1
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Osman K, Desjardins SD, Simmonds J, Burridge AJ, Kanyuka K, Henderson IR, Edwards KJ, Uauy C, Franklin FCH, Higgins JD, Sanchez-Moran E. FIGL1 prevents aberrant chromosome associations and fragmentation and limits crossovers in polyploid wheat meiosis. New Phytol 2024. [PMID: 38584326 DOI: 10.1111/nph.19716] [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] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/10/2024] [Indexed: 04/09/2024]
Abstract
Meiotic crossovers (COs) generate genetic diversity and are crucial for viable gamete production. Plant COs are typically limited to 1-3 per chromosome pair, constraining the development of improved varieties, which in wheat is exacerbated by an extreme distal localisation bias. Advances in wheat genomics and related technologies provide new opportunities to investigate, and possibly modify, recombination in this important crop species. Here, we investigate the disruption of FIGL1 in tetraploid and hexaploid wheat as a potential strategy for modifying CO frequency/position. We analysed figl1 mutants and virus-induced gene silencing lines cytogenetically. Genetic mapping was performed in the hexaploid. FIGL1 prevents abnormal meiotic chromosome associations/fragmentation in both ploidies. It suppresses class II COs in the tetraploid such that CO/chiasma frequency increased 2.1-fold in a figl1 msh5 quadruple mutant compared with a msh5 double mutant. It does not appear to affect class I COs based on HEI10 foci counts in a hexaploid figl1 triple mutant. Genetic mapping in the triple mutant suggested no significant overall increase in total recombination across examined intervals but revealed large increases in specific individual intervals. Notably, the tetraploid figl1 double mutant was sterile but the hexaploid triple mutant was moderately fertile, indicating potential utility for wheat breeding.
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Affiliation(s)
- Kim Osman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stuart D Desjardins
- Department of Genetics and Genome Biology, University of Leicester, University Road, Adrian Building, Leicester, LE1 7RH, UK
| | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Amanda J Burridge
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | | | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Keith J Edwards
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - F Chris H Franklin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, University Road, Adrian Building, Leicester, LE1 7RH, UK
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2
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Lin X, Xu Y, Wang D, Yang Y, Zhang X, Bie X, Gui L, Chen Z, Ding Y, Mao L, Zhang X, Lu F, Zhang X, Uauy C, Fu X, Xiao J. Systematic identification of wheat spike developmental regulators by integrated multi-omics, transcriptional network, GWAS, and genetic analyses. Mol Plant 2024; 17:438-459. [PMID: 38310351 DOI: 10.1016/j.molp.2024.01.010] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 02/05/2024]
Abstract
The spike architecture of wheat plays a crucial role in determining grain number, making it a key trait for optimization in wheat breeding programs. In this study, we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages, revealing coordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering transition. We constructed a core transcriptional regulatory network (TRN) that drives wheat spike formation and experimentally validated a multi-layer regulatory module involving TaSPL15, TaAGLG1, and TaFUL2. By integrating the TRN with genome-wide association studies, we identified 227 transcription factors, including 42 with known functions and 185 with unknown functions. Further investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time, such as TaMYC2-A1, TaMYB30-A1, and TaWRKY37-A1. Of particular interest, TaMYB30-A1, downstream of and repressed by WFZP, was found to regulate fertile spikelet number. Notably, the excellent haplotype of TaMYB30-A1, which contains a C allele at the WFZP binding site, was enriched during wheat breeding improvement in China, leading to improved agronomic traits. Finally, we constructed a free and open access Wheat Spike Multi-Omic Database (http://39.98.48.156:8800/#/). Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development, with practical value for wheat breeding.
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Affiliation(s)
- Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongxin Xu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongzhi Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiaoyu Zhang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin Bie
- Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Lixuan Gui
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan 610000, China
| | - Zhongxu Chen
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan 610000, China
| | - Yiliang Ding
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Long Mao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fei Lu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, CAS, Beijing 100101, China
| | - Xiansheng Zhang
- Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xiangdong Fu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, CAS, Beijing 100101, China.
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3
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Horsnell R, Leigh FJ, Wright TIC, Burridge AJ, Ligeza A, Przewieslik-Allen AM, Howell P, Uauy C, Edwards KJ, Bentley AR. A wheat chromosome segment substitution line series supports characterization and use of progenitor genetic variation. Plant Genome 2024; 17:e20288. [PMID: 36718796 DOI: 10.1002/tpg2.20288] [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] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/20/2022] [Indexed: 06/18/2023]
Abstract
Genome-wide introgression and substitution lines have been developed in many plant species, enhancing mapping precision, gene discovery, and the identification and exploitation of variation from wild relatives. Created over multiple generations of crossing and/or backcrossing accompanied by marker-assisted selection, the resulting introgression lines are a fixed genetic resource. In this study we report the development of spring wheat (Triticum aestivum L.) chromosome segment substitution lines (CSSLs) generated to systematically capture genetic variation from tetraploid (T. turgidum ssp. dicoccoides) and diploid (Aegilops tauschii) progenitor species. Generated in a common genetic background over four generations of backcrossing, this is a base resource for the mapping and characterization of wheat progenitor variation. To facilitate further exploitation the final population was genetically characterized using a high-density genotyping array and a range of agronomic and grain traits assessed to demonstrate the potential use of the populations for trait localization in wheat.
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Affiliation(s)
- Richard Horsnell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | - Fiona J Leigh
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | - Tally I C Wright
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | | | - Aleksander Ligeza
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | | | - Philip Howell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
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4
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Zeng V, Uauy C, Chen Y. Identification of a novel SNP in the miR172 binding site of Q homoeolog AP2L-D5 is associated with spike compactness and agronomic traits in wheat (Triticum aestivum L.). Theor Appl Genet 2023; 137:13. [PMID: 38142253 DOI: 10.1007/s00122-023-04514-8] [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] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/23/2023] [Indexed: 12/25/2023]
Abstract
KEY MESSAGE This study found that the compact spike locus of ANK-15 is on chromosome 5D instead of 2B. We have identified a new allele of AP2L-D5 as the candidate causal polymorphism. Spike architecture is a key determinant of wheat yield, a crop which supports much of the human diet but whose yield gains are stagnating. Spike architecture mutants offer opportunities to identify genetic factors contributing to inflorescence development. Here, we investigate the locus underlying the compact spike phenotype of mutant line ANK-15 by conducting mRNA-sequencing and genetic mapping using ANK-15 and its non-compact spike near-isogenic line Novosibirskaya 67 (N67). Previous literature has placed the compact spike locus of ANK-15 to chromosome 2B. However, based on the single nucleotide polymorphisms (SNPs) identified using mRNA-seq data, we were unable to detect polymorphisms between N67 and ANK-15 in the putative chromosome 2B region. We performed differential expression analysis of developing rachis and found that AP2L-D5, the D homoeolog of the domestication Q gene, is upregulated in ANK-15 in comparison to N67. ANK-15 carries a SNP in the microRNA172 binding site of AP2L-D5, which is predicted to lead to higher expression of AP2L-D5 due to decreased miRNA172-mediated degradation. Furthermore, we performed genetic mapping using an ANK-15 × N67 F2 population and found a single quantitative trait locus on chromosome 5D coinciding with the position of AP2L-D5. This result suggests that AP2L-D5 is likely the underlying causal gene for the compact spike phenotype in ANK-15. We performed a field trial to investigate the effect of the AP2L-D5 allele on agronomic traits and found that the AP2L-D5 allele from ANK-15 is associated with a significant reduction in height, increased thousand grain weight (TGW), and increased grain width.
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Affiliation(s)
- Victoria Zeng
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yi Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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5
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Sharma PK, Ahmed HI, Heuberger M, Koo DH, Quiroz-Chavez J, Adhikari L, Raupp J, Cauet S, Rodde N, Cravero C, Callot C, Yadav IS, Kathiresan N, Athiyannan N, Ramirez-Gonzalez RH, Uauy C, Wicker T, Abrouk M, Gu YQ, Poland J, Krattinger SG, Lazo GR, Tiwari VK. An online database for einkorn wheat to aid in gene discovery and functional genomics studies. Database (Oxford) 2023; 2023:baad079. [PMID: 37971714 PMCID: PMC10653128 DOI: 10.1093/database/baad079] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/02/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help wheat research and breeding. Database URL https://wheat.pw.usda.gov/GG3/pangenome.
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Affiliation(s)
- Parva Kumar Sharma
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
| | - Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, 107, Zurich, Zollikerstrasse CH-8008, Switzerland
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, 4024 Throckmorton, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jesus Quiroz-Chavez
- John Innes Centre John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Laxman Adhikari
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - John Raupp
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, 4024 Throckmorton, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Stéphane Cauet
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Nathalie Rodde
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Charlotte Cravero
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Caroline Callot
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Inderjit Singh Yadav
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
| | - Nagarajan Kathiresan
- Supercomputing Core Lab, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | | | - Cristobal Uauy
- John Innes Centre John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 107, Zurich, Zollikerstrasse CH-8008, Switzerland
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Yong Q Gu
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Gerard R Lazo
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
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6
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López-Fernández M, García-Abadillo J, Uauy C, Ruiz M, Giraldo P, Pascual L. Genome wide association in Spanish bread wheat landraces identifies six key genomic regions that constitute potential targets for improving grain yield related traits. Theor Appl Genet 2023; 136:244. [PMID: 37957405 PMCID: PMC10643358 DOI: 10.1007/s00122-023-04492-x] [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] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023]
Abstract
KEY MESSAGE Association mapping conducted in 189 Spanish bread wheat landraces revealed six key genomic regions that constitute stable QTLs for yield and include 15 candidate genes. Genetically diverse landraces provide an ideal population to conduct association analysis. In this study, association mapping was conducted in a collection of 189 Spanish bread wheat landraces whose genomic diversity had been previously assessed. These genomic data were combined with characterization for yield-related traits, including grain size and shape, and phenological traits screened across five seasons. The association analysis revealed a total of 881 significant marker trait associations, involving 434 markers across the genome, that could be grouped in 366 QTLs based on linkage disequilibrium. After accounting for days to heading, we defined 33 high density QTL genomic regions associated to at least four traits. Considering the importance of detecting stable QTLs, 6 regions associated to several grain traits and thousand kernel weight in at least three environments were selected as the most promising ones to harbour targets for breeding. To dissect the genetic cause of the observed associations, we studied the function and in silico expression of the 413 genes located inside these six regions. This identified 15 candidate genes that provide a starting point for future analysis aimed at the identification and validation of wheat yield related genes.
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Affiliation(s)
- Matilde López-Fernández
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering (ETSIAAB), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Julián García-Abadillo
- Department of Biotechnology and Plant Biology, Centre for Biotechnology and Plant Genomics (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Magdalena Ruiz
- Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), CSIC, Autovía A2, Km. 36.2. Finca La Canaleja, 28805, Alcalá de Henares, Madrid, Spain
| | - Patricia Giraldo
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering (ETSIAAB), Universidad Politécnica de Madrid (UPM), Madrid, Spain.
| | - Laura Pascual
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering (ETSIAAB), Universidad Politécnica de Madrid (UPM), Madrid, Spain
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7
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Backhaus AE, Griffiths C, Vergara-Cruces A, Simmonds J, Lee R, Morris RJ, Uauy C. Delayed development of basal spikelets in wheat explains their increased floret abortion and rudimentary nature. J Exp Bot 2023; 74:5088-5103. [PMID: 37338600 PMCID: PMC10498016 DOI: 10.1093/jxb/erad233] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/15/2023] [Indexed: 06/21/2023]
Abstract
Large differences exist in the number of grains per spikelet across an individual wheat (Triticum aestivum L.) spike. The central spikelets produce the highest number of grains, while apical and basal spikelets are less productive, and the most basal spikelets are commonly only developed in rudimentary form. Basal spikelets are delayed in initiation, yet they continue to develop and produce florets. The precise timing or the cause of their abortion remains largely unknown. Here, we investigated the underlying causes of basal spikelet abortion using shading applications in the field. We found that basal spikelet abortion is likely to be the consequence of complete floret abortion, as both occur concurrently and have the same response to shading treatments. We detected no differences in assimilate availability across the spike. Instead, we show that the reduced developmental age of basal florets pre-anthesis is strongly associated with their increased abortion. Using the developmental age pre-abortion, we were able to predict final grain set per spikelet across the spike, alongside the characteristic gradient in the number of grains from basal to central spikelets. Future efforts to improve spikelet homogeneity across the spike could thus focus on improving basal spikelet establishment and increasing floret development rates pre-abortion.
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Affiliation(s)
| | - Cara Griffiths
- Plant Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | | | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Rebecca Lee
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Richard J Morris
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
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8
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Ahmed HI, Heuberger M, Schoen A, Koo DH, Quiroz-Chavez J, Adhikari L, Raupp J, Cauet S, Rodde N, Cravero C, Callot C, Lazo GR, Kathiresan N, Sharma PK, Moot I, Yadav IS, Singh L, Saripalli G, Rawat N, Datla R, Athiyannan N, Ramirez-Gonzalez RH, Uauy C, Wicker T, Tiwari VK, Abrouk M, Poland J, Krattinger SG. Einkorn genomics sheds light on history of the oldest domesticated wheat. Nature 2023; 620:830-838. [PMID: 37532937 PMCID: PMC10447253 DOI: 10.1038/s41586-023-06389-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 06/29/2023] [Indexed: 08/04/2023]
Abstract
Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.
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Affiliation(s)
- Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Adam Schoen
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - Laxman Adhikari
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - John Raupp
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Stéphane Cauet
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Nathalie Rodde
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Charlotte Cravero
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Caroline Callot
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Gerard R Lazo
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, CA, USA
| | - Nagarajan Kathiresan
- KAUST Supercomputing Core Lab (KSL), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Parva K Sharma
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Ian Moot
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Inderjit Singh Yadav
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Lovepreet Singh
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Gautam Saripalli
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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9
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Boden SA, McIntosh RA, Uauy C, Krattinger SG, Dubcovsky J, Rogers WJ, Xia XC, Badaeva ED, Bentley AR, Brown-Guedira G, Caccamo M, Cattivelli L, Chhuneja P, Cockram J, Contreras-Moreira B, Dreisigacker S, Edwards D, González FG, Guzmán C, Ikeda TM, Karsai I, Nasuda S, Pozniak C, Prins R, Sen TZ, Silva P, Simkova H, Zhang Y. Updated guidelines for gene nomenclature in wheat. Theor Appl Genet 2023; 136:72. [PMID: 36952017 PMCID: PMC10036449 DOI: 10.1007/s00122-023-04253-w] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/10/2022] [Indexed: 06/18/2023]
Abstract
Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community. The last decade has seen a proliferation in genomic resources for wheat, including reference- and pan-genome assemblies with gene annotations, which provide new opportunities to detect, characterise, and describe genes that influence traits of interest. The expansion of genetic information has supported growth of the wheat research community and catalysed strong interest in the genes that control agronomically important traits, such as yield, pathogen resistance, grain quality, and abiotic stress tolerance. To accommodate these developments, we present an updated set of guidelines for gene nomenclature in wheat. These guidelines can be used to describe loci identified based on morphological or phenotypic features or to name genes based on sequence information, such as similarity to genes characterised in other species or the biochemical properties of the encoded protein. The updated guidelines provide a flexible system that is not overly prescriptive but provides structure and a common framework for naming genes in wheat, which may be extended to related cereal species. We propose these guidelines be used henceforth by the wheat research community to facilitate integration of data from independent studies and allow broader and more efficient use of text and data mining approaches, which will ultimately help further accelerate wheat research and breeding.
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Affiliation(s)
- S. A. Boden
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064 Australia
| | - R. A. McIntosh
- School of Life and Environmental Sciences, University of Sydney, Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW 2570 Australia
| | - C. Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - S. G. Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
- The Wheat Initiative, 14195 Berlin, Germany
| | - J. Dubcovsky
- Department of Plant Science, University of California, Davis, CA 95616 USA
- The Wheat Initiative, 14195 Berlin, Germany
| | - W. J. Rogers
- Departamento de Biología Aplicada, Facultad de Agronomía (CIISAS, CIC-BIOLAB AZUL, CONICET-INBIOTEC, CRESCA), Universidad Nacional del Centro de La Provincia de Buenos Aires, Av. República Italia 780, C.C. 47, (7300), Azul, Provincia de Buenos Aires Argentina
- The Wheat Initiative, 14195 Berlin, Germany
| | - X. C. Xia
- Institute of Crop Science, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South St, Beijing, 100081 China
| | - E. D. Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia 119991
| | - A. R. Bentley
- International Maize and Wheat Improvement Center (CIMMYT), Apdo Postal 6-641, Mexico, D.F., Mexico
- The Wheat Initiative, 14195 Berlin, Germany
| | - G. Brown-Guedira
- USDA-ARS Plant Science Research, North Carolina State University, William Hall 4114A, Raleigh, NC 27695 USA
- The Wheat Initiative, 14195 Berlin, Germany
| | - M. Caccamo
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
- The Wheat Initiative, 14195 Berlin, Germany
| | - L. Cattivelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Via S. Protaso, 302, 29017 Fiorenzuola d’Arda, PC Italy
- The Wheat Initiative, 14195 Berlin, Germany
| | - P. Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141 004 India
| | - J. Cockram
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
- The Wheat Initiative, 14195 Berlin, Germany
| | | | - S. Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Apdo Postal 6-641, Mexico, D.F., Mexico
- The Wheat Initiative, 14195 Berlin, Germany
| | - D. Edwards
- School of Biological Sciences, University of Western Australia, Perth, 6009 Australia
- The Wheat Initiative, 14195 Berlin, Germany
| | - F. G. González
- Instituto Nacional de Tecnología Agropecuaria (INTA), EEA Pergamino, y Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA, CONICET-UNNOBA-UNSADA), Ruta 32. Km 4.5, CP 2700, Pergamino, Buenos Aires Argentina
- The Wheat Initiative, 14195 Berlin, Germany
| | - C. Guzmán
- Department of Genetics, School of Agricultural and Forest Engineering, Universidad de Córdoba, Córdoba, Spain
- The Wheat Initiative, 14195 Berlin, Germany
| | - T. M. Ikeda
- Agroecosystem and Crop Breeding Group, Western Region Agricultural Research Center, Fukuyama, Hiroshima 721-8514 Japan
- The Wheat Initiative, 14195 Berlin, Germany
| | - I. Karsai
- Centre for Agricultural Research, ELKH, 2462 Martonvasar, Hungary
- The Wheat Initiative, 14195 Berlin, Germany
| | - S. Nasuda
- Laboratory of Plant Breeding, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8224 Japan
| | - C. Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
- The Wheat Initiative, 14195 Berlin, Germany
| | - R. Prins
- CenGen Pty Ltd., Worcester, 6850 South Africa
- Department of Genetics, Stellenbosch University, Matieland, 7602 South Africa
| | - T. Z. Sen
- Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan St, Albany, CA 94710 USA
- The Wheat Initiative, 14195 Berlin, Germany
| | - P. Silva
- Programa Nacional de Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, 70006 Colonia, Uruguay
| | - H. Simkova
- Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Y. Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
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10
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Harrington SA, Connorton JM, Nyangoma NIM, McNelly R, Morgan YML, Aslam MF, Sharp PA, Johnson AAT, Uauy C, Balk J. A two-gene strategy increases iron and zinc concentrations in wheat flour, improving mineral bioaccessibility. Plant Physiol 2023; 191:528-541. [PMID: 36308454 PMCID: PMC9806615 DOI: 10.1093/plphys/kiac499] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/13/2022] [Indexed: 05/09/2023]
Abstract
Dietary deficiencies of iron and zinc cause human malnutrition that can be mitigated by biofortified staple crops. Conventional breeding approaches to increase grain mineral concentrations in wheat (Triticum aestivum L.) have had only limited success, and our understanding of the genetic and physiological barriers to altering this trait is incomplete. Here we demonstrate that a transgenic approach combining endosperm-specific expression of the wheat VACUOLAR IRON TRANSPORTER gene TaVIT2-D with constitutive expression of the rice (Oryza sativa) NICOTIANAMINE SYNTHASE gene OsNAS2 significantly increases the total concentration of zinc and relocates iron to white-flour fractions. In two distinct bread wheat cultivars, we show that the so called VIT-NAS construct led to a two-fold increase in zinc in wholemeal flour, to ∼50 µg g-1. Total iron was not significantly increased, but redistribution within the grain resulted in a three-fold increase in iron in highly pure, roller-milled white flour, to ∼25 µg g-1. Interestingly, expression of OsNAS2 partially restored iron translocation to the aleurone, which is iron depleted in grain overexpressing TaVIT2 alone. A greater than three-fold increase in the level of the natural plant metal chelator nicotianamine in the grain of VIT-NAS lines corresponded with improved iron and zinc bioaccessibility in white flour. The growth of VIT-NAS plants in the greenhouse was indistinguishable from untransformed controls. Our results provide insights into mineral translocation and distribution in wheat grain and demonstrate that the individual and combined effects of the two transgenes can enhance the nutritional quality of wheat beyond what is possible by conventional breeding.
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Affiliation(s)
| | - James M Connorton
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Rose McNelly
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Yvie M L Morgan
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Mohamad F Aslam
- Department of Nutritional Sciences, King’s College London, London SE1 9NH, UK
| | - Paul A Sharp
- Department of Nutritional Sciences, King’s College London, London SE1 9NH, UK
| | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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11
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Yadav IS, Bhardwaj SC, Kaur J, Singla D, Kaur S, Kaur H, Rawat N, Tiwari VK, Saunders D, Uauy C, Chhuneja P. Whole genome resequencing and comparative genome analysis of three Puccinia striiformis f. sp. tritici pathotypes prevalent in India. PLoS One 2022; 17:e0261697. [PMID: 36327308 PMCID: PMC9632834 DOI: 10.1371/journal.pone.0261697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/05/2021] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Stripe rust disease of wheat, caused by Puccinia striiformis f. sp. tritici, (Pst) is one of the most serious diseases of wheat worldwide. In India, virulent stripe rust races have been constantly evolving in the North-Western Plains Zone leading to the failure of some of the most widely grown resistant varieties in the region. With the goal of studying the recent evolution of virulent races in this region, we conducted whole-genome re-sequencing of three prevalent Indian Pst pathotypes Pst46S119, Pst78S84 and Pst110S119. We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively and found that pathotypes were highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene families expansion were also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known United States, European, African, and Asian races. Diagnostic markers developed for the identification of three Pst pathotypes will help tracking of yellow rust at farmers field and strategizing resistance gene deployment.
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Affiliation(s)
- Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - S. C. Bhardwaj
- Regional Station, Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, India
| | - Jaspal Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Deepak Singla
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Harmandeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland College Park, College Park, Maryland, United States of America
| | - Vijay Kumar Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland College Park, College Park, Maryland, United States of America
| | - Diane Saunders
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- * E-mail:
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12
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Millan-Blanquez M, Hartley M, Bird N, Manes Y, Uauy C, Boden SA. A scalable phenotyping approach for female floral organ development and senescence in the absence of pollination in wheat. Development 2022; 149:dev200889. [PMID: 35993314 PMCID: PMC9573784 DOI: 10.1242/dev.200889] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022]
Abstract
In the absence of pollination, female reproductive organs senesce, leading to an irrevocable loss in the reproductive potential of the flower, which directly affects seed set. In self-pollinating crops like wheat (Triticum aestivum), the post-anthesis viability of unpollinated carpels has been overlooked, despite its importance for hybrid seed production systems. To advance our knowledge of carpel development in the absence of pollination, we created a high-throughput phenotyping approach to quantify stigma and ovary morphology. We demonstrate the suitability of the approach, which uses light-microscopy imaging and machine learning, for the analysis of floral organ traits in field-grown plants using fresh and fixed samples. We show that the unpollinated carpel undergoes a well-defined initial growth phase, followed by a peak phase in which stigma area reaches its maximum and the radial expansion of the ovary slows, and a final deterioration phase. These developmental dynamics were consistent across years and could be used to classify male-sterile cultivars. This phenotyping approach provides a new tool for examining carpel development, which we hope will advance research into female fertility of wheat.
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Affiliation(s)
| | - Matthew Hartley
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Yann Manes
- Syngenta France S.A.S., Le Jardin des Entreprises, 28 000 Chartres, France
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Scott A. Boden
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond 5064, South Australia, Australia
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13
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Chen Y, Liu Y, Zhang J, Torrance A, Watanabe N, Adamski NM, Uauy C. The Triticum ispahanicum elongated glume locus P2 maps to chromosome 6A and is associated with the ectopic expression of SVP-A1. Theor Appl Genet 2022; 135:2313-2331. [PMID: 35583655 PMCID: PMC9271103 DOI: 10.1007/s00122-022-04114-y] [Citation(s) in RCA: 2] [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: 01/28/2022] [Accepted: 04/21/2022] [Indexed: 05/26/2023]
Abstract
We propose the MADS-box transcription factor SVP-A1 as a promising candidate gene for the elongated glume locus P2, which maps to chromosome 6A instead of the previously proposed chromosome 7B. In rice and wheat, glume and floral organ length are positively correlated with grain size, making them an important target to increase grain size and potentially yield. The wheat subspecies Triticum ispahanicum is known to develop elongated glumes and floral organs as well as long grains. These multiple phenotypic effects are controlled by the P2 locus, which was previously mapped to wheat chromosome 7B. Using three mapping populations, we show that the long glume locus P2 does not map to chromosome 7B, but instead maps to a 1.68 Mbp interval on chromosome 6A. Within this interval, we identified SVP-A1, a MADS box transcription factor which is the direct ortholog of the maize gene underlying the 'pod corn' Tunicate locus and is a paralog to the T. polonicum elongated glume P1 gene. In T. ispahanicum, we identified a unique allele which has a 482-bp deletion in the SVP-A1 promoter and is associated with ectopic and higher expression of SVP-A1 in the elongated glumes and floral organs. We used near-isogenic lines (NILs) to show that P2 has a consistent positive effect on the length of glume, lemma, palea, spike and grain. Based on the mapping data, natural variation, biological function of SVP genes in cereals and expression analyses, we propose the MADS-box transcription factor SVP-A1 as a promising candidate for P2.
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Affiliation(s)
- Yi Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yinqi Liu
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Adam Torrance
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nobuyoshi Watanabe
- The Little Nursery, 1152 Ina, Toride, Ibaraki, 302-0026, Japan
- College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami, Inashiki, Ibaraki, 300-0393, Japan
| | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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14
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Backhaus AE, Lister A, Tomkins M, Adamski NM, Simmonds J, Macaulay I, Morris RJ, Haerty W, Uauy C. High expression of the MADS-box gene VRT2 increases the number of rudimentary basal spikelets in wheat. Plant Physiol 2022; 189:1536-1552. [PMID: 35377414 PMCID: PMC9237664 DOI: 10.1093/plphys/kiac156] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/13/2022] [Indexed: 05/03/2023]
Abstract
Spikelets are the fundamental building blocks of Poaceae inflorescences, and their development and branching patterns determine the various inflorescence architectures and grain yield of grasses. In wheat (Triticum aestivum), the central spikelets produce the most and largest grains, while spikelet size gradually decreases acropetally and basipetally, giving rise to the characteristic lanceolate shape of wheat spikes. The acropetal gradient corresponds with the developmental age of spikelets; however, the basal spikelets are developed first, and the cause of their small size and rudimentary development is unclear. Here, we adapted G&T-seq, a low-input transcriptomics approach, to characterize gene expression profiles within spatial sections of individual spikes before and after the establishment of the lanceolate shape. We observed larger differences in gene expression profiles between the apical, central, and basal sections of a single spike than between any section belonging to consecutive developmental time points. We found that SHORT VEGETATIVE PHASE MADS-box transcription factors, including VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (VRT-A2), are expressed highest in the basal section of the wheat spike and display the opposite expression gradient to flowering E-class SEPALLATA1 genes. Based on multi-year field trials and transgenic lines, we show that higher expression of VRT-A2 in the basal sections of the spike is associated with increased numbers of rudimentary basal spikelets. Our results, supported by computational modeling, suggest that the delayed transition of basal spikelets from vegetative to floral developmental programs results in the lanceolate shape of wheat spikes. This study highlights the value of spatially resolved transcriptomics to gain insights into developmental genetics pathways of grass inflorescences.
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Affiliation(s)
- Anna E Backhaus
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ashleigh Lister
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Melissa Tomkins
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Iain Macaulay
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | | | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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15
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Desjardins SD, Simmonds J, Guterman I, Kanyuka K, Burridge AJ, Tock AJ, Sanchez-Moran E, Franklin FCH, Henderson IR, Edwards KJ, Uauy C, Higgins JD. FANCM promotes class I interfering crossovers and suppresses class II non-interfering crossovers in wheat meiosis. Nat Commun 2022; 13:3644. [PMID: 35752733 PMCID: PMC9233680 DOI: 10.1038/s41467-022-31438-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 02/22/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022] Open
Abstract
FANCM suppresses crossovers in plants by unwinding recombination intermediates. In wheat, crossovers are skewed toward the chromosome ends, thus limiting generation of novel allelic combinations. Here, we observe that FANCM maintains the obligate crossover in tetraploid and hexaploid wheat, thus ensuring that every chromosome pair exhibits at least one crossover, by localizing class I crossover protein HEI10 at pachytene. FANCM also suppresses class II crossovers that increased 2.6-fold in fancm msh5 quadruple mutants. These data are consistent with a role for FANCM in second-end capture of class I designated crossover sites, whilst FANCM is also required to promote formation of non-crossovers. In hexaploid wheat, genetic mapping reveals that crossovers increase by 31% in fancm compared to wild type, indicating that fancm could be an effective tool to accelerate breeding. Crossover rate differences in fancm correlate with wild type crossover distributions, suggesting that chromatin may influence the recombination landscape in similar ways in both wild type and fancm. The FANCM helicase functions in limiting crossovers (COs) by unwinding inter-homolog repair intermediates. Here, the authors generate null mutants of fancm in tetraploid and hexaploid wheat and show that FANCM promotes class I interfering COs and suppresses class II noninterfering COs in wheat meiosis.
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Affiliation(s)
- Stuart D Desjardins
- Department of Genetics and Genome Biology, Adrian Building, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - James Simmonds
- Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - Inna Guterman
- Department of Genetics and Genome Biology, Adrian Building, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Kostya Kanyuka
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.,Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Amanda J Burridge
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | | | - F Chris H Franklin
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Keith J Edwards
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - James D Higgins
- Department of Genetics and Genome Biology, Adrian Building, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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16
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Dixon LE, Pasquariello M, Badgami R, Levin KA, Poschet G, Ng PQ, Orford S, Chayut N, Adamski NM, Brinton J, Simmonds J, Steuernagel B, Searle IR, Uauy C, Boden SA. MicroRNA-resistant alleles of HOMEOBOX DOMAIN-2 modify inflorescence branching and increase grain protein content of wheat. Sci Adv 2022; 8:eabn5907. [PMID: 35544571 PMCID: PMC9094671 DOI: 10.1126/sciadv.abn5907] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/25/2022] [Indexed: 05/26/2023]
Abstract
Plant and inflorescence architecture determine the yield potential of crops. Breeders have harnessed natural diversity for inflorescence architecture to improve yields, and induced genetic variation could provide further gains. Wheat is a vital source of protein and calories; however, little is known about the genes that regulate the development of its inflorescence. Here, we report the identification of semidominant alleles for a class III homeodomain-leucine zipper transcription factor, HOMEOBOX DOMAIN-2 (HB-2), on wheat A and D subgenomes, which generate more flower-bearing spikelets and enhance grain protein content. These alleles increase HB-2 expression by disrupting a microRNA 165/166 complementary site with conserved roles in plants; higher HB-2 expression is associated with modified leaf and vascular development and increased amino acid supply to the inflorescence during grain development. These findings enhance our understanding of genes that control wheat inflorescence development and introduce an approach to improve the nutritional quality of grain.
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Affiliation(s)
- Laura E. Dixon
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Marianna Pasquariello
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Roshani Badgami
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Kara A. Levin
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Gernot Poschet
- Centre of Organismal Studies (COS), University of Heidelberg, Heidelberg 69120, Germany
| | - Pei Qin Ng
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Simon Orford
- Germplasm Resources Unit, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Noam Chayut
- Germplasm Resources Unit, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Nikolai M. Adamski
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jemima Brinton
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - James Simmonds
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Burkhard Steuernagel
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Iain R. Searle
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Scott A. Boden
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
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17
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Polturak G, Dippe M, Stephenson MJ, Chandra Misra R, Owen C, Ramirez-Gonzalez RH, Haidoulis JF, Schoonbeek HJ, Chartrain L, Borrill P, Nelson DR, Brown JK, Nicholson P, Uauy C, Osbourn A. Pathogen-induced biosynthetic pathways encode defense-related molecules in bread wheat. Proc Natl Acad Sci U S A 2022; 119:e2123299119. [PMID: 35412884 PMCID: PMC9169793 DOI: 10.1073/pnas.2123299119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 01/05/2022] [Accepted: 02/14/2022] [Indexed: 12/23/2022] Open
Abstract
Wheat is a widely grown food crop that suffers major yield losses due to attack by pests and pathogens. A better understanding of biotic stress responses in wheat is thus of major importance. The recently assembled bread wheat genome coupled with extensive transcriptomic resources provides unprecedented new opportunities to investigate responses to pathogen challenge. Here, we analyze gene coexpression networks to identify modules showing consistent induction in response to pathogen exposure. Within the top pathogen-induced modules, we identify multiple clusters of physically adjacent genes that correspond to six pathogen-induced biosynthetic pathways that share a common regulatory network. Functional analysis reveals that these pathways, all of which are encoded by biosynthetic gene clusters, produce various different classes of compounds—namely, flavonoids, diterpenes, and triterpenes, including the defense-related compound ellarinacin. Through comparative genomics, we also identify associations with the known rice phytoalexins momilactones, as well as with a defense-related gene cluster in the grass model plant Brachypodium distachyon. Our results significantly advance the understanding of chemical defenses in wheat and open up avenues for enhancing disease resistance in this agriculturally important crop. They also exemplify the power of transcriptional networks to discover the biosynthesis of chemical defenses in plants with large, complex genomes.
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Affiliation(s)
- Guy Polturak
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Martin Dippe
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Michael J. Stephenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Rajesh Chandra Misra
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Charlotte Owen
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | | | - John F. Haidoulis
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Henk-Jan Schoonbeek
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Laetitia Chartrain
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Philippa Borrill
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163
| | - James K.M. Brown
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Paul Nicholson
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
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18
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Shorinola O, Simmonds J, Wingen LU, Uauy C. Trend, population structure, and trait mapping from 15 years of national varietal trials of UK winter wheat. G3 Genes|Genomes|Genetics 2022; 12:6460332. [PMID: 34897454 PMCID: PMC9210278 DOI: 10.1093/g3journal/jkab415] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/22/2021] [Indexed: 11/15/2022]
Abstract
There are now a rich variety of genomic and genotypic resources available to wheat researchers and breeders. However, the generation of high-quality and field-relevant phenotyping data which is required to capture the complexities of gene × environment interactions remains a major bottleneck. Historical datasets from national variety performance trials (NVPT) provide sufficient dimensions, in terms of numbers of years and locations, to examine phenotypic trends and study gene × environment interactions. Using NVPT for winter wheat varieties grown in the United Kingdom between 2002 and 2017, we examined temporal trends for eight traits related to yield, adaptation, and grain quality performance. We show a non-stationary linear trend for yield, grain protein content, Hagberg Falling Number (HFN), and days to ripening. Our data also show high environmental stability for yield, grain protein content, and specific weight in UK winter wheat varieties and high environmental sensitivity for HFN. We also show that UK varieties released within this period cluster into four main population groups. Using the historical NVPT data in a genome-wide association analysis, we uncovered a significant marker-trait association peak on wheat chromosome 6A spanning the NAM-A1 gene that have been previously associated with early senescence. Together, our results show the value of utilizing the data routinely collected during national variety evaluation process for examining breeding progress and the genetic architecture of important traits.
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Affiliation(s)
- Oluwaseyi Shorinola
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Bioscience Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI), Nairobi 00100, Kenya
| | - James Simmonds
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Luzie U Wingen
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Cristobal Uauy
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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19
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Wamalwa MN, Wanyera R, Rodriguez-Algaba J, Boyd LA, Owuoche J, Ogendo J, Bhavani S, Uauy C, Justesen AF, Hovmøller M. Distribution of Puccinia striiformis f. sp. tritici Races and Virulence in Wheat Growing Regions of Kenya from 1970 to 2014. Plant Dis 2022; 106:701-710. [PMID: 34633239 DOI: 10.1094/pdis-11-20-2341-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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] [Indexed: 06/13/2023]
Abstract
Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici, is a major threat to wheat (Triticum spp.) production worldwide. The objective of this study was to determine the virulence of P. striiformis f. sp. tritici races prevalent in the main wheat growing regions of Kenya, which includes Mt. Kenya, Eastern Kenya, and the Rift Valley (Central, Southern, and Northern Rift). Fifty P. striiformis f. sp. tritici isolates collected from 1970 to 1992 and from 2009 to 2014 were virulence phenotyped with stripe rust differential sets, and 45 isolates were genotyped with sequence characterized amplified region (SCAR) markers to differentiate the isolates and identify aggressive strains PstS1 and PstS2. Virulence corresponding to stripe rust resistance genes Yr1, Yr2, Yr3, Yr6, Yr7, Yr8, Yr9, Yr17, Yr25, and Yr27 and the seedling resistance in genotype Avocet S were detected. Ten races were detected in the P. striiformis f. sp. tritici samples obtained from 1970 to 1992, and three additional races were detected from 2009 to 2014, with a single race being detected in both periods. The SCAR markers detected both Pst1 and Pst2 strains in the collection. Increasing P. striiformis f. sp. tritici virulence was found in the Kenyan P. striiformis f. sp. tritici population, and different P. striiformis f. sp. tritici race groups were found to dominate different wheat growing regions. Moreover, recent P. striiformis f. sp. tritici races in East Africa indicated possible migration of some race groups into Kenya from other regions. This study is important in elucidating P. striiformis f. sp. tritici evolution and virulence diversity and useful in breeding wheat cultivars with effective resistance to stripe rust.
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Affiliation(s)
| | - Ruth Wanyera
- Kenya Agricultural and Livestock Research Organization Njoro, Private Bag 20107, Kenya
| | | | - Lesley A Boyd
- National Institute of Agricultural Botany, Cambridge CB3 0LE, UK
| | | | | | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 UH, UK
| | - Annemarie F Justesen
- Global Rust Reference Center, Aarhus University, Flakkebjerg, Slagelse DK-4200, Denmark
| | - Mogens Hovmøller
- Global Rust Reference Center, Aarhus University, Flakkebjerg, Slagelse DK-4200, Denmark
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20
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Saccomanno B, Berbezy P, Findlay K, Shoesmith J, Uauy C, Viallis B, Trafford K. Characterization of wheat lacking B-type starch granules. J Cereal Sci 2022; 104:103398. [PMID: 35340793 PMCID: PMC8935375 DOI: 10.1016/j.jcs.2021.103398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/03/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022]
Abstract
The physicochemical and agronomic properties of a new form of bread wheat lacking B-type starch granules (BlessT) were assessed. Three BlessT mutant lines made by combining homoeologous deletions of BGC1, a gene responsible for the control of B-granule content, were compared with two sibling lines with normal starch phenotype and the parent line, cv. Paragon. Quantification of starch granule size and number in developing grain confirmed the lack of small, B-type starch granules throughout development in BlessT. Most starch, flour, grain and loaf characteristics did not vary between BlessT and the wild type sibling controls. However, BlessT starches had higher water absorption, reduced grain hardness and higher protein content, and dough made from BlessT flour required more water and had increased elasticity. Despite the lack of B-granules, BlessT lines do not display a significant decrease in total starch content suggesting that it should be possible to produce commercial wheat varieties that lack B-type starch granules without compromising yield. These findings support the potential utility of this novel type of wheat as a specialist crop in applications ranging from bread making and alcohol production to improved industrial starch products. BlessT lines lack small, B-type starch granules throughout grain development. BlessT starches have higher water absorption, reduced grain hardness and higher protein content. BlessT flours do not display a significant decrease in total starch content.
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Affiliation(s)
- Benedetta Saccomanno
- The National Institute of Agricultural Botany, Huntingdon Road, Cambridge, Cambridgeshire, CB3 0LE, UK
| | - Pierre Berbezy
- Limagrain Céréale Ingrédients, ZAC les Porte de Riom, Avenue George Gershwin, 63200, RIOM, France
| | - Kim Findlay
- The John Innes Centre, Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7UH, UK
| | - Jennifer Shoesmith
- The National Institute of Agricultural Botany, Huntingdon Road, Cambridge, Cambridgeshire, CB3 0LE, UK
| | - Cristobal Uauy
- The John Innes Centre, Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7UH, UK
| | - Bruno Viallis
- Limagrain Céréale Ingrédients, ZAC les Porte de Riom, Avenue George Gershwin, 63200, RIOM, France
| | - Kay Trafford
- The National Institute of Agricultural Botany, Huntingdon Road, Cambridge, Cambridgeshire, CB3 0LE, UK
- Corresponding author.
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21
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Yang X, Yu H, Sun W, Ding L, Li J, Cheema J, Ramirez-Gonzalez R, Zhao X, Martín AC, Lu F, Liu B, Uauy C, Ding Y, Zhang H. Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry. Genome Biol 2021; 22:326. [PMID: 34847934 PMCID: PMC8638558 DOI: 10.1186/s13059-021-02549-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/12/2021] [Accepted: 11/19/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Polyploidy, especially allopolyploidy, which entails merging divergent genomes via hybridization and whole-genome duplication (WGD), is a major route to speciation in plants. The duplication among the parental genomes (subgenomes) often leads to one subgenome becoming dominant over the other(s), resulting in subgenome asymmetry in gene content and expression. Polyploid wheats are allopolyploids with most genes present in two (tetraploid) or three (hexaploid) functional copies, which commonly show subgenome expression asymmetry. It is unknown whether a similar subgenome asymmetry exists during translation. We aim to address this key biological question and explore the major contributing factors to subgenome translation asymmetry. RESULTS Here, we obtain the first tetraploid wheat translatome and reveal that subgenome expression asymmetry exists at the translational level. We further perform in vivo RNA structure profiling to obtain the wheat RNA structure landscape and find that mRNA structure has a strong impact on translation, independent of GC content. We discover a previously uncharacterized contribution of RNA structure in subgenome translation asymmetry. We identify 3564 single-nucleotide variations (SNVs) across the transcriptomes between the two tetraploid wheat subgenomes, which induce large RNA structure disparities. These SNVs are highly conserved within durum wheat cultivars but are divergent in both domesticated and wild emmer wheat. CONCLUSIONS We successfully determine both the translatome and in vivo RNA structurome in tetraploid wheat. We reveal that RNA structure serves as an important modulator of translational subgenome expression asymmetry in polyploids. Our work provides a new perspective for molecular breeding of major polyploid crops.
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Affiliation(s)
- Xiaofei Yang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Haopeng Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wenqing Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Ling Ding
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Ji Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Jitender Cheema
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Xuebo Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Azahara C Martín
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China.
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22
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Tock AJ, Holland DM, Jiang W, Osman K, Sanchez-Moran E, Higgins JD, Edwards KJ, Uauy C, Franklin FCH, Henderson IR. Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation. Genome Res 2021; 31:1614-1628. [PMID: 34426514 PMCID: PMC8415368 DOI: 10.1101/gr.273672.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 11/03/2020] [Accepted: 07/20/2021] [Indexed: 12/18/2022]
Abstract
The hexaploid bread wheat genome comprises over 16 gigabases of sequence across 21 chromosomes. Meiotic crossovers are highly polarized along the chromosomes, with elevation in the gene-dense distal regions and suppression in the Gypsy retrotransposon-dense centromere-proximal regions. We profiled the genomic landscapes of the meiotic recombinase DMC1 and the chromosome axis protein ASY1 in wheat and investigated their relationships with crossovers, chromatin state, and genetic diversity. DMC1 and ASY1 chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed strong co-enrichment in the distal, crossover-active regions of the wheat chromosomes. Distal ChIP-seq enrichment is consistent with spatiotemporally biased cytological immunolocalization of DMC1 and ASY1 close to the telomeres during meiotic prophase I. DMC1 and ASY1 ChIP-seq peaks show significant overlap with genes and transposable elements in the Mariner and Mutator superfamilies. However, DMC1 and ASY1 ChIP-seq peaks were detected along the length of each chromosome, including in low-crossover regions. At the fine scale, crossover elevation at DMC1 and ASY1 peaks and genes correlates with enrichment of the Polycomb histone modification H3K27me3. This indicates a role for facultative heterochromatin, coincident with high DMC1 and ASY1, in promoting crossovers in wheat and is reflected in distalized H3K27me3 enrichment observed via ChIP-seq and immunocytology. Genes with elevated crossover rates and high DMC1 and ASY1 ChIP-seq signals are overrepresented for defense-response and immunity annotations, have higher sequence polymorphism, and exhibit signatures of selection. Our findings are consistent with meiotic recombination promoting genetic diversity, shaping host–pathogen co-evolution, and accelerating adaptation by increasing the efficiency of selection.
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Affiliation(s)
- Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Daniel M Holland
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Wei Jiang
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Kim Osman
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | | | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Keith J Edwards
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | | | - F Chris H Franklin
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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23
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Adamski NM, Simmonds J, Brinton JF, Backhaus AE, Chen Y, Smedley M, Hayta S, Florio T, Crane P, Scott P, Pieri A, Hall O, Barclay JE, Clayton M, Doonan JH, Nibau C, Uauy C. Ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner. Plant Cell 2021; 33:2296-2319. [PMID: 34009390 PMCID: PMC8364232 DOI: 10.1093/plcell/koab119] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/17/2021] [Indexed: 05/20/2023]
Abstract
Flower development is an important determinant of grain yield in crops. In wheat (Triticum spp.), natural variation for the size of spikelet and floral organs is particularly evident in Triticum turgidum ssp. polonicum (also termed Triticum polonicum), a tetraploid subspecies of wheat with long glumes, lemmas, and grains. Using map-based cloning, we identified VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (VRT2), which encodes a MADS-box transcription factor belonging to the SHORT VEGETATIVE PHASE family, as the gene underlying the T. polonicum long-glume (P1) locus. The causal P1 mutation is a sequence rearrangement in intron-1 that results in ectopic expression of the T. polonicum VRT-A2 allele. Based on allelic variation studies, we propose that the intron-1 mutation in VRT-A2 is the unique T. polonicum subspecies-defining polymorphism, which was later introduced into hexaploid wheat via natural hybridizations. Near-isogenic lines differing for the P1 locus revealed a gradient effect of P1 across spikelets and within florets. Transgenic lines of hexaploid wheat carrying the T. polonicum VRT-A2 allele show that expression levels of VRT-A2 are highly correlated with spike, glume, grain, and floral organ length. These results highlight how changes in expression profiles, through variation in cis-regulation, can affect agronomic traits in a dosage-dependent manner in polyploid crops.
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Affiliation(s)
| | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Yi Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mark Smedley
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sadiye Hayta
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Tobin Florio
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Pamela Crane
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Peter Scott
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alice Pieri
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Olyvia Hall
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Myles Clayton
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY23 3EE, UK
| | - John H. Doonan
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY23 3EE, UK
| | - Candida Nibau
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY23 3EE, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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24
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Bansal M, Adamski NM, Toor PI, Kaur S, Sharma A, Srivastava P, Bansal U, Uauy C, Chhuneja P. A robust KASP marker for selection of four pairs of linked leaf rust and stripe rust resistance genes introgressed on chromosome arm 5DS from different wheat genomes. Mol Biol Rep 2021; 48:5209-5216. [PMID: 34213711 DOI: 10.1007/s11033-021-06525-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/25/2021] [Indexed: 11/24/2022]
Abstract
Stripe rust and leaf rust are among the most devastating diseases of wheat, limiting its production globally. Wheat wild relatives harbour genetic diversity for new genes and alleles for all major wheat diseases. However, the use of this genetic variation from wild progenitor and non-progenitor species has been limited in the breeding programs. Reasons include limited recombination of donor and recipient genomes and the lack of tertiary gene pool markers. Here, we describe the development of a SNP based marker from the flow-sorted and sequenced Aegilops umbellulata chromosome 5U which can be used for marker assisted selection of four pair of alien leaf rust and stripe rust resistance genes. Lr57-Yr40_CAPS16 marker was reported earlier to be linked with alien leaf and stripe rust resistance genes introgressed on wheat chromosome 5DS. Due to its dominant nature and laborious to work with, a new SNP-based KASP marker, XTa5DS-2754099_kasp23, was developed from the same CAPS marker contig. XTa5DS-2754099_kasp23 was tested in Aegilops umbellulata, Ae. geniculata, Ae. peregrina and Ae. caudata derived alien introgression lines, which harbour four pairs of linked leaf and stripe rust genes; Lr76-Yr70, Lr57-Yr40, LrP- YrP, LrAc-YrAc, respectively. This KASP marker was found to be effective for the selection of the aforesaid four pairs of leaf rust and stripe rust resistance genes. Further, we tested and validated XTa5DS-2754099_kasp23 on commercial varieties and advanced breeding lines from four countries (India, Egypt, Australia and UK) including hexaploid and durum wheat. Our results provide evidence that KASP marker, XTa5DS-2754099_kasp23 can be used in marker-assisted selection of the four pairs of rust resistance alien genes in wheat breeding programmes.
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Affiliation(s)
- Mitaly Bansal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
| | | | - Puneet Inder Toor
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
| | - Achla Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
| | - Urmil Bansal
- University of Sydney Plant Breeding Institute-Cobbitty, PMB 4011, Narellan, NSW, 2567, Australia
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India.
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25
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Ober ES, Alahmad S, Cockram J, Forestan C, Hickey LT, Kant J, Maccaferri M, Marr E, Milner M, Pinto F, Rambla C, Reynolds M, Salvi S, Sciara G, Snowdon RJ, Thomelin P, Tuberosa R, Uauy C, Voss-Fels KP, Wallington E, Watt M. Wheat root systems as a breeding target for climate resilience. Theor Appl Genet 2021; 134:1645-1662. [PMID: 33900415 PMCID: PMC8206059 DOI: 10.1007/s00122-021-03819-w] [Citation(s) in RCA: 10] [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] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/18/2021] [Indexed: 05/08/2023]
Abstract
In the coming decades, larger genetic gains in yield will be necessary to meet projected demand, and this must be achieved despite the destabilizing impacts of climate change on crop production. The root systems of crops capture the water and nutrients needed to support crop growth, and improved root systems tailored to the challenges of specific agricultural environments could improve climate resiliency. Each component of root initiation, growth and development is controlled genetically and responds to the environment, which translates to a complex quantitative system to navigate for the breeder, but also a world of opportunity given the right tools. In this review, we argue that it is important to know more about the 'hidden half' of crop plants and hypothesize that crop improvement could be further enhanced using approaches that directly target selection for root system architecture. To explore these issues, we focus predominantly on bread wheat (Triticum aestivum L.), a staple crop that plays a major role in underpinning global food security. We review the tools available for root phenotyping under controlled and field conditions and the use of these platforms alongside modern genetics and genomics resources to dissect the genetic architecture controlling the wheat root system. To contextualize these advances for applied wheat breeding, we explore questions surrounding which root system architectures should be selected for, which agricultural environments and genetic trait configurations of breeding populations are these best suited to, and how might direct selection for these root ideotypes be implemented in practice.
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Affiliation(s)
- Eric S Ober
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
| | - Samir Alahmad
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - James Cockram
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Cristian Forestan
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Lee T Hickey
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Josefine Kant
- Forschungszentrum Jülich, IBG-2, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Emily Marr
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | - Francisco Pinto
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Estado de Mexico, Mexico
| | - Charlotte Rambla
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Matthew Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Estado de Mexico, Mexico
| | - Silvio Salvi
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | | | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127, Bologna, Italy
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Kai P Voss-Fels
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Michelle Watt
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
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26
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Alemu SK, Huluka AB, Tesfaye K, Haileselassie T, Uauy C. Genome-wide association mapping identifies yellow rust resistance loci in Ethiopian durum wheat germplasm. PLoS One 2021; 16:e0243675. [PMID: 33999918 PMCID: PMC8128278 DOI: 10.1371/journal.pone.0243675] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 11/24/2020] [Accepted: 04/16/2021] [Indexed: 12/28/2022] Open
Abstract
Durum wheat is an important cereal grown in Ethiopia, a country which is also its center for genetic diversity. Yellow (stripe) rust caused by Puccinia striiformis fsp tritici is one of the most devastating diseases threatening Ethiopian wheat production. To identify sources of genetic resistance and combat this pathogen, we conducted a genome wide association study of yellow rust resistance on 300 durum wheat accessions comprising 261 landraces and 39 cultivars. The accessions were evaluated for their field resistance using a modified Cobb scale at Meraro, Kulumsa and Chefe Donsa in the 2015 and 2016 main growing seasons. Analysis of the 35K Axiom Array genotyping data of the panel resulted in a total of 8,797 polymorphic SNPs of which 7,093 were used in subsequent analyses. Population structure analysis suggested two groups in which the cultivars clearly stood out separately from the landraces. Eleven SNPs significantly associated with yellow rust resistance were identified on four chromosomes (1A, 1B, 2B, and 5A) which defined at least five genomic loci. Six of the SNPs were consistently identified on chromosome 1B singly at each and combined overall environments which explained 62.6–64.0% of the phenotypic variation (R2). Resistant allele frequency ranged from 14.0–71.0%; Zooming in to the identified resistance loci revealed the presence of disease resistance related genes involved in the plant defense system such as the ABC transporter gene family, disease resistance protein RPM1 (NBS-LRR class), Receptor kinases and Protein kinases. This study has provided SNPs for tracking the loci associated with yellow rust resistance and a diversity panel which can be used for association study of other agriculturally important traits in durum wheat.
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Affiliation(s)
- Sisay Kidane Alemu
- National Agricultural Biotechnology Research Center, Holeta, Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
- * E-mail:
| | - Ayele Badebo Huluka
- International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology and DMCMB, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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27
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Vu LD, Xu X, Zhu T, Pan L, van Zanten M, de Jong D, Wang Y, Vanremoortele T, Locke AM, van de Cotte B, De Winne N, Stes E, Russinova E, De Jaeger G, Van Damme D, Uauy C, Gevaert K, De Smet I. The membrane-localized protein kinase MAP4K4/TOT3 regulates thermomorphogenesis. Nat Commun 2021; 12:2842. [PMID: 33990595 PMCID: PMC8121802 DOI: 10.1038/s41467-021-23112-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 04/10/2020] [Accepted: 04/12/2021] [Indexed: 12/14/2022] Open
Abstract
Plants respond to mild warm temperature conditions by increased elongation growth of organs to enhance cooling capacity, in a process called thermomorphogenesis. To this date, the regulation of thermomorphogenesis has been exclusively shown to intersect with light signalling pathways. To identify regulators of thermomorphogenesis that are conserved in flowering plants, we map changes in protein phosphorylation in both dicots and monocots exposed to warm temperature. We identify MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE KINASE4 (MAP4K4)/TARGET OF TEMPERATURE3 (TOT3) as a regulator of thermomorphogenesis that impinges on brassinosteroid signalling in Arabidopsis thaliana. In addition, we show that TOT3 plays a role in thermal response in wheat, a monocot crop. Altogether, the conserved thermal regulation by TOT3 expands our knowledge of thermomorphogenesis beyond the well-studied pathways and can contribute to ensuring food security under a changing climate. Plants respond to warmth via growth processes termed thermomorphogenesis. Here, via a phosphoproteomics approach, the authors show that the mitogen activated protein kinase TOT3 regulates thermomorphogenesis in both wheat and Arabidopsis and modifies brassinosteroid signaling in Arabidopsis.
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Affiliation(s)
- Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, B-9000, Ghent, Belgium.,VIB Center for Medical Biotechnology, B-9000, Ghent, Belgium
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Tingting Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Lixia Pan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - Dorrit de Jong
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Yaowei Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Tim Vanremoortele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Anna M Locke
- Soybean & Nitrogen Fixation Research Unit, United States Department of Agriculture- Agricultural Research Service, Raleigh, NC, 27695, USA.,Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Brigitte van de Cotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Elisabeth Stes
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, B-9000, Ghent, Belgium.,VIB Center for Medical Biotechnology, B-9000, Ghent, Belgium.,VIB Headquarters, 9052, Gent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, NR4 7UH, UK
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, B-9000, Ghent, Belgium. .,VIB Center for Medical Biotechnology, B-9000, Ghent, Belgium.
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium. .,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium.
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28
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Juery C, Concia L, De Oliveira R, Papon N, Ramírez-González R, Benhamed M, Uauy C, Choulet F, Paux E. New insights into homoeologous copy number variations in the hexaploid wheat genome. Plant Genome 2021; 14:e20069. [PMID: 33155760 DOI: 10.1002/tpg2.20069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.
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Affiliation(s)
- Caroline Juery
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, 63000, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, 91405, France
- Current address: Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Romain De Oliveira
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, 63000, France
| | - Nathan Papon
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, 63000, France
| | | | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, 91405, France
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Frédéric Choulet
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, 63000, France
| | - Etienne Paux
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, 63000, France
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29
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Marchal C, Haberer G, Spannagl M, Uauy C. Comparative Genomics and Functional Studies of Wheat BED-NLR Loci. Genes (Basel) 2020; 11:E1406. [PMID: 33256067 PMCID: PMC7761493 DOI: 10.3390/genes11121406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 02/13/2020] [Revised: 04/30/2020] [Accepted: 05/10/2020] [Indexed: 12/01/2022] Open
Abstract
Nucleotide-binding leucine-rich-repeat (LRR) receptors (NLRs) with non-canonical integrated domains (NLR-IDs) are widespread in plant genomes. Zinc-finger BED (named after the Drosophila proteins Boundary Element-Associated Factor and DNA Replication-related Element binding Factor, named BED hereafter) are among the most frequently found IDs. Five BED-NLRs conferring resistance against bacterial and fungal pathogens have been characterized. However, it is unknown whether BED-NLRs function in a manner similar to other NLR-IDs. Here, we used chromosome-level assemblies of wheat to explore the Yr7 and Yr5a genomic regions and show that, unlike known NLR-ID loci, there is no evidence for a NLR-partner in their vicinity. Using neighbor-network analyses, we observed that BED domains from BED-NLRs share more similarities with BED domains from single-BED proteins and from BED-containing proteins harboring domains that are conserved in transposases. We identified a nuclear localization signal (NLS) in Yr7, Yr5, and the other characterized BED-NLRs. We thus propose that this is a feature of BED-NLRs that confer resistance to plant pathogens. We show that the NLS was functional in truncated versions of the Yr7 protein when expressed in N. benthamiana. We did not observe cell-death upon the overexpression of Yr7 full-length, truncated, and 'MHD' variants in N. benthamiana. This suggests that either this system is not suitable to study BED-NLR signaling or that BED-NLRs require additional components to trigger cell death. These results define novel future directions to further understand the role of BED domains in BED-NLR mediated resistance.
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Affiliation(s)
| | | | - Georg Haberer
- Plant Genome and Systems Biology, Helmholtz Center Munich, D-85764 Neuherberg, Germany; (G.H.); (M.S.)
| | - Manuel Spannagl
- Plant Genome and Systems Biology, Helmholtz Center Munich, D-85764 Neuherberg, Germany; (G.H.); (M.S.)
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK;
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30
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Nilsen KT, Walkowiak S, Xiang D, Gao P, Quilichini TD, Willick IR, Byrns B, N'Diaye A, Ens J, Wiebe K, Ruan Y, Cuthbert RD, Craze M, Wallington EJ, Simmonds J, Uauy C, Datla R, Pozniak CJ. Copy number variation of TdDof controls solid-stemmed architecture in wheat. Proc Natl Acad Sci U S A 2020; 117:28708-28718. [PMID: 33127757 PMCID: PMC7682410 DOI: 10.1073/pnas.2009418117] [Citation(s) in RCA: 11] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Stem solidness is an important agronomic trait of durum (Triticum turgidum L. var. durum) and bread (Triticum aestivum L.) wheat that provides resistance to the wheat stem sawfly. This dominant trait is conferred by the SSt1 locus on chromosome 3B. However, the molecular identity and mechanisms underpinning stem solidness have not been identified. Here, we demonstrate that copy number variation of TdDof, a gene encoding a putative DNA binding with one finger protein, controls the stem solidness trait in wheat. Using map-based cloning, we localized TdDof to within a physical interval of 2.1 Mb inside the SSt1 locus. Molecular analysis revealed that hollow-stemmed wheat cultivars such as Kronos carry a single copy of TdDof, whereas solid-stemmed cultivars such as CDC Fortitude carry multiple identical copies of the gene. Deletion of all TdDof copies from CDC Fortitude resulted in the loss of stem solidness, whereas the transgenic overexpression of TdDof restored stem solidness in the TdDof deletion mutant pithless1 and conferred stem solidness in Kronos. In solid-stemmed cultivars, increased TdDof expression was correlated with the down-regulation of genes whose orthologs have been implicated in programmed cell death (PCD) in other species. Anatomical and histochemical analyses revealed that hollow-stemmed lines had stronger PCD-associated signals in the pith cells compared to solid-stemmed lines, which suggests copy number-dependent expression of TdDof could be directly or indirectly involved in the negative regulation of PCD. These findings provide opportunities to manipulate stem development in wheat and other monocots for agricultural or industrial purposes.
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Affiliation(s)
- Kirby T Nilsen
- Crop Development Centre and Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB R7A 5Y3, Canada
| | - Sean Walkowiak
- Crop Development Centre and Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
- Grain Research Laboratory, Canadian Grain Commission, Winnipeg, MB R3C 3G8, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Saskatoon, SK S7N 0W9, Canada
| | - Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Saskatoon, SK S7N 0W9, Canada
| | - Ian R Willick
- Crop Development Centre and Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Brook Byrns
- Crop Development Centre and Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Jennifer Ens
- Crop Development Centre and Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Krystalee Wiebe
- Crop Development Centre and Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada
| | - Richard D Cuthbert
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada
| | | | | | | | | | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Curtis J Pozniak
- Crop Development Centre and Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada;
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31
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Harrington SA, Backhaus AE, Fox S, Rogers C, Borrill P, Uauy C, Richardson A. A heat-shock inducible system for flexible gene expression in cereals. Plant Methods 2020; 16:137. [PMID: 33072173 PMCID: PMC7557097 DOI: 10.1186/s13007-020-00677-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 06/02/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Functional characterisation of genes using transgenic methods is increasingly common in cereal crops. Yet standard methods of gene over-expression can lead to undesirable developmental phenotypes, or even embryo lethality, due to ectopic gene expression. Inducible expression systems allow the study of such genes by preventing their expression until treatment with the specific inducer. When combined with the Cre-Lox recombination system, inducible promoters can be used to initiate constitutive expression of a gene of interest. Yet while these systems are well established in dicot model plants, like Arabidopsis thaliana, they have not yet been implemented in grasses. RESULTS Here we present an irreversible heat-shock inducible system developed using Golden Gate-compatible components which utilises Cre recombinase to drive constitutive gene expression in barley and wheat. We show that a heat shock treatment of 38 °C is sufficient to activate the construct and drive expression of the gene of interest. Modulating the duration of heat shock controls the density of induced cells. Short durations of heat shock cause activation of the construct in isolated single cells, while longer durations lead to global construct activation. The system can be successfully activated in multiple tissues and at multiple developmental stages and shows no activation at standard growth temperatures (~ 20 °C). CONCLUSIONS This system provides an adaptable framework for use in gene functional characterisation in cereal crops. The developed vectors can be easily adapted for specific genes of interest within the Golden Gate cloning system. By using an environmental signal to induce activation of the construct, the system avoids pitfalls associated with consistent and complete application of chemical inducers. As with any inducible system, care must be taken to ensure that the expected construct activation has indeed taken place.
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Affiliation(s)
| | | | - Samantha Fox
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Christian Rogers
- ENSA, Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR UK
| | - Philippa Borrill
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Annis Richardson
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF UK
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32
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Harrington SA, Backhaus AE, Singh A, Hassani-Pak K, Uauy C. The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat. G3 (Bethesda) 2020; 10:3675-3686. [PMID: 32747342 PMCID: PMC7534433 DOI: 10.1534/g3.120.401436] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 08/01/2020] [Indexed: 11/18/2022]
Abstract
Gene regulatory networks are powerful tools which facilitate hypothesis generation and candidate gene discovery. However, the extent to which the network predictions are biologically relevant is often unclear. Recently a GENIE3 network which predicted targets of wheat transcription factors was produced. Here we used an independent RNA-Seq dataset to test the predictions of the wheat GENIE3 network for the senescence-regulating transcription factor NAM-A1 (TraesCS6A02G108300). We re-analyzed the RNA-Seq data against the RefSeqv1.0 genome and identified a set of differentially expressed genes (DEGs) between the wild-type and nam-a1 mutant which recapitulated the known role of NAM-A1 in senescence and nutrient remobilisation. We found that the GENIE3-predicted target genes of NAM-A1 overlap significantly with the DEGs, more than would be expected by chance. Based on high levels of overlap between GENIE3-predicted target genes and the DEGs, we identified candidate senescence regulators. We then explored genome-wide trends in the network related to polyploidy and found that only homeologous transcription factors are likely to share predicted targets in common. However, homeologs which vary in expression levels across tissues are less likely to share predicted targets than those that do not, suggesting that they may be more likely to act in distinct pathways. This work demonstrates that the wheat GENIE3 network can provide biologically-relevant predictions of transcription factor targets, which can be used for candidate gene prediction and for global analyses of transcription factor function. The GENIE3 network has now been integrated into the KnetMiner web application, facilitating its use in future studies.
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Affiliation(s)
- Sophie A Harrington
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Anna E Backhaus
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Ajit Singh
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom
| | - Keywan Hassani-Pak
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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Sansaloni C, Franco J, Santos B, Percival-Alwyn L, Singh S, Petroli C, Campos J, Dreher K, Payne T, Marshall D, Kilian B, Milne I, Raubach S, Shaw P, Stephen G, Carling J, Pierre CS, Burgueño J, Crosa J, Li H, Guzman C, Kehel Z, Amri A, Kilian A, Wenzl P, Uauy C, Banziger M, Caccamo M, Pixley K. Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints. Nat Commun 2020; 11:4572. [PMID: 32917907 PMCID: PMC7486412 DOI: 10.1038/s41467-020-18404-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [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: 07/04/2019] [Accepted: 08/16/2020] [Indexed: 11/09/2022] Open
Abstract
Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 domesticated tetraploid and 3,903 crop wild relatives in a massive-scale genotyping and diversity analysis. Using DArTseqTM technology, we identify more than 300,000 high-quality SNPs and SilicoDArT markers and align them to three reference maps: the IWGSC RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Svevo), and the DArT genetic map. On average, 72% of the markers are uniquely placed on these maps and 50% are linked to genes. The analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection. This provides fertile ground to develop wheat varieties of the future by exploring specific gene or chromosome regions and identifying germplasm conserving allelic diversity missing in current breeding programs. Genebanks hold comprehensive collections of wild species, wild relatives, and landraces that are useful for genetic improvement. Here, the authors report the genotype of nearly 80,000 wheat accessions using DArTseq technology to show the less explored genetic diversity.
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Affiliation(s)
- Carolina Sansaloni
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico.
| | - Jorge Franco
- Departamento de Biometria y Estadística, Facultad de agronomía, Universidad de la República, Ruta 3, km 363, Paysandú, C.P., 60000, Uruguay
| | - Bruno Santos
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | - Sukhwinder Singh
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico.,Geneshifters, 222 Mary Jena Lane, Pullman, WA, 99163, USA
| | - Cesar Petroli
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - Jaime Campos
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - Kate Dreher
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - Thomas Payne
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - David Marshall
- Information and Computational Science, The James Hutton Institute, Invergowrie Dundee, DD2 5DA, Scotland
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz Der Vereinten Nationen 7, Bonn, 53113, Germany
| | - Iain Milne
- Information and Computational Science, The James Hutton Institute, Invergowrie Dundee, DD2 5DA, Scotland
| | - Sebastian Raubach
- Information and Computational Science, The James Hutton Institute, Invergowrie Dundee, DD2 5DA, Scotland
| | - Paul Shaw
- Information and Computational Science, The James Hutton Institute, Invergowrie Dundee, DD2 5DA, Scotland
| | - Gordon Stephen
- Information and Computational Science, The James Hutton Institute, Invergowrie Dundee, DD2 5DA, Scotland
| | - Jason Carling
- Diversity Arrays Technology, Building 3, Level D, University of Canberra, Monana St., Bruce, ACT, 2617, Australia
| | - Carolina Saint Pierre
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - Juan Burgueño
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - José Crosa
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - HuiHui Li
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - Carlos Guzman
- Departamento de Genética Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Universidad de Córdoba, Córdoba, Spain
| | - Zakaria Kehel
- Genetic Resouces Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Rabat-Salé-Zemmour-Zaër, Morocco
| | - Ahmed Amri
- Genetic Resouces Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Rabat-Salé-Zemmour-Zaër, Morocco
| | - Andrzej Kilian
- Diversity Arrays Technology, Building 3, Level D, University of Canberra, Monana St., Bruce, ACT, 2617, Australia
| | - Peter Wenzl
- Genetic Resouces Program, International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira CP 763537 Apartado Aéreo 6713, Cali, Colombia
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Marianne Banziger
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - Mario Caccamo
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Kevin Pixley
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
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Benbow HR, Brennan CJ, Zhou B, Christodoulou T, Berry S, Uauy C, Mullins E, Doohan FM. Insights into the resistance of a synthetically-derived wheat to Septoria tritici blotch disease: less is more. BMC Plant Biol 2020; 20:407. [PMID: 32883202 PMCID: PMC7469286 DOI: 10.1186/s12870-020-02612-z] [Citation(s) in RCA: 2] [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] [Received: 12/30/2019] [Accepted: 08/18/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Little is known about the initial, symptomless (latent) phase of the devastating wheat disease Septoria tritici blotch. However, speculations as to its impact on fungal success and disease severity in the field have suggested that a long latent phase is beneficial to the host and can reduce inoculum build up in the field over a growing season. The winter wheat cultivar Stigg is derived from a synthetic hexaploid wheat and contains introgressions from wild tetraploid wheat Triticum turgidum subsp. dicoccoides, which contribute to cv. Stigg's exceptional STB resistance, hallmarked by a long latent phase. We compared the early transcriptomic response to Zymoseptoria tritici of cv. Stigg to a susceptible wheat cultivar, to elucidate the mechanisms of and differences in pathogen recognition and disease response in these two hosts. RESULTS The STB-susceptible cultivar Longbow responds to Z. tritici infection with a stress response, including activation of hormone-responsive transcription factors, post translational modifications, and response to oxidative stress. The activation of key genes associated with these pathways in cv. Longbow was independently observed in a second susceptible wheat cultivar based on an independent gene expression study. By comparison, cv. Stigg is apathetic in response to STB, and appears to fail to activate a range of defence pathways that cv. Longbow employs. Stigg also displays some evidence of sub-genome bias in its response to Z. tritici infection, whereas the susceptible cv. Longbow shows even distribution of Z. tritici responsive genes across the three wheat sub-genomes. CONCLUSIONS We identify a suite of disease response genes that are involved in early pathogen response in susceptible wheat cultivars that may ultimately lead to susceptibility. In comparison, we hypothesise that rather than an active defence response to stave off disease progression, cv. Stigg's defence strategy is molecular lethargy, or a lower-amplitude of pathogen recognition that may stem from cv. Stigg's wild wheat-derived ancestry. Overall, we present insights into cv. Stigg's exceptional resistance to STB, and present key biological processes for further characterisation in this pathosystem.
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Affiliation(s)
- Harriet R Benbow
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
| | - Ciarán J Brennan
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
| | - Binbin Zhou
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
| | - Thalia Christodoulou
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
| | - Simon Berry
- Limagrain UK Ltd, Windmill Avenue, Woolpit, Suffolk, IP30 9UP, UK
| | | | - Ewen Mullins
- Teagasc Crops Research, Oak Park, Co. Carlow, Ireland
| | - Fiona M Doohan
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland.
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland.
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland.
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Goddard R, Steed A, Chinoy C, Ferreira JR, Scheeren PL, Maciel JLN, Caierão E, Torres GAM, Consoli L, Santana FM, Fernandes JMC, Simmonds J, Uauy C, Cockram J, Nicholson P. Dissecting the genetic basis of wheat blast resistance in the Brazilian wheat cultivar BR 18-Terena. BMC Plant Biol 2020; 20:398. [PMID: 32854622 PMCID: PMC7451118 DOI: 10.1186/s12870-020-02592-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 01/23/2020] [Accepted: 08/12/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Wheat blast, caused by Magnaporthe oryzae Triticum (MoT) pathotype, is a global threat to wheat (Triticum aestivum L.) production. Few blast resistance (R) genes have been identified to date, therefore assessing potential sources of resistance in wheat is important. The Brazilian wheat cultivar BR 18-Terena is considered one of the best sources of resistance to blast and has been widely used in Brazilian breeding programmes, however the underlying genetics of this resistance are unknown. RESULTS BR 18-Terena was used as the common parent in the development of two recombinant inbred line (RIL) F6 populations with the Brazilian cultivars Anahuac 75 and BRS 179. Populations were phenotyped for resistance at the seedling and heading stage using the sequenced MoT isolate BR32, with transgressive segregation being observed. Genetic maps containing 1779 and 1318 markers, were produced for the Anahuac 75 × BR 18-Terena and BR 18-Terena × BRS 179 populations, respectively. Five quantitative trait loci (QTL) associated with seedling resistance, on chromosomes 2B, 4B (2 QTL), 5A and 6A, were identified, as were four QTL associated with heading stage resistance (1A, 2B, 4A and 5A). Seedling and heading stage QTL did not co-locate, despite a significant positive correlation between these traits, indicating that resistance at these developmental stages is likely to be controlled by different genes. BR 18-Terena provided the resistant allele for six QTL, at both developmental stages, with the largest phenotypic effect conferred by a QTL being 24.8% suggesting that BR 18-Terena possesses quantitative resistance. Haplotype analysis of 100 Brazilian wheat cultivars indicates that 11.0% of cultivars already possess a BR 18-Terena-like haplotype for more than one of the identified heading stage QTL. CONCLUSIONS This study suggests that BR 18-Terena possesses quantitative resistance to wheat blast, with nine QTL associated with resistance at either the seedling or heading stage being detected. Wheat blast resistance is also largely tissue-specific. Identification of durable quantitative resistances which can be combined with race-specific R gene-mediated resistance is critical to effectively control wheat blast. Collectively, this work facilitates marker-assisted selection to develop new varieties for cultivation in regions at risk from this emerging disease.
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Affiliation(s)
- Rachel Goddard
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK.
| | - Andrew Steed
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Catherine Chinoy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | | | | | | | | | | | | | - James Simmonds
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Paul Nicholson
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
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Hazard B, Trafford K, Lovegrove A, Griffiths S, Uauy C, Shewry P. Strategies to improve wheat for human health. Nat Food 2020; 1:475-480. [PMID: 37128081 DOI: 10.1038/s43016-020-0134-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/17/2020] [Indexed: 05/03/2023]
Abstract
Despite their economic importance and growing demand, concerns are emerging around wheat-based foods and human health. Most wheat-based foods are made from refined white flour rather than wholemeal flour, and the overconsumption of these products may contribute to the increasing global prevalence of chronic diseases, particularly type 2 diabetes and obesity. Here, we review how the amount, composition and interactions of starch and cell wall polysaccharides, the major carbohydrate components in refined wheat products, impact human health. We discuss strategies and challenges to manipulate these components for improved diet and health using newly developed wheat genomics tools and resources. Commercial foods developed from these novel approaches must be produced without adverse effects on cost, consumer acceptability and processing properties.
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37
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Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Ćwiek-Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, Krajewski P, Lange M, Laporte MA, Michotey C, Oppermann M, Ostler R, Poorter H, Ramı Rez-Gonzalez R, Ramšak Ž, Reif JC, Rocca-Serra P, Sansone SA, Scholz U, Tardieu F, Uauy C, Usadel B, Visser RGF, Weise S, Kersey PJ, Miguel CM, Adam-Blondon AF, Pommier C. Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytol 2020. [PMID: 32171029 DOI: 10.15454/1yxvzv] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.
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Affiliation(s)
- Evangelia A Papoutsoglou
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Daniel Faria
- BioData.pt, Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
- INESC-ID, 1000-029, Lisboa, Portugal
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Elizabeth Arnaud
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Ioannis N Athanasiadis
- Geo-Information Science and Remote Sensing Laboratory, Wageningen University, Droevendaalsesteeg 3, Wageningen, 6708PB, the Netherlands
| | - Inês Chaves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | | | - Bruno V Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal
| | - Hanna Ćwiek-Kupczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Bert Droesbeke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Richard Finkers
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2577, Australia
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Marie-Angélique Laporte
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Célia Michotey
- Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Richard Ostler
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | | | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - François Tardieu
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, UMR759, Montpellier, 34060, France
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Björn Usadel
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Institute for Biology I, BioSC, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | | | - Célia M Miguel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal
| | | | - Cyril Pommier
- Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France
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Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Ćwiek‐Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, Krajewski P, Lange M, Laporte M, Michotey C, Oppermann M, Ostler R, Poorter H, Ramírez‐Gonzalez R, Ramšak Ž, Reif JC, Rocca‐Serra P, Sansone S, Scholz U, Tardieu F, Uauy C, Usadel B, Visser RGF, Weise S, Kersey PJ, Miguel CM, Adam‐Blondon A, Pommier C. Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytol 2020; 227:260-273. [PMID: 32171029 PMCID: PMC7317793 DOI: 10.1111/nph.16544] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [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: 11/22/2019] [Accepted: 02/24/2020] [Indexed: 05/21/2023]
Abstract
Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.
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39
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Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Ćwiek-Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, Krajewski P, Lange M, Laporte MA, Michotey C, Oppermann M, Ostler R, Poorter H, Ramı Rez-Gonzalez R, Ramšak Ž, Reif JC, Rocca-Serra P, Sansone SA, Scholz U, Tardieu F, Uauy C, Usadel B, Visser RGF, Weise S, Kersey PJ, Miguel CM, Adam-Blondon AF, Pommier C. Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytol 2020. [PMID: 32171029 DOI: 10.15454/ah6u4a] [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] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.
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Affiliation(s)
- Evangelia A Papoutsoglou
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Daniel Faria
- BioData.pt, Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
- INESC-ID, 1000-029, Lisboa, Portugal
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Elizabeth Arnaud
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Ioannis N Athanasiadis
- Geo-Information Science and Remote Sensing Laboratory, Wageningen University, Droevendaalsesteeg 3, Wageningen, 6708PB, the Netherlands
| | - Inês Chaves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | | | - Bruno V Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal
| | - Hanna Ćwiek-Kupczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Bert Droesbeke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Richard Finkers
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2577, Australia
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Marie-Angélique Laporte
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Célia Michotey
- Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Richard Ostler
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | | | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - François Tardieu
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, UMR759, Montpellier, 34060, France
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Björn Usadel
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Institute for Biology I, BioSC, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | | | - Célia M Miguel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal
| | | | - Cyril Pommier
- Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France
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Steuernagel B, Witek K, Krattinger SG, Ramirez-Gonzalez RH, Schoonbeek HJ, Yu G, Baggs E, Witek AI, Yadav I, Krasileva KV, Jones JDG, Uauy C, Keller B, Ridout CJ, Wulff BBH. The NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire. Plant Physiol 2020; 183:468-482. [PMID: 32184345 PMCID: PMC7271791 DOI: 10.1104/pp.19.01273] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/06/2020] [Indexed: 05/19/2023]
Abstract
Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR-encoding genes. The availability of the hexaploid wheat (Triticum aestivum) cultivar Chinese Spring reference genome allows a detailed study of its NLR complement. However, low NLR expression and high intrafamily sequence homology hinder their accurate annotation. Here, we developed NLR-Annotator, a software tool for in silico NLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. We applied our tool to wheat and combined it with a transcript-validated subset of genes from the reference gene annotation to characterize the structure, phylogeny, and expression profile of the NLR gene family. We detected 3,400 full-length NLR loci, of which 1,560 were confirmed as expressed genes with intact open reading frames. NLRs with integrated domains mostly group in specific subclades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains, suggesting a paired helper function. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts). In young leaves subjected to biotic stress, we found up-regulation of 266 of the NLRs To illustrate the utility of our tool for the positional cloning of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease-resistant varieties.
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Affiliation(s)
| | - Kamil Witek
- Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | | | - Guotai Yu
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Erin Baggs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Agnieszka I Witek
- Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Inderjit Yadav
- School of Agricultural Biotechnology, Dr. G.S. Khush Laboratories, Punjab Agricultural University, Ludhiana-141 004, Punjab, India
| | - Ksenia V Krasileva
- Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Jonathan D G Jones
- Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | | | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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Orman-Ligeza B, Borrill P, Chia T, Chirico M, Doležel J, Drea S, Karafiátová M, Schatlowski N, Solomon CU, Steuernagel B, Wulff BBH, Uauy C, Trafford K. LYS3 encodes a prolamin-box-binding transcription factor that controls embryo growth in barley and wheat. J Cereal Sci 2020; 93:102965. [PMID: 32508376 PMCID: PMC7263734 DOI: 10.1016/j.jcs.2020.102965] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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] [Indexed: 12/29/2022]
Abstract
Mutations at the LYS3 locus in barley have multiple effects on grain development, including an increase in embryo size and a decrease in endosperm starch content. The gene underlying LYS3 was identified by genetic mapping and mutations in this gene were identified in all four barley lys3 alleles. LYS3 encodes a transcription factor called Prolamin Binding Factor (PBF). Its role in controlling embryo size was confirmed using wheat TILLING mutants. To understand how PBF controls embryo development, we studied its spatial and temporal patterns of expression in developing grains. The PBF gene is expressed in both the endosperm and the embryos, but the timing of expression in these organs differs. PBF expression in wild-type embryos precedes the onset of embryo enlargement in lys3 mutants, suggesting that PBF suppresses embryo growth. We predicted the down-stream target genes of PBF in wheat and found them to be involved in a wide range of biological processes, including organ development and starch metabolism. Our work suggests that PBF may influence embryo size and endosperm starch synthesis via separate gene control networks. LYS3 encodes a transcription factor called Prolamin Binding Factor (PBF) that is expressed in grains only. Wheat and barley LYS3/PBF mutants have enlarged embryos suggesting that this gene suppresses embryo growth. The predicted targets of wheat PBF are involved in a wide range of biological processes, including organ development.
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Affiliation(s)
| | - Philippa Borrill
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Tansy Chia
- NIAB, Genetics and Breeding, Huntington Road, Cambridge, CB3 0LE, UK
| | - Marcella Chirico
- NIAB, Genetics and Breeding, Huntington Road, Cambridge, CB3 0LE, UK
| | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Sinead Drea
- Department of Genetics, University of Leicester, Adrian Building University Road, Leicester, LE1 7RH, UK
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Charles U Solomon
- Department of Genetics, University of Leicester, Adrian Building University Road, Leicester, LE1 7RH, UK.,Department of Plant Science and Biotechnology, Abia State University, PMB 2000, Uturu, Nigeria
| | | | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Kay Trafford
- NIAB, Genetics and Breeding, Huntington Road, Cambridge, CB3 0LE, UK
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Orman-Ligeza B, Harwood W, Hedley PE, Hinchcliffe A, Macaulay M, Uauy C, Trafford K. TRA1: A Locus Responsible for Controlling Agrobacterium-Mediated Transformability in Barley. Front Plant Sci 2020; 11:355. [PMID: 32373138 PMCID: PMC7176908 DOI: 10.3389/fpls.2020.00355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/10/2020] [Indexed: 05/18/2023]
Abstract
In barley (Hordeum vulgare L.), Agrobacterium-mediated transformation efficiency is highly dependent on genotype with very few cultivars being amenable to transformation. Golden Promise is the cultivar most widely used for barley transformation and developing embryos are the most common donor tissue. We tested whether barley mutants with abnormally large embryos were more or less amenable to transformation and discovered that mutant M1460 had a transformation efficiency similar to that of Golden Promise. The large-embryo phenotype of M1460 is due to mutation at the LYS3 locus. There are three other barley lines with independent mutations at the same LYS3 locus, and one of these, Risø1508 has an identical missense mutation to that in M1460. However, none of the lys3 mutants except M1460 were transformable showing that the locus responsible for transformation efficiency, TRA1, was not LYS3 but another locus unique to M1460. To identify TRA1, we generated a segregating population by crossing M1460 to the cultivar Optic, which is recalcitrant to transformation. After four rounds of backcrossing to Optic, plants were genotyped and their progeny were tested for transformability. Some of the progeny lines were transformable at high efficiencies similar to those seen for the parent M1460 and some were not transformable, like Optic. A region on chromosome 2H inherited from M1460 is present in transformable lines only. We propose that one of the 225 genes in this region is TRA1.
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Affiliation(s)
- Beata Orman-Ligeza
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Wendy Harwood
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Pete E. Hedley
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | | | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Kay Trafford
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
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Adamski NM, Borrill P, Brinton J, Harrington SA, Marchal C, Bentley AR, Bovill WD, Cattivelli L, Cockram J, Contreras-Moreira B, Ford B, Ghosh S, Harwood W, Hassani-Pak K, Hayta S, Hickey LT, Kanyuka K, King J, Maccaferrri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BBH, Uauy C. A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. eLife 2020; 9:e55646. [PMID: 32208137 PMCID: PMC7093151 DOI: 10.7554/elife.55646] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [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: 02/03/2020] [Accepted: 03/12/2020] [Indexed: 02/04/2023] Open
Abstract
Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite their importance, a lack of genomic information and resources has hindered the functional characterisation of genes in major crops. The recent release of high-quality reference sequences for these crops underpins a suite of genetic and genomic resources that support basic research and breeding. For wheat, these include gene model annotations, expression atlases and gene networks that provide information about putative function. Sequenced mutant populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources. This review provides a helpful guide for plant scientists, especially those expanding into crop research, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of crops of vital importance for food and nutrition security.
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Affiliation(s)
| | - Philippa Borrill
- School of Biosciences, University of BirminghamBirminghamUnited Kingdom
| | - Jemima Brinton
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | | | | | - William D Bovill
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and BioinformaticsFiorenzuola d'ArdaItaly
| | | | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Brett Ford
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Sreya Ghosh
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Wendy Harwood
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | - Sadiye Hayta
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandSt LuciaAustralia
| | | | - Julie King
- Division of Plant and Crop Sciences, The University of Nottingham, Sutton Bonington CampusLoughboroughUnited Kingdom
| | - Marco Maccaferrri
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna (University of Bologna)BolognaItaly
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Curtis J Pozniak
- Crop Development Centre, University of SaskatchewanSaskatoonCanada
| | | | | | - Ben Trevaskis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luzie U Wingen
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Brande BH Wulff
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
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Bansal M, Adamski NM, Toor PI, Kaur S, Molnár I, Holušová K, Vrána J, Doležel J, Valárik M, Uauy C, Chhuneja P. Aegilops umbellulata introgression carrying leaf rust and stripe rust resistance genes Lr76 and Yr70 located to 9.47-Mb region on 5DS telomeric end through a combination of chromosome sorting and sequencing. Theor Appl Genet 2020; 133:903-915. [PMID: 31894365 DOI: 10.1007/s00122-019-03514-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 12/17/2019] [Indexed: 05/13/2023]
Abstract
Lr76 and Yr70 have been fine mapped using the sequence of flow-sorted recombinant 5D chromosome from wheat-Ae. umbellulata introgression line. The alien introgression has been delineated to 9.47-Mb region on short arm of wheat chromosome 5D. Leaf rust and stripe rust are among the most damaging diseases of wheat worldwide. Wheat cultivation based on limited number of rust resistance genes deployed over vast areas expedites the emergence of new pathotypes warranting a continuous deployment of new resistance genes. In this paper, fine mapping of Aegilops umbellulata-derived leaf rust and stripe rust resistance genes Lr76 and Yr70 is being reported. We flow sorted and paired-end sequenced 5U chromosome of Ae. umbellulata, recombinant chromosome 5D (5DIL) from wheat-Ae. umbellulata introgression line pau16057 and 5DRP of recurrent parent WL711. Chromosome 5U reads were mapped against the reference Chinese Spring chromosome 5D sequence, and alien-specific SNPs were identified. Chromosome 5DIL and 5DRP sequences were de novo assembled, and alien introgression-specific markers were designed by selecting 5U- and 5D-specific SNPs. Overall, 27 KASP markers were mapped in high-resolution population consisting of 1404 F5 RILs. The mapping population segregated for single gene each for leaf rust and stripe rust resistance. The physical order of the SNPs in pau16057 was defined by projecting the 27 SNPs against the IWGSC RefSeq v1.0 sequence. Based on this physical map, the size of Ae. umbellulata introgression was determined to be 9.47 Mb on the distal most end of the short arm of chromosome 5D. This non-recombining alien segment carries six NB-LRR encoding genes based on NLR annotation of assembled chromosome 5DIL sequence and IWGSC RefSeq v1.1 gene models. The presence of SNPs and other sequence variations in these genes between pau16057 and WL711 suggested that they are candidates for Lr76 and Yr70.
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Affiliation(s)
- Mitaly Bansal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
| | | | - Puneet Inder Toor
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India
| | - István Molnár
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 783 71, Olomouc, Czech Republic
- Centre for Agricultural Research, Agricultural Institute, Hungarian Academy of Sciences, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 783 71, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 783 71, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 783 71, Olomouc, Czech Republic
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 783 71, Olomouc, Czech Republic
| | | | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141 004, India.
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Martinez SA, Shorinola O, Conselman S, See D, Skinner DZ, Uauy C, Steber CM. Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype. Theor Appl Genet 2020; 133:719-736. [PMID: 31993676 PMCID: PMC7021667 DOI: 10.1007/s00122-019-03503-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/06/2019] [Indexed: 05/09/2023]
Abstract
Using bulked segregant analysis of exome sequence, we fine-mapped the ABA-hypersensitive mutant ERA8 in a wheat backcross population to the TaMKK3-A locus of chromosome 4A. Preharvest sprouting (PHS) is the germination of mature grain on the mother plant when it rains before harvest. The ENHANCED RESPONSE TO ABA8 (ERA8) mutant increases seed dormancy and, consequently, PHS tolerance in soft white wheat 'Zak.' ERA8 was mapped to chromosome 4A in a Zak/'ZakERA8' backcross population using bulked segregant analysis of exome sequenced DNA (BSA-exome-seq). ERA8 was fine-mapped relative to mutagen-induced SNPs to a 4.6 Mb region containing 70 genes. In the backcross population, the ERA8 ABA-hypersensitive phenotype was strongly linked to a missense mutation in TaMKK3-A-G1093A (LOD 16.5), a gene associated with natural PHS tolerance in barley and wheat. The map position of ERA8 was confirmed in an 'Otis'/ZakERA8 but not in a 'Louise'/ZakERA8 mapping population. This is likely because Otis carries the same natural PHS susceptible MKK3-A-A660S allele as Zak, whereas Louise carries the PHS-tolerant MKK3-A-C660R allele. Thus, the variation for grain dormancy and PHS tolerance in the Louise/ZakERA8 population likely resulted from segregation of other loci rather than segregation for PHS tolerance at the MKK3 locus. This inadvertent complementation test suggests that the MKK3-A-G1093A mutation causes the ERA8 phenotype. Moreover, MKK3 was a known ABA signaling gene in the 70-gene 4.6 Mb ERA8 interval. None of these 70 genes showed the differential regulation in wild-type Zak versus ERA8 expected of a promoter mutation. Thus, the working model is that the ERA8 phenotype results from the MKK3-A-G1093A mutation.
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Affiliation(s)
- Shantel A Martinez
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | | | - Samantha Conselman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Deven See
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, Washington State University, Pullman, WA, 99164-6420, USA
| | - Daniel Z Skinner
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, Washington State University, Pullman, WA, 99164-6420, USA
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Camille M Steber
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
- USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, Washington State University, Pullman, WA, 99164-6420, USA.
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Pasquariello M, Berry S, Burt C, Uauy C, Nicholson P. Yield reduction historically associated with the Aegilops ventricosa 7D V introgression is genetically and physically distinct from the eyespot resistance gene Pch1. Theor Appl Genet 2020; 133:707-717. [PMID: 31834441 PMCID: PMC7021663 DOI: 10.1007/s00122-019-03502-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/27/2019] [Indexed: 05/27/2023]
Abstract
Yield penalty and increased grain protein content traits associated with Aegilops ventricosa 7D introgression have been mapped for the first time, and they are physically distinct from the eyespot resistance locus Pch1. Wheat wild relatives represent an important source of genetic variation, but introgression of agronomically relevant genes, such as for disease resistance, may lead to the simultaneous introduction of genetically linked deleterious traits. Pch1 is a dominant gene, conferring resistance to eyespot and was introgressed to wheat from Aegilops ventricosa as part of a large segment of the 7DV chromosome. This introgression has been associated with a significant yield reduction and a concomitant increase in grain protein content. In this study, we evaluated both traits and their relationship to the location of the Pch1 gene. We found that both QTLs were clearly distinct from the Pch1 gene, being located on a different linkage group to Pch1. In addition, we found that the QTL for increased grain protein content was strong and consistent across field trials, whereas the yield penalty QTL was unstable and environmentally dependent. The yield and grain protein content QTLs were genetically linked and located in the same linkage group. This finding is due in part to the small size of the population, and to the restricted recombination between wheat 7D and Ae. ventricosa 7Dv chromosomes. Although recombination in this interval is rare, it does occur. A recombinant line containing Pch1 and 7D_KASP6, the marker associated with increase in grain protein content, but not Xwmc221, the marker associated with the yield penalty effect, was identified.
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Affiliation(s)
| | - Simon Berry
- Limagrain UK Ltd, Rothwell, Market Rasen, Lincolnshire, LN7 6DT, UK
| | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Paul Nicholson
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
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Tkacz A, Pini F, Turner TR, Bestion E, Simmonds J, Howell P, Greenland A, Cheema J, Emms DM, Uauy C, Poole PS. Agricultural Selection of Wheat Has Been Shaped by Plant-Microbe Interactions. Front Microbiol 2020; 11:132. [PMID: 32117153 PMCID: PMC7015950 DOI: 10.3389/fmicb.2020.00132] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/21/2020] [Indexed: 12/26/2022] Open
Abstract
The influence of wheat (modern wheat, both bread and pasta, their wild ancestors and synthetic hybrids) on the microbiota of their roots and surrounding soil is characterized. We isolated lines of bread wheat by hybridizing diploid (Aegilops tauschii) with tetraploid Triticum durum and crossed it with a modern cultivar of Triticum aestivum. The newly created, synthetic hybrid wheat, which recapitulate the breeding history of wheat through artificial selection, is found to support a microbiome enriched in beneficial Glomeromycetes fungi, but also in, potentially detrimental, Nematoda. We hypothesize that during wheat domestication this plant-microbe interaction diminished, suggesting an evolutionary tradeoff; sacrificing advantageous nutrient acquisition through fungal interactions to minimize interaction with pathogenic fungi. Increased plant selection for Glomeromycetes and Nematoda is correlated with the D genome derived from A. tauschii. Despite differences in their soil microbiota communities, overall wheat plants consistently show a low ratio of eukaryotes to prokaryotes. We propose that this is a mechanism for protection against soil-borne fungal disease and appears to be deeply rooted in the wheat genome. We suggest that the influence of plants on the composition of their associated microbiota is an integral factor, hitherto overlooked, but intrinsic to selection during wheat domestication.
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Affiliation(s)
- Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Francesco Pini
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Thomas R Turner
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Eloïne Bestion
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Phil Howell
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Andy Greenland
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Jitender Cheema
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - David M Emms
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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48
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Chia T, Chirico M, King R, Ramirez-Gonzalez R, Saccomanno B, Seung D, Simmonds J, Trick M, Uauy C, Verhoeven T, Trafford K. A carbohydrate-binding protein, B-GRANULE CONTENT 1, influences starch granule size distribution in a dose-dependent manner in polyploid wheat. J Exp Bot 2020; 71:105-115. [PMID: 31633795 DOI: 10.1093/jxb/erz405] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 07/03/2019] [Accepted: 08/29/2019] [Indexed: 05/19/2023]
Abstract
In Triticeae endosperm (e.g. wheat and barley), starch granules have a bimodal size distribution (with A- and B-type granules) whereas in other grasses the endosperm contains starch granules with a unimodal size distribution. Here, we identify the gene, BGC1 (B-GRANULE CONTENT 1), responsible for B-type starch granule content in Aegilops and wheat. Orthologues of this gene are known to influence starch synthesis in diploids such as rice, Arabidopsis, and barley. However, using polyploid Triticeae species, we uncovered a more complex biological role for BGC1 in starch granule initiation: BGC1 represses the initiation of A-granules in early grain development but promotes the initiation of B-granules in mid grain development. We provide evidence that the influence of BGC1 on starch synthesis is dose dependent and show that three very different starch phenotypes are conditioned by the gene dose of BGC1 in polyploid wheat: normal bimodal starch granule morphology; A-granules with few or no B-granules; or polymorphous starch with few normal A- or B-granules. We conclude from this work that BGC1 participates in controlling B-type starch granule initiation in Triticeae endosperm and that its precise effect on granule size and number varies with gene dose and stage of development.
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Affiliation(s)
| | | | - Rob King
- Rothamsted Research, West Common, Harpenden, UK
| | | | | | - David Seung
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich, UK
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Ingvardsen CR, Massange-Sánchez JA, Borum F, Uauy C, Gregersen PL. Development of mlo-based resistance in tetraploid wheat against wheat powdery mildew. Theor Appl Genet 2019; 132:3009-3022. [PMID: 31317234 DOI: 10.1007/s00122-019-03402-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/11/2019] [Indexed: 05/12/2023]
Abstract
Powdery mildew is a severe disease in wheat. In barley, durable resistance exists, based on non-functionality of the Mlo gene. As a model to analyse the effects of mutagenesis in the homoeologous Mlo genes of wheat, we developed mlo-based powdery mildew resistance in tetraploid durum wheat. To obtain Mlo mutations, we screened a TILLING population developed in tetraploid wheat "Kronos" for which the captured exome sequence of > 1500 lines is available. This resulted in 23 mutants for Mlo-A1 and 26 non-redundant mutants for Mlo-B1. Two Mlo-A1 and four Mlo-B1 mutants were crossed to obtain eight F2 mutant lines that showed a range of phenotypes from susceptibility to full resistance. Pot experiments under semi-field conditions confirmed the resistance levels for six of the mutants without any signs of adverse pleiotropic effects. Resistance ranking was similar across six powdery mildew isolates, indicating no isolate specificity of the mlo-based resistance. The effect of mutations in the Mlo-B1 gene was stronger than in the Mlo-A1 gene, probably reflecting differences in wild-type Mlo gene expression levels. Strong partial resistance effects were observed with single mlo-B1 mutations hence, revealing a dosage effect of mlo mutant alleles. Two of the four mlo-B1 mutations (W163* and P335L) were very strong; however, the highest combined effect was observed with the MloA-P335S/MloB-P335L combination, suggesting that non-functional, but full-length Mlo proteins might have the strongest effect compared with nonsense mutations. Our results show that mlo-based resistance might offer possibilities to introduce durable protection in tetraploid wheat against powdery mildew.
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Affiliation(s)
- Christina R Ingvardsen
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Slagelse, Denmark
| | - Julio A Massange-Sánchez
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Slagelse, Denmark
- CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Per L Gregersen
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Slagelse, Denmark.
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50
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Alabdullah AK, Borrill P, Martin AC, Ramirez-Gonzalez RH, Hassani-Pak K, Uauy C, Shaw P, Moore G. A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization. Front Plant Sci 2019; 10:1325. [PMID: 31681395 PMCID: PMC6813927 DOI: 10.3389/fpls.2019.01325] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/24/2019] [Indexed: 05/05/2023]
Abstract
Polyploidization has played an important role in plant evolution. However, upon polyploidization, the process of meiosis must adapt to ensure the proper segregation of increased numbers of chromosomes to produce balanced gametes. It has been suggested that meiotic gene (MG) duplicates return to a single copy following whole genome duplication to stabilize the polyploid genome. Therefore, upon the polyploidization of wheat, a hexaploid species with three related (homeologous) genomes, the stabilization process may have involved rapid changes in content and expression of MGs on homeologous chromosomes (homeologs). To examine this hypothesis, sets of candidate MGs were identified in wheat using co-expression network analysis and orthology informed approaches. In total, 130 RNA-Seq samples from a range of tissues including wheat meiotic anthers were used to define co-expressed modules of genes. Three modules were significantly correlated with meiotic tissue samples but not with other tissue types. These modules were enriched for GO terms related to cell cycle, DNA replication, and chromatin modification and contained orthologs of known MGs. Overall, 74.4% of genes within these meiosis-related modules had three homeologous copies which was similar to other tissue-related modules. Amongst wheat MGs identified by orthology, rather than co-expression, the majority (93.7%) were either retained in hexaploid wheat at the same number of copies (78.4%) or increased in copy number (15.3%) compared to ancestral wheat species. Furthermore, genes within meiosis-related modules showed more balanced expression levels between homeologs than genes in non-meiosis-related modules. Taken together, our results do not support extensive gene loss nor changes in homeolog expression of MGs upon wheat polyploidization. The construction of the MG co-expression network allowed identification of hub genes and provided key targets for future studies.
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Affiliation(s)
| | - Philippa Borrill
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | | | | | - Keywan Hassani-Pak
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Peter Shaw
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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