotypes. Subsequently, an Illumina GoldenGate assay for 1,536 SNPs was developed. A total of 1,519 SNPs were successfully assayed across 92 recombinant inbred lines (RILs), of which 761 SNPs were polymorphic between the two parents. In addition, the next generation sequencing (NGS)-based GBS was applied to the same population generating 29,464 high quality SNPs. These SNPs were clustered into 626 recombination bins based on common segregation patterns. Data from the two approaches were used for the construction of a genetic map using a population derived from an intraspecific cross. The map consisted of 1,336 SNPs including 604 RAD recombination bins and 732 SNPs from Illumina GoldenGate assay. The map covered 653 cM of the chickpea genome with an average distance between adjacent markers of 0.5 cM. To date, this is the most extensive genetic map of chickpea using an intraspecific population. The alignment of the map with the CDC Frontier genome assembly revealed an overall conserved marker order; however, a few local inconsistencies within the Cicer arietinum pseudochromosome 1 (Ca1), Ca5 and Ca8 were detected. The map enabled the alignment of 215 unplaced scaffolds from the CDC Frontier draft genome assembly. The alignment also revealed varying degrees of recombination rates and hotspots across the chickpea genome. CONCLUSIONS A high-density genetic map using RAD-Seq GBS and Illumina GoldenGate assay was developed and aligned with the existing kabuli chickpea draft genome sequence. The analysis revealed an overall conserved marker order, although some localized inversions between draft genome assembly and the genetic map were detected. The current analysis provides an insight of the recombination rates and hotspots across the chickpea genome.
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Affiliation(s)
| | | | | | | | | | | | | | - Bunyamin Tar'an
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr, Saskatoon, SK S7N 5A8, Canada.
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Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VHD, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CHD, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014. [PMID: 25146293 DOI: 10.1126/science.125343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
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Affiliation(s)
- Boulos Chalhoub
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France.
| | - France Denoeud
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, MD 20850, USA. Center for Genomics and Biotechnology, Fujian Agriculture and Forestry, University, Fuzhou 350002, Fujian Province, China
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. Center of Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei 063000, China
| | - Julien Chiquet
- Laboratoire de Mathématiques et Modélisation d'Evry-UMR 8071 CNRS/Université d'Evry val d'Essonne-USC INRA, Evry, France
| | - Harry Belcram
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Birgit Samans
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Margot Corréa
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jérémy Just
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Cyril Falentin
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Chu Shin Koh
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Isabelle Le Clainche
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Maria Bernard
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Pascal Bento
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Benjamin Noel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Adriana Alberti
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Mathieu Charles
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Dominique Arnaud
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - Salman Alamery
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kamel Jabbari
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France. Cologne Center for Genomics, University of Cologne, Weyertal 115b, 50931 Köln, Germany
| | - Meixia Zhao
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Houda Chelaifa
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - David Tack
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Gilles Lassalle
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Imen Mestiri
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Nicolas Schnel
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Marie-Christine Le Paslier
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Guangyi Fan
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Victor Renault
- Fondation Jean Dausset-Centre d'Étude du Polymorphisme Humain, 27 rue Juliette Dodu, 75010 Paris, France
| | - Philippe E Bayer
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Agnieszka A Golicz
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Sahana Manoli
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Vinh Ha Dinh Thi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Smahane Chalabi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Reece Tollenaere
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Yunhai Lu
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Christophe Battail
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Aurélie Canaguier
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Chauveau
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Bérard
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Gwenaëlle Deniot
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Mei Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Fengming Sun
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon-305764, South Korea
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, USA
| | | | - Ian Bancroft
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Dominique Brunel
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Régine Delourme
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Michel Renard
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Keith L Adams
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Jacqueline Batley
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia
| | - Rod J Snowdon
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - David Edwards
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia.
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France.
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37
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Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VHD, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CHD, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014; 345:950-3. [PMID: 25146293 DOI: 10.1126/science.1253435] [Citation(s) in RCA: 1357] [Impact Index Per Article: 135.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
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Affiliation(s)
- Boulos Chalhoub
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France.
| | - France Denoeud
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, MD 20850, USA. Center for Genomics and Biotechnology, Fujian Agriculture and Forestry, University, Fuzhou 350002, Fujian Province, China
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. Center of Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei 063000, China
| | - Julien Chiquet
- Laboratoire de Mathématiques et Modélisation d'Evry-UMR 8071 CNRS/Université d'Evry val d'Essonne-USC INRA, Evry, France
| | - Harry Belcram
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Birgit Samans
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Margot Corréa
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jérémy Just
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Cyril Falentin
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Chu Shin Koh
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Isabelle Le Clainche
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Maria Bernard
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Pascal Bento
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Benjamin Noel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Adriana Alberti
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Mathieu Charles
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Dominique Arnaud
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - Salman Alamery
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kamel Jabbari
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France. Cologne Center for Genomics, University of Cologne, Weyertal 115b, 50931 Köln, Germany
| | - Meixia Zhao
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Houda Chelaifa
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - David Tack
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Gilles Lassalle
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Imen Mestiri
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Nicolas Schnel
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Marie-Christine Le Paslier
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Guangyi Fan
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Victor Renault
- Fondation Jean Dausset-Centre d'Étude du Polymorphisme Humain, 27 rue Juliette Dodu, 75010 Paris, France
| | - Philippe E Bayer
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Agnieszka A Golicz
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Sahana Manoli
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Vinh Ha Dinh Thi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Smahane Chalabi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Reece Tollenaere
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Yunhai Lu
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Christophe Battail
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Aurélie Canaguier
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Chauveau
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Bérard
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Gwenaëlle Deniot
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Mei Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Fengming Sun
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon-305764, South Korea
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, USA
| | | | - Ian Bancroft
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Dominique Brunel
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Régine Delourme
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Michel Renard
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Keith L Adams
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Jacqueline Batley
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia
| | - Rod J Snowdon
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - David Edwards
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia.
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France.
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Kagale S, Robinson SJ, Nixon J, Xiao R, Huebert T, Condie J, Kessler D, Clarke WE, Edger PP, Links MG, Sharpe AG, Parkin IAP. Polyploid evolution of the Brassicaceae during the Cenozoic era. Plant Cell 2014; 26:2777-91. [PMID: 25035408 PMCID: PMC4145113 DOI: 10.1105/tpc.114.126391] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/07/2014] [Accepted: 06/19/2014] [Indexed: 05/18/2023]
Abstract
The Brassicaceae (Cruciferae) family, owing to its remarkable species, genetic, and physiological diversity as well as its significant economic potential, has become a model for polyploidy and evolutionary studies. Utilizing extensive transcriptome pyrosequencing of diverse taxa, we established a resolved phylogeny of a subset of crucifer species. We elucidated the frequency, age, and phylogenetic position of polyploidy and lineage separation events that have marked the evolutionary history of the Brassicaceae. Besides the well-known ancient α (47 million years ago [Mya]) and β (124 Mya) paleopolyploidy events, several species were shown to have undergone a further more recent (∼7 to 12 Mya) round of genome multiplication. We identified eight whole-genome duplications corresponding to at least five independent neo/mesopolyploidy events. Although the Brassicaceae family evolved from other eudicots at the beginning of the Cenozoic era of the Earth (60 Mya), major diversification occurred only during the Neogene period (0 to 23 Mya). Remarkably, the widespread species divergence, major polyploidy, and lineage separation events during Brassicaceae evolution are clustered in time around epoch transitions characterized by prolonged unstable climatic conditions. The synchronized diversification of Brassicaceae species suggests that polyploid events may have conferred higher adaptability and increased tolerance toward the drastically changing global environment, thus facilitating species radiation.
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Affiliation(s)
- Sateesh Kagale
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada National Research Council Canada, Saskatoon SK S7N 0W9, Canada
| | | | - John Nixon
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Rong Xiao
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Terry Huebert
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Janet Condie
- National Research Council Canada, Saskatoon SK S7N 0W9, Canada
| | - Dallas Kessler
- Plant Gene Resources of Canada, Saskatoon SK S7N 0X2, Canada
| | - Wayne E Clarke
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Matthew G Links
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Andrew G Sharpe
- National Research Council Canada, Saskatoon SK S7N 0W9, Canada
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Parkin IAP, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL, Denoeud F, Belcram H, Links MG, Just J, Clarke C, Bender T, Huebert T, Mason AS, Pires JC, Barker G, Moore J, Walley PG, Manoli S, Batley J, Edwards D, Nelson MN, Wang X, Paterson AH, King G, Bancroft I, Chalhoub B, Sharpe AG. Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol 2014; 15:R77. [PMID: 24916971 PMCID: PMC4097860 DOI: 10.1186/gb-2014-15-6-r77] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 06/10/2014] [Indexed: 01/24/2023] Open
Abstract
Background Brassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus. Results We generate an assembly representing 75% of the predicted B. oleracea genome using a hybrid Illumina/Roche 454 approach. Two dense genetic maps are generated to anchor almost 92% of the assembled scaffolds to nine pseudo-chromosomes. Over 50,000 genes are annotated and 40% of the genome predicted to be repetitive, thus contributing to the increased genome size of B. oleracea compared to its close relative B. rapa. A snapshot of both the leaf transcriptome and methylome allows comparisons to be made across the triplicated sub-genomes, which resulted from the most recent Brassiceae-specific polyploidy event. Conclusions Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture. Although cytosine methylation does not correlate with individual gene dominance, the independent methylation patterns of triplicated copies suggest epigenetic mechanisms play a role in the functional diversification of duplicate genes.
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Nayidu NK, Kagale S, Taheri A, Withana-Gamage TS, Parkin IAP, Sharpe AG, Gruber MY. Comparison of five major trichome regulatory genes in Brassica villosa with orthologues within the Brassicaceae. PLoS One 2014; 9:e95877. [PMID: 24755905 PMCID: PMC3995807 DOI: 10.1371/journal.pone.0095877] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 03/31/2014] [Indexed: 01/21/2023] Open
Abstract
Coding sequences for major trichome regulatory genes, including the positive regulators GLABRA 1(GL1), GLABRA 2 (GL2), ENHANCER OF GLABRA 3 (EGL3), and TRANSPARENT TESTA GLABRA 1 (TTG1) and the negative regulator TRIPTYCHON (TRY), were cloned from wild Brassica villosa, which is characterized by dense trichome coverage over most of the plant. Transcript (FPKM) levels from RNA sequencing indicated much higher expression of the GL2 and TTG1 regulatory genes in B. villosa leaves compared with expression levels of GL1 and EGL3 genes in either B. villosa or the reference genome species, glabrous B. oleracea; however, cotyledon TTG1 expression was high in both species. RNA sequencing and Q-PCR also revealed an unusual expression pattern for the negative regulators TRY and CPC, which were much more highly expressed in trichome-rich B. villosa leaves than in glabrous B. oleracea leaves and in glabrous cotyledons from both species. The B. villosa TRY expression pattern also contrasted with TRY expression patterns in two diploid Brassica species, and with the Arabidopsis model for expression of negative regulators of trichome development. Further unique sequence polymorphisms, protein characteristics, and gene evolution studies highlighted specific amino acids in GL1 and GL2 coding sequences that distinguished glabrous species from hairy species and several variants that were specific for each B. villosa gene. Positive selection was observed for GL1 between hairy and non-hairy plants, and as expected the origin of the four expressed positive trichome regulatory genes in B. villosa was predicted to be from B. oleracea. In particular the unpredicted expression patterns for TRY and CPC in B. villosa suggest additional characterization is needed to determine the function of the expanded families of trichome regulatory genes in more complex polyploid species within the Brassicaceae.
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Affiliation(s)
- Naghabushana K. Nayidu
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon SK, Canada
| | - Sateesh Kagale
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK, Canada
- National Research Council (NRC), Saskatoon SK, Canada
| | - Ali Taheri
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK, Canada
| | | | - Isobel A. P. Parkin
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK, Canada
| | | | - Margaret Y. Gruber
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK, Canada
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Clarke WE, Parkin IA, Gajardo HA, Gerhardt DJ, Higgins E, Sidebottom C, Sharpe AG, Snowdon RJ, Federico ML, Iniguez-Luy FL. Genomic DNA enrichment using sequence capture microarrays: a novel approach to discover sequence nucleotide polymorphisms (SNP) in Brassica napus L. PLoS One 2013; 8:e81992. [PMID: 24312619 PMCID: PMC3849492 DOI: 10.1371/journal.pone.0081992] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/20/2013] [Indexed: 12/24/2022] Open
Abstract
Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola (Brassica napus L., AACC, 2n=38). The main goal of this project was to combine sequence capture with next generation sequencing (NGS) to discover single nucleotide polymorphisms (SNPs) in specific areas of the B. napus genome historically associated (via quantitative trait loci –QTL– analysis) to traits of agronomical and nutritional importance. A 2.1 million feature sequence capture platform was designed to interrogate DNA sequence variation across 47 specific genomic regions, representing 51.2 Mb of the Brassica A and C genomes, in ten diverse rapeseed genotypes. All ten genotypes were sequenced using the 454 Life Sciences chemistry and to assess the effect of increased sequence depth, two genotypes were also sequenced using Illumina HiSeq chemistry. As a result, 589,367 potentially useful SNPs were identified. Analysis of sequence coverage indicated a four-fold increased representation of target regions, with 57% of the filtered SNPs falling within these regions. Sixty percent of discovered SNPs corresponded to transitions while 40% were transversions. Interestingly, fifty eight percent of the SNPs were found in genic regions while 42% were found in intergenic regions. Further, a high percentage of genic SNPs was found in exons (65% and 64% for the A and C genomes, respectively). Two different genotyping assays were used to validate the discovered SNPs. Validation rates ranged from 61.5% to 84% of tested SNPs, underpinning the effectiveness of this SNP discovery approach. Most importantly, the discovered SNPs were associated with agronomically important regions of the B. napus genome generating a novel data resource for research and breeding this crop species.
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Affiliation(s)
- Wayne E. Clarke
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Isobel A. Parkin
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Humberto A. Gajardo
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Louisiana, United States of America Araucanía, Chile
| | | | - Erin Higgins
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Christine Sidebottom
- Plant Biotechnology Institute, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Andrew G. Sharpe
- Plant Biotechnology Institute, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Maria L. Federico
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Louisiana, United States of America Araucanía, Chile
| | - Federico L. Iniguez-Luy
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Louisiana, United States of America Araucanía, Chile
- * E-mail:
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Raman H, Raman R, Kilian A, Detering F, Long Y, Edwards D, Parkin IAP, Sharpe AG, Nelson MN, Larkan N, Zou J, Meng J, Aslam MN, Batley J, Cowling WA, Lydiate D. A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: applications in genetic dissection of qualitative and quantitative traits. BMC Genomics 2013; 14:277. [PMID: 23617817 PMCID: PMC3641989 DOI: 10.1186/1471-2164-14-277] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 04/06/2013] [Indexed: 12/03/2022] Open
Abstract
Background Dense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive molecular breeding, and map-based gene cloning. This report describes the construction of the first B. napus consensus map consisting of a 1,359 anchored array based genotyping platform; Diversity Arrays Technology (DArT), and non-DArT markers from six populations originating from Australia, Canada, China and Europe. We aligned the B. napus DArT sequences with genomic scaffolds from Brassica rapa and Brassica oleracea, and identified DArT loci that showed linkage with qualitative and quantitative loci associated with agronomic traits. Results The integrated consensus map covered a total of 1,987.2 cM and represented all 19 chromosomes of the A and C genomes, with an average map density of one marker per 1.46 cM, corresponding to approximately 0.88 Mbp of the haploid genome. Through in silico physical mapping 2,457 out of 3,072 (80%) DArT clones were assigned to the genomic scaffolds of B. rapa (A genome) and B. oleracea (C genome). These were used to orientate the genetic consensus map with the chromosomal sequences. The DArT markers showed linkage with previously identified non-DArT markers associated with qualitative and quantitative trait loci for plant architecture, phenological components, seed and oil quality attributes, boron efficiency, sucrose transport, male sterility, and race-specific resistance to blackleg disease. Conclusions The DArT markers provide increased marker density across the B. napus genome. Most of the DArT markers represented on the current array were sequenced and aligned with the B. rapa and B. oleracea genomes, providing insight into the Brassica A and C genomes. This information can be utilised for comparative genomics and genomic evolution studies. In summary, this consensus map can be used to (i) integrate new generation markers such as SNP arrays and next generation sequencing data; (ii) anchor physical maps to facilitate assembly of B. napus genome sequences; and (iii) identify candidate genes underlying natural genetic variation for traits of interest.
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Affiliation(s)
- Harsh Raman
- EH Graham Centre for Agricultural Innovation (an alliance between NSWDPI and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
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Navabi ZK, Huebert T, Sharpe AG, O’Neill CM, Bancroft I, Parkin IAP. Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea. BMC Genomics 2013; 14:250. [PMID: 23586706 PMCID: PMC3765694 DOI: 10.1186/1471-2164-14-250] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 04/04/2013] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The Brassica B genome is known to carry several important traits, yet there has been limited analyses of its underlying genome structure, especially in comparison to the closely related A and C genomes. A bacterial artificial chromosome (BAC) library of Brassica nigra was developed and screened with 17 genes from a 222 kb region of A. thaliana that had been well characterised in both the Brassica A and C genomes. RESULTS Fingerprinting of 483 apparently non-redundant clones defined physical contigs for the corresponding regions in B. nigra. The target region is duplicated in A. thaliana and six homologous contigs were found in B. nigra resulting from the whole genome triplication event shared by the Brassiceae tribe. BACs representative of each region were sequenced to elucidate the level of microscale rearrangements across the Brassica species divide. CONCLUSIONS Although the B genome species separated from the A/C lineage some 6 Mya, comparisons between the three paleopolyploid Brassica genomes revealed extensive conservation of gene content and sequence identity. The level of fractionation or gene loss varied across genomes and genomic regions; however, the greatest loss of genes was observed to be common to all three genomes. One large-scale chromosomal rearrangement differentiated the B genome suggesting such events could contribute to the lack of recombination observed between B genome species and those of the closely related A/C lineage.
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Affiliation(s)
- Zahra-Katy Navabi
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Terry Huebert
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Andrew G Sharpe
- DNA Technologies Laboratory, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Carmel M O’Neill
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Ian Bancroft
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Isobel AP Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
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Liao D, Cram D, Sharpe AG, Marsolais F. Transcriptome Profiling Identifies Candidate Genes Associated with the Accumulation of Distinct Sulfur γ-Glutamyl Dipeptides in Phaseolus vulgaris and Vigna mungo Seeds. Front Plant Sci 2013; 4:60. [PMID: 23532826 PMCID: PMC3606967 DOI: 10.3389/fpls.2013.00060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 03/04/2013] [Indexed: 05/29/2023]
Abstract
Common bean (Phaseolus vulgaris) and black gram (Vigna mungo) accumulate γ-Glutamyl-S-methylcysteine and γ-Glutamyl-methionine in seed, respectively. Transcripts were profiled by 454 pyrosequencing data at a similar developmental stage coinciding with the beginning of the accumulation of these metabolites. Expressed sequence tags were assembled into Unigenes, which were assigned to specific genes in the early release chromosomal assembly of the P. vulgaris genome. Genes involved in multiple sulfur metabolic processes were expressed in both species. Expression of Sultr3 members was predominant in P. vulgaris, whereas expression of Sultr5 members predominated in V. mungo. Expression of the cytosolic SERAT1;1 and -1;2 was approximately fourfold higher in P. vulgaris while expression of the plastidic SERAT2;1 was twofold higher in V. mungo. Among BSAS family members, BSAS4;1, encoding a cytosolic cysteine desulfhydrase, and BSAS1;1, encoding a cytosolic O-acetylserine sulphydrylase were most highly expressed in both species. This was followed by BSAS3;1 encoding a plastidic β-cyanoalanine synthase which was more highly expressed by 10-fold in P. vulgaris. The data identify BSAS3;1 as a candidate enzyme for the biosynthesis of S-methylcysteine through the use of methanethiol as substrate instead of cyanide. Expression of GLC1 would provide a complete sequence leading to the biosynthesis of γ-Glutamyl-S-methylcysteine in plastids. The detection of S-methylhomoglutathione in P. vulgaris suggested that homoglutathione synthetase may accept, to some extent, γ-Glutamyl-S-methylcysteine as substrate, which might lead to the formation of S-methylated phytochelatins. In conclusion, 454 sequencing was effective at revealing differences in the expression of sulfur metabolic genes, providing information on candidate genes for the biosynthesis of distinct sulfur amino acid γ-Glutamyl dipeptides between P. vulgaris and V. mungo.
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Affiliation(s)
- Dengqun Liao
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food CanadaLondon, ON, Canada
| | - Dustin Cram
- National Research Council CanadaSaskatoon, SK, Canada
| | | | - Frédéric Marsolais
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food CanadaLondon, ON, Canada
- Department of Biology, University of Western OntarioLondon, ON, Canada
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Sharpe AG, Ramsay L, Sanderson LA, Fedoruk MJ, Clarke WE, Li R, Kagale S, Vijayan P, Vandenberg A, Bett KE. Ancient orphan crop joins modern era: gene-based SNP discovery and mapping in lentil. BMC Genomics 2013; 14:192. [PMID: 23506258 PMCID: PMC3635939 DOI: 10.1186/1471-2164-14-192] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 02/22/2013] [Indexed: 12/22/2022] Open
Abstract
Background The genus Lens comprises a range of closely related species within the galegoid clade of the Papilionoideae family. The clade includes other important crops (e.g. chickpea and pea) as well as a sequenced model legume (Medicago truncatula). Lentil is a global food crop increasing in importance in the Indian sub-continent and elsewhere due to its nutritional value and quick cooking time. Despite this importance there has been a dearth of genetic and genomic resources for the crop and this has limited the application of marker-assisted selection strategies in breeding. Results We describe here the development of a deep and diverse transcriptome resource for lentil using next generation sequencing technology. The generation of data in multiple cultivated (L. culinaris) and wild (L. ervoides) genotypes together with the utilization of a bioinformatics workflow enabled the identification of a large collection of SNPs and the subsequent development of a genotyping platform that was used to establish the first comprehensive genetic map of the L. culinaris genome. Extensive collinearity with M. truncatula was evident on the basis of sequence homology between mapped markers and the model genome and large translocations and inversions relative to M. truncatula were identified. An estimate for the time divergence of L. culinaris from L. ervoides and of both from M. truncatula was also calculated. Conclusions The availability of the genomic and derived molecular marker resources presented here will help change lentil breeding strategies and lead to increased genetic gain in the future.
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Affiliation(s)
- Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
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Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe AG, Wong GKS, Wang J, Deyholos MK. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J 2012; 72:461-73. [PMID: 22757964 DOI: 10.1111/j.1365-313x.2012.05093.x] [Citation(s) in RCA: 252] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.
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Affiliation(s)
- Zhiwen Wang
- BGI-Shenzen, Bei Shan Industrial Zone, Yantian District, Shenzhen 518083, China
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Sharpe AG, Parkin IA, Keith DJ, Lydiate DJ. Frequent nonreciprocal translocations in the amphidiploid genome of oilseed rape (Brassica napus). Genome 2012; 38:1112-21. [PMID: 18470235 DOI: 10.1139/g95-148] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A RFLP map of Brassica napus, consisting of 277 loci arranged in 19 linkage groups, was produced from genetic segregation in a combined population of 174 doubled-haploid microspore-derived lines. The integration of this map with a B. napus map derived from a resynthesized B. napus x oilseed rape cross allowed the 10 linkage groups of the B. napus A genome and the 9 linkage groups of the C genome to be identified. Collinear patterns of marker loci on different linkage groups suggested potential partial homoeologues. RFLP patterns consistent with aberrant chromosomes were observed in 9 of the 174 doubled-haploid lines. At least 4 of these lines carried nonreciprocal, homoeologous translocations. These translocations were probably the result of homoeologous recombination in the amphidiploid genome of oilseed rape, suggesting that domesticated B. napus is unable to control chromosome pairing completely. Evidence for genome homogenization in oilseed rape is presented and its implications on genetic mapping in amphidiploid species is discussed. The level of polymorphism in the A genome was higher than that in the C genome and this might be a general property of oilseed rape crosses.
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Parkin IA, Sharpe AG, Keith DJ, Lydiate DJ. Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). Genome 2012; 38:1122-31. [PMID: 18470236 DOI: 10.1139/g95-149] [Citation(s) in RCA: 280] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A genetic linkage map consisting of 399 RFLP-defined loci was generated from a cross between resynthesized Brassica napus (an interspecific B. rapa x B. oleracea hybrid) and "natural" oilseed rape. The majority of loci exhibited disomic inheritance of parental alleles demonstrating that B. rapa chromosomes were each pairing exclusively with recognisable A-genome homologues in B. napus and that B. oleracea chromosomes were pairing similarly with C-genome homologues. This behaviour identified the 10 A genome and 9 C genome linkage groups of B. napus and demonstrated that the nuclear genomes of B. napus, B. rapa, and B. oleracea have remained essentially unaltered since the formation of the amphidiploid species, B. napus. A range of unusual marker patterns, which could be explained by aneuploidy and nonreciprocal translocations, were observed in the mapping population. These chromosome abnormalities were probably caused by associations between homoeologous chromosomes at meiosis in the resynthesized parent and the F1 plant leading to nondisjunction and homoeologous recombination.
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Kelly AL, Sharpe AG, Nixon JH, Lydiate DJ, Evans EJ. Indistinguishable patterns of recombination resulting from male and female meioses in Brassica napus (oilseed rape). Genome 2012; 40:49-56. [PMID: 18464807 DOI: 10.1139/g97-007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An F1 individual derived from a cross between two distinct lines of spring oilseed rape (Brassica napus) was used to produce a pair of complementary backcross populations, each consisting of 90 individuals. The F1 donated male gametes to the Male population and female gametes to the Female population. Genetic maps were generated from both populations and aligned using 117 common loci to form an integrated genome map of B. napus with 243 RFLP-defined loci. A comparison of the frequency and distribution of crossovers in the two populations of F1 gametes (assayed in the Male and Female populations) detected no differences. The genetic maps derived from the Male and Female populations each consisted of 19 linkage groups spanning 1544 and 1577 cM, respectively. The maps were aligned with other B. napus maps, and all 19 equivalent linkage groups were unambiguously assigned. The genetic size and general organisation of the new maps were comparable with those of pre-existing B. napus maps in most respects, except that the levels of polymorphism in the constituent A and C genomes were unusually similar in the new cross.
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Liao D, Pajak A, Karcz SR, Chapman BP, Sharpe AG, Austin RS, Datla R, Dhaubhadel S, Marsolais F. Transcripts of sulphur metabolic genes are co-ordinately regulated in developing seeds of common bean lacking phaseolin and major lectins. J Exp Bot 2012; 63:6283-95. [PMID: 23066144 PMCID: PMC3481216 DOI: 10.1093/jxb/ers280] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The lack of phaseolin and phytohaemagglutinin in common bean (dry bean, Phaseolus vulgaris) is associated with an increase in total cysteine and methionine concentrations by 70% and 10%, respectively, mainly at the expense of an abundant non-protein amino acid, S-methyl-cysteine. Transcripts were profiled between two genetically related lines differing for this trait at four stages of seed development using a high density microarray designed for common bean. Transcripts of multiple sulphur-rich proteins were elevated, several previously identified by proteomics, including legumin, basic 7S globulin, albumin-2, defensin, albumin-1, the Bowman-Birk type proteinase inhibitor, the double-headed trypsin inhibitor, and the Kunitz trypsin inhibitor. A co-ordinated regulation of transcripts coding for sulphate transporters, sulphate assimilatory enzymes, serine acetyltransferases, cystathionine β-lyase, homocysteine S-methyltransferase and methionine gamma-lyase was associated with changes in cysteine and methionine concentrations. Differential gene expression of sulphur-rich proteins preceded that of sulphur metabolic enzymes, suggesting a regulation by demand from the protein sink. Up-regulation of SERAT1;1 and -1;2 expression revealed an activation of cytosolic O-acetylserine biosynthesis. Down-regulation of SERAT2;1 suggested that cysteine and S-methyl-cysteine biosynthesis may be spatially separated in different subcellular compartments. Analysis of free amino acid profiles indicated that enhanced cysteine biosynthesis was correlated with a depletion of O-acetylserine. These results contribute to our understanding of the regulation of sulphur metabolism in developing seed in response to a change in the composition of endogenous proteins.
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Affiliation(s)
- Dengqun Liao
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Agnieszka Pajak
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Steven R. Karcz
- Agriculture and Agri-Food Canada, Bioproducts and Bioprocesses, Saskatoon Research Centre, 107 Science Place, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - B. Patrick Chapman
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Andrew G. Sharpe
- National Research Council Canada, Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Ryan S. Austin
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Raju Datla
- National Research Council Canada, Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sangeeta Dhaubhadel
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Frédéric Marsolais
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada
- * To whom correspondence should be addressed. E-mail:
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