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Qi Z, Meng X, Xu M, Du Y, Yu J, Song T, Pan X, Zhang R, Cao H, Yu M, Telebanco-Yanoria MJ, Lu G, Zhou B, Liu Y. A novel Pik allele confers extended resistance to rice blast. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39087779 DOI: 10.1111/pce.15072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
In the ongoing arms race between rice and Magnaporthe oryzae, the pathogen employs effectors to evade the immune response, while the host develops resistance genes to recognise these effectors and confer resistance. In this study, we identified a novel Pik allele, Pik-W25, from wild rice WR25 through bulked-segregant analysis, creating the Pik-W25 NIL (Near-isogenic Lines) named G9. Pik-W25 conferred resistance to isolates expressing AvrPik-C/D/E alleles. CRISPR-Cas9 editing was used to generate transgenic lines with a loss of function in Pik-W25-1 and Pik-W25-2, resulting in loss of resistance in G9 to isolates expressing the three alleles, confirming that Pik-W25-induced immunity required both Pik-W25-1 and Pik-W25-2. Yeast two-hybrid (Y2H) and split luciferase complementation assays showed interactions between Pik-W25-1 and the three alleles, while Pik-W25-2 could not interact with AvrPik-C, -D, and -E alleles with Y2H assay, indicating Pik-W25-1 acts as an adaptor and Pik-W25-2 transduces the signal to trigger resistance. The Pik-W25 NIL exhibited enhanced field resistance to leaf and panicle blast without significant changes in morphology or development compared to the parent variety CO39, suggesting its potential for resistance breeding. These findings advance our knowledge of rice blast resistance mechanisms and offer valuable resources for effective and sustainable control strategies.
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Affiliation(s)
- Zhongqiang Qi
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
- IRRI-JAAS Joint Laboratory, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Xiuli Meng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Genetics and Biotechnology Division, International Rice Research Institute, College, Los Banos, Laguna, Philippines
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Ming Xu
- High-throughput Genotyping Shared Laboratory, Seed Administration Department of Jiangsu Province, Nanjing, China
| | - Yan Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Junjie Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Tianqiao Song
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Xiayan Pan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Rongsheng Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Huijuan Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Mina Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | | | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Bo Zhou
- IRRI-JAAS Joint Laboratory, Jiangsu Academy of Agricultural Science, Nanjing, China
- Genetics and Biotechnology Division, International Rice Research Institute, College, Los Banos, Laguna, Philippines
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
- IRRI-JAAS Joint Laboratory, Jiangsu Academy of Agricultural Science, Nanjing, China
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Chen T, Niu Y, Yang C, Liang Y, Xu J. Screening of Rice ( Oryza sativa L.) Genotypes for Salinity Tolerance and Dissecting Determinants of Tolerance Mechanism. PLANTS (BASEL, SWITZERLAND) 2024; 13:1036. [PMID: 38611565 PMCID: PMC11013488 DOI: 10.3390/plants13071036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
Soil salinity imposes osmotic, ionic, and oxidative stresses on plants, resulting in growth inhibition, developmental changes, metabolic adaptations, and ion sequestration or exclusion. Identifying salinity-tolerant resources and understanding physiological and molecular mechanisms of salinity tolerance could lay a foundation for the improvement of salinity tolerance in rice. In this study, a series of salinity-tolerance-related morphological and physiological traits were investigated in 46 rice genotypes, including Sea Rice 86, to reveal the main strategies of rice in responding to salinity stress at the seedling stage. No genotypes showed the same tolerance level as the two landraces Pokkali and Nona Bokra, which remain the donors for improving the salinity tolerance of rice. However, due to undesirable agronomic traits of these donors, alternative cultivars such as JC118S and R1 are recommended as novel source of salinity tolerance. Correlation and principal component analyses revealed that the salinity tolerance of rice seedlings is not only controlled by growth vigor but also regulated by ion transport pathways such as long-distance Na+ transport, root Na+ sequestration, and root K+ retention. Therefore, such key traits should be targeted in future breeding programs as the strategy of obtaining better Na+ exclusion is still the bottleneck for improving salinity tolerance in rice.
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Affiliation(s)
- Tianxiao Chen
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China; (T.C.); (C.Y.)
| | - Yanan Niu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Changdeng Yang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China; (T.C.); (C.Y.)
| | - Yan Liang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China; (T.C.); (C.Y.)
| | - Jianlong Xu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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Kamble U, Mishra CN, Govindan V, Sharma AK, Pawar S, Kumar S, Krishnappa G, Gupta OP, Singh GP, Singh G. Ensuring Nutritional Security in India through Wheat Biofortification: A Review. Genes (Basel) 2022; 13:genes13122298. [PMID: 36553565 PMCID: PMC9778289 DOI: 10.3390/genes13122298] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Undernourishment of nutrients, also known as hidden hunger, affects over 2 billion populace globally. Even though stunting among children below five years of age has decreased in India in the last ten years, India is home to roughly thirty percent of the world's population of stunted pre-schoolers. A significant improvement has been witnessed in the targeted development and deployment of biofortified crops; approximately 20 million farm households from developing counties benefit from cultivating and consuming biofortified crops. There is ample scope for including biofortified varieties in the seed chain, ensuring nutritional security. Wheat is a dietary staple in India, typically consumed as wholemeal flour in the form of flatbreads such as chapatti and roti. Wheat contributes to nearly one fifth of global energy requirements and can also provide better amounts of iron (Fe) and zinc (Zn). As a result, biofortified wheat can serve as a medium for delivery of essential micronutrients such as Fe and Zn to end users. This review discusses wheat biofortification components such as Fe and Zn dynamics, its uptake and movement in plants, the genetics of their buildup, and the inclusion of biofortified wheat varieties in the seed multiplication chain concerning India.
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Affiliation(s)
- Umesh Kamble
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - Chandra Nath Mishra
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
- Correspondence: ; Tel.: +91-946-8251-294
| | | | - Amit Kumar Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - Sushma Pawar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | | | - Om Prakash Gupta
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | | | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
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Genomic revolution of US weedy rice in response to 21st century agricultural technologies. Commun Biol 2022; 5:885. [PMID: 36076028 PMCID: PMC9458635 DOI: 10.1038/s42003-022-03803-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/04/2022] [Indexed: 11/08/2022] Open
Abstract
Weedy rice is a close relative of cultivated rice that devastates rice productivity worldwide. In the southern United States, two distinct strains have been historically predominant, but the 21st century introduction of hybrid rice and herbicide resistant rice technologies has dramatically altered the weedy rice selective landscape. Here, we use whole-genome sequences of 48 contemporary weedy rice accessions to investigate the genomic consequences of crop-weed hybridization and selection for herbicide resistance. We find that population dynamics have shifted such that most contemporary weeds are now crop-weed hybrid derivatives, and that their genomes have subsequently evolved to be more like their weedy ancestors. Haplotype analysis reveals extensive adaptive introgression of cultivated alleles at the resistance gene ALS, but also uncovers evidence for convergent molecular evolution in accessions with no signs of hybrid origin. The results of this study suggest a new era of weedy rice evolution in the United States.
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Thomson MJ, Biswas S, Tsakirpaloglou N, Septiningsih EM. Functional Allele Validation by Gene Editing to Leverage the Wealth of Genetic Resources for Crop Improvement. Int J Mol Sci 2022; 23:ijms23126565. [PMID: 35743007 PMCID: PMC9223900 DOI: 10.3390/ijms23126565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 02/05/2023] Open
Abstract
Advances in molecular technologies over the past few decades, such as high-throughput DNA marker genotyping, have provided more powerful plant breeding approaches, including marker-assisted selection and genomic selection. At the same time, massive investments in plant genetics and genomics, led by whole genome sequencing, have led to greater knowledge of genes and genetic pathways across plant genomes. However, there remains a gap between approaches focused on forward genetics, which start with a phenotype to map a mutant locus or QTL with the goal of cloning the causal gene, and approaches using reverse genetics, which start with large-scale sequence data and work back to the gene function. The recent establishment of efficient CRISPR-Cas-based gene editing promises to bridge this gap and provide a rapid method to functionally validate genes and alleles identified through studies of natural variation. CRISPR-Cas techniques can be used to knock out single or multiple genes, precisely modify genes through base and prime editing, and replace alleles. Moreover, technologies such as protoplast isolation, in planta transformation, and the use of developmental regulatory genes promise to enable high-throughput gene editing to accelerate crop improvement.
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Understanding the Dynamics of Blast Resistance in Rice-Magnaporthe oryzae Interactions. J Fungi (Basel) 2022; 8:jof8060584. [PMID: 35736067 PMCID: PMC9224618 DOI: 10.3390/jof8060584] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 01/09/2023] Open
Abstract
Rice is a global food grain crop for more than one-third of the human population and a source for food and nutritional security. Rice production is subjected to various stresses; blast disease caused by Magnaporthe oryzae is one of the major biotic stresses that has the potential to destroy total crop under severe conditions. In the present review, we discuss the importance of rice and blast disease in the present and future global context, genomics and molecular biology of blast pathogen and rice, and the molecular interplay between rice–M. oryzae interaction governed by different gene interaction models. We also elaborated in detail on M. oryzae effector and Avr genes, and the role of noncoding RNAs in disease development. Further, rice blast resistance QTLs; resistance (R) genes; and alleles identified, cloned, and characterized are discussed. We also discuss the utilization of QTLs and R genes for blast resistance through conventional breeding and transgenic approaches. Finally, we review the demonstrated examples and potential applications of the latest genome-editing tools in understanding and managing blast disease in rice.
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7
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Khan ZA, Kumar R, Dasgupta I. CRISPR/Cas-Mediated Resistance against Viruses in Plants. Int J Mol Sci 2022; 23:ijms23042303. [PMID: 35216418 PMCID: PMC8879314 DOI: 10.3390/ijms23042303] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 11/16/2022] Open
Abstract
CRISPR/Cas9 provides a robust and widely adaptable system with enormous potential for genome editing directed towards generating useful products. It has been used extensively to generate resistance against viruses infecting plants with more effective and prolonged efficiency as compared with previous antiviral approaches, thus holding promise to alleviate crop losses. In this review, we have discussed the reports of CRISPR/Cas-based virus resistance strategies against plant viruses. These strategies include approaches targeting single or multiple genes (or non-coding region) in the viral genome and targeting host factors essential for virus propagation. In addition, the utilization of base editing has been discussed to generate transgene-free plants resistant to viruses. This review also compares the efficiencies of these approaches. Finally, we discuss combinatorial approaches, including multiplexing, to increase editing efficiency and bypass the generation of escape mutants.
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Exploring the legacy of Central European historical winter wheat landraces. Sci Rep 2021; 11:23915. [PMID: 34903761 PMCID: PMC8668957 DOI: 10.1038/s41598-021-03261-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/29/2021] [Indexed: 11/14/2022] Open
Abstract
Historical wheat landraces are rich sources of genetic diversity offering untapped reservoirs for broadening the genetic base of modern varieties. Using a 20K SNP array, we investigated the accessible genetic diversity in a Central European bread wheat landrace collection with great drought, heat stress tolerance and higher tillering capacity. We discovered distinct differences in the number of average polymorphisms between landraces and modern wheat cultivars, and identified a set of novel rare alleles present at low frequencies in the landrace collection. The detected polymorphisms were unevenly distributed along the wheat genome, and polymorphic markers co-localized with genes of great agronomic importance. The geographical distribution of the inferred Bayesian clustering revealed six genetically homogenous ancestral groups among the collection, where the Central European core bared an admixed background originating from four ancestral groups. We evaluated the effective population sizes (Ne) of the Central European collection and assessed changes in diversity over time, which revealed a dramatic ~ 97% genetic erosion between 1955 and 2015.
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Volante A, Barabaschi D, Marino R, Brandolini A. Genome-wide association study for morphological, phenological, quality, and yield traits in einkorn (Triticum monococcum L. subsp. monococcum). G3 (BETHESDA, MD.) 2021; 11:jkab281. [PMID: 34849796 PMCID: PMC8527505 DOI: 10.1093/g3journal/jkab281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/27/2021] [Indexed: 11/12/2022]
Abstract
Einkorn (Triticum monococcum L. subsp. monococcum, 2n = 2× = 14, AmAm) is a diploid wheat whose cultivation was widespread in the Mediterranean and European area till the Bronze Age, before it was replaced by the more productive durum and bread wheats. Although scarcely cultivated nowadays, it has gained renewed interest due to its relevant nutritional properties and as source of genetic diversity for crop breeding. However, the molecular basis of many traits of interest in einkorn remain still unknown. A panel of 160 einkorn landraces, from different parts of the distribution area, was characterized for several phenotypic traits related to morphology, phenology, quality, and yield for 4 years in two locations. An approach based on co-linearity with the A genome of bread wheat, supported also by that with Triticum urartu genome, was exploited to perform association mapping, even without an einkorn anchored genome. The association mapping approach uncovered numerous marker-trait associations; for 37 of these, a physical position was inferred by homology with the bread wheat genome. Moreover, numerous associated regions were also assigned to the available T. monococcum contigs. Among the intervals detected in this work, three overlapped with regions previously described as involved in the same trait, while four other regions were localized in proximity of loci previously described and presumably refer to the same gene/QTL. The remaining associated regions identified in this work could represent a novel and useful starting point for breeding approaches to improve the investigated traits in this neglected species.
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Affiliation(s)
- Andrea Volante
- CREA—Research Centre for Cereal and Industrial Crops, 13100 Vercelli, Italy
| | - Delfina Barabaschi
- CREA—Research Centre for Genomics and Bioinformatics, 29017 Fiorenzuola d’Arda, Italy and
| | - Rosanna Marino
- CREA—Research Centre for Animal Production and Aquaculture, 26900 Lodi, Italy
| | - Andrea Brandolini
- CREA—Research Centre for Animal Production and Aquaculture, 26900 Lodi, Italy
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Shariatipour N, Heidari B, Tahmasebi A, Richards C. Comparative Genomic Analysis of Quantitative Trait Loci Associated With Micronutrient Contents, Grain Quality, and Agronomic Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:709817. [PMID: 34712248 PMCID: PMC8546302 DOI: 10.3389/fpls.2021.709817] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/06/2021] [Indexed: 05/02/2023]
Abstract
Comparative genomics and meta-quantitative trait loci (MQTLs) analysis are important tools for the identification of reliable and stable QTLs and functional genes controlling quantitative traits. We conducted a meta-analysis to identify the most stable QTLs for grain yield (GY), grain quality traits, and micronutrient contents in wheat. A total of 735 QTLs retrieved from 27 independent mapping populations reported in the last 13 years were used for the meta-analysis. The results showed that 449 QTLs were successfully projected onto the genetic consensus map which condensed to 100 MQTLs distributed on wheat chromosomes. This consolidation of MQTLs resulted in a three-fold reduction in the confidence interval (CI) compared with the CI for the initial QTLs. Projection of QTLs revealed that the majority of QTLs and MQTLs were in the non-telomeric regions of chromosomes. The majority of micronutrient MQTLs were located on the A and D genomes. The QTLs of thousand kernel weight (TKW) were frequently associated with QTLs for GY and grain protein content (GPC) with co-localization occurring at 55 and 63%, respectively. The co- localization of QTLs for GY and grain Fe was found to be 52% and for QTLs of grain Fe and Zn, it was found to be 66%. The genomic collinearity within Poaceae allowed us to identify 16 orthologous MQTLs (OrMQTLs) in wheat, rice, and maize. Annotation of promising candidate genes (CGs) located in the genomic intervals of the stable MQTLs indicated that several CGs (e.g., TraesCS2A02G141400, TraesCS3B02G040900, TraesCS4D02G323700, TraesCS3B02G077100, and TraesCS4D02G290900) had effects on micronutrients contents, yield, and yield-related traits. The mapping refinements leading to the identification of these CGs provide an opportunity to understand the genetic mechanisms driving quantitative variation for these traits and apply this information for crop improvement programs.
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Affiliation(s)
- Nikwan Shariatipour
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Heidari
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ahmad Tahmasebi
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Christopher Richards
- USDA ARS National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
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The influence of QTL allelic diversity on QTL detection in multi-parent populations: a simulation study in sugar beet. BMC Genom Data 2021; 22:4. [PMID: 33568071 PMCID: PMC7860181 DOI: 10.1186/s12863-021-00960-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multi-parent populations (MPPs) are important resources for studying plant genetic architecture and detecting quantitative trait loci (QTLs). In MPPs, the QTL effects can show various levels of allelic diversity, which can be an important factor influencing the detection of QTLs. In MPPs, the allelic effects can be more or less specific. They can depend on an ancestor, a parent or the combination of parents in a cross. In this paper, we evaluated the effect of QTL allelic diversity on the QTL detection power in MPPs. RESULTS We simulated: a) cross-specific QTLs; b) parental and ancestral QTLs; and c) bi-allelic QTLs. Inspired by a real application in sugar beet, we tested different MPP designs (diallel, chessboard, factorial, and NAM) derived from five or nine parents to explore the ability to sample genetic diversity and detect QTLs. Using a fixed total population size, the QTL detection power was larger in MPPs with fewer but larger crosses derived from a reduced number of parents. The use of a larger set of parents was useful to detect rare alleles with a large phenotypic effect. The benefit of using a larger set of parents was however conditioned on an increase of the total population size. We also determined empirical confidence intervals for QTL location to compare the resolution of different designs. For QTLs representing 6% of the phenotypic variation, using 1600 F2 offspring individuals, we found average 95% confidence intervals over different designs of 49 and 25 cM for cross-specific and bi-allelic QTLs, respectively. CONCLUSIONS MPPs derived from less parents with few but large crosses generally increased the QTL detection power. Using a larger set of parents to cover a wider genetic diversity can be useful to detect QTLs with a reduced minor allele frequency when the QTL effect is large and when the total population size is increased.
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Lin YL, Wu DH, Wu CC, Huang YF. Explore the genetics of weedy traits using rice 3K database. BOTANICAL STUDIES 2021; 62:2. [PMID: 33432466 PMCID: PMC7801593 DOI: 10.1186/s40529-020-00309-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Weedy rice, a conspecific weedy counterpart of the cultivated rice (Oryza sativa L.), has been problematic in rice-production area worldwide. Although we started to know about the origin of some weedy traits for some rice-growing regions, an overall assessment of weedy trait-related loci was not yet available. On the other hand, the advances in sequencing technologies, together with community efforts, have made publicly available a large amount of genomic data. Given the availability of public data and the need of "weedy" allele mining for a better management of weedy rice, the objective of the present study was to explore the genetic architecture of weedy traits based on publicly available data, mainly from the 3000 Rice Genome Project (3K-RGP). RESULTS Based on the results of population structure analysis, we have selected 1378 individuals from four sub-populations (aus, indica, temperate japonica, tropical japonica) without admixed genomic composition for genome-wide association analysis (GWAS). Five traits were investigated: awn color, seed shattering, seed threshability, seed coat color, and seedling height. GWAS was conducted for each sub-population × trait combination and we have identified 66 population-specific trait-associated SNPs. Eleven significant SNPs fell into an annotated gene and four other SNPs were close to a putative candidate gene (± 25 kb). SNPs located in or close to Rc were particularly predictive of the occurrence of seed coat color and our results showed that different sub-populations required different SNPs for a better seed coat color prediction. We compared the data of 3K-RGP to a publicly available weedy rice dataset. The profile of allele frequency, phenotype-genotype segregation of target SNP, as well as GWAS results for the presence and absence of awns diverged between the two sets of data. CONCLUSIONS The genotype of trait-associated SNPs identified in this study, especially those located in or close to Rc, can be developed to diagnostic SNPs to trace the origin of weedy trait occurred in the field. The difference of results from the two publicly available datasets used in this study emphasized the importance of laboratory experiments to confirm the allele mining results based on publicly available data.
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Affiliation(s)
- Yu-Lan Lin
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Da'an Dist., Taipei, 10617, Taiwan
| | - Dong-Hong Wu
- Taiwan Agricultural Research Institute, Council of Agriculture, Executive Yuan, No. 189, Zhongzheng Rd, Wufeng Dist, Taichung City, 41362, Taiwan
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Institute of Plant Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Da'an Dist., Taipei, 10617, Taiwan
| | - Yung-Fen Huang
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Da'an Dist., Taipei, 10617, Taiwan.
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Pramanik D, Shelake RM, Kim MJ, Kim JY. CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement. MOLECULAR PLANT 2021; 14:127-150. [PMID: 33152519 DOI: 10.1016/j.molp.2020.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/14/2020] [Accepted: 11/02/2020] [Indexed: 05/03/2023]
Abstract
The central dogma (CD) of molecular biology is the transfer of genetic information from DNA to RNA to protein. Major CD processes governing genetic flow include the cell cycle, DNA replication, chromosome packaging, epigenetic changes, transcription, posttranscriptional alterations, translation, and posttranslational modifications. The CD processes are tightly regulated in plants to maintain genetic integrity throughout the life cycle and to pass genetic materials to next generation. Engineering of various CD processes involved in gene regulation will accelerate crop improvement to feed the growing world population. CRISPR technology enables programmable editing of CD processes to alter DNA, RNA, or protein, which would have been impossible in the past. Here, an overview of recent advancements in CRISPR tool development and CRISPR-based CD modulations that expedite basic and applied plant research is provided. Furthermore, CRISPR applications in major thriving areas of research, such as gene discovery (allele mining and cryptic gene activation), introgression (de novo domestication and haploid induction), and application of desired traits beneficial to farmers or consumers (biotic/abiotic stress-resilient crops, plant cell factories, and delayed senescence), are described. Finally, the global regulatory policies, challenges, and prospects for CRISPR-mediated crop improvement are discussed.
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Affiliation(s)
- Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
| | - Mi Jung Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
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Scott MF, Ladejobi O, Amer S, Bentley AR, Biernaskie J, Boden SA, Clark M, Dell'Acqua M, Dixon LE, Filippi CV, Fradgley N, Gardner KA, Mackay IJ, O'Sullivan D, Percival-Alwyn L, Roorkiwal M, Singh RK, Thudi M, Varshney RK, Venturini L, Whan A, Cockram J, Mott R. Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding. Heredity (Edinb) 2020; 125:396-416. [PMID: 32616877 PMCID: PMC7784848 DOI: 10.1038/s41437-020-0336-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 11/21/2022] Open
Abstract
Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.
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Affiliation(s)
| | | | - Samer Amer
- University of Reading, Reading, RG6 6AH, UK
- Faculty of Agriculture, Alexandria University, Alexandria, 23714, Egypt
| | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Jay Biernaskie
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Scott A Boden
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | | | | | - Laura E Dixon
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Carla V Filippi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Nicolas Repetto y Los Reseros s/n, 1686, Hurlingham, Buenos Aires, Argentina
| | - Nick Fradgley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Keith A Gardner
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Ian J Mackay
- SRUC, West Mains Road, Kings Buildings, Edinburgh, EH9 3JG, UK
| | | | | | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rakesh Kumar Singh
- International Center for Biosaline Agriculture, Academic City, Dubai, United Arab Emirates
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev Kumar Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Alex Whan
- CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - James Cockram
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Richard Mott
- UCL Genetics Institute, Gower Street, London, WC1E 6BT, UK
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15
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Satturu V, Vattikuti JL, J DS, Kumar A, Singh RK, M SP, Zaw H, Jubay ML, Satish L, Rathore A, Mulinti S, Lakshmi VG I, Fiyaz R. A, Chakraborty A, Thirunavukkarasu N. Multiple Genome Wide Association Mapping Models Identify Quantitative Trait Nucleotides for Brown Planthopper ( Nilaparvata lugens) Resistance in MAGIC Indica Population of Rice. Vaccines (Basel) 2020; 8:vaccines8040608. [PMID: 33066559 PMCID: PMC7712083 DOI: 10.3390/vaccines8040608] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023] Open
Abstract
Brown planthopper (BPH), one of the most important pests of the rice (Oryza sativa) crop, becomes catastrophic under severe infestations and causes up to 60% yield loss. The highly disastrous BPH biotype in the Indian sub-continent is Biotype 4, which also known as the South Asian Biotype. Though many resistance genes were mapped until now, the utility of the resistance genes in the breeding programs is limited due to the breakdown of resistance and emergence of new biotypes. Hence, to identify the resistance genes for this economically important pest, we have used a multi-parent advanced generation intercross (MAGIC) panel consisting of 391 lines developed from eight indica founder parents. The panel was phenotyped at the controlled conditions for two consecutive years. A set of 27,041 cured polymorphic single nucleotide polymorphism (SNPs) and across-year phenotypic data were used for the identification of marker–trait associations. Genome-wide association analysis was performed to find out consistent associations by employing four single and two multi-locus models. Sixty-one SNPs were consistently detected by all six models. A set of 190 significant marker-associations identified by fixed and random model circulating probability unification (FarmCPU) were considered for searching resistance candidate genes. The highest number of annotated genes were found in chromosome 6 followed by 5 and 1. Ninety-two annotated genes identified across chromosomes of which 13 genes are associated BPH resistance including NB-ARC (nucleotide binding in APAF-1, R gene products, and CED-4) domain-containing protein, NHL repeat-containing protein, LRR containing protein, and WRKY70. The significant SNPs and resistant lines identified from our study could be used for an accelerated breeding program to develop new BPH resistant cultivars.
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Affiliation(s)
- Vanisri Satturu
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India; (D.S.J.); (I.L.V.)
- Correspondence: ; Tel.: +91-8186945838
| | - Jhansi Lakshmi Vattikuti
- Entomology, Pathology and Plant breeding Division, Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad 500030, India; (J.L.V.); (S.P.M.); (A.F.R.)
| | - Durga Sai J
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India; (D.S.J.); (I.L.V.)
| | - Arvind Kumar
- Plant Breeding Division, International Rice Research Institute (IRRI)-South Asia Hub (SAH), Patancheru, Hyderabad 502324, India;
| | - Rakesh Kumar Singh
- Plant Breeding Division, International Rice Research Institute (IRRI), Metro Manila 1226, Philippines; (R.K.S.); (H.Z.); (M.L.J.)
- Program Leader and Principal Scientist (Plant Breeding), Crop Diversification and Genetics, International Center for Biosaline Agriculture, Academic City, Dubai 14660, UAE
| | - Srinivas Prasad M
- Entomology, Pathology and Plant breeding Division, Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad 500030, India; (J.L.V.); (S.P.M.); (A.F.R.)
| | - Hein Zaw
- Plant Breeding Division, International Rice Research Institute (IRRI), Metro Manila 1226, Philippines; (R.K.S.); (H.Z.); (M.L.J.)
- Department of Agriculture, Plant Biotechnology Center, Shwe Nanthar, Mingalardon Township, Yangon 11021, Myanmar
| | - Mona Liza Jubay
- Plant Breeding Division, International Rice Research Institute (IRRI), Metro Manila 1226, Philippines; (R.K.S.); (H.Z.); (M.L.J.)
| | - Lakkakula Satish
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Abhishek Rathore
- Agriculture Statistics Division, International Crops Research for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502324, India;
| | - Sreedhar Mulinti
- MFPI-Quality Control Lab, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India;
| | - Ishwarya Lakshmi VG
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India; (D.S.J.); (I.L.V.)
| | - Abdul Fiyaz R.
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India; (D.S.J.); (I.L.V.)
| | - Animikha Chakraborty
- Plant Breeding Division, Indian Institute of Millets Research (ICAR-IIMR), Rajendranagar, Hyderabad 500030, India; (A.C.); (N.T.)
| | - Nepolean Thirunavukkarasu
- Plant Breeding Division, Indian Institute of Millets Research (ICAR-IIMR), Rajendranagar, Hyderabad 500030, India; (A.C.); (N.T.)
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16
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Assessment of Genetic Heritability in Rice Breeding Lines Based on Morphological Traits and Caryopsis Ultrastructure. Sci Rep 2020; 10:7830. [PMID: 32385288 PMCID: PMC7210993 DOI: 10.1038/s41598-020-63976-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/03/2020] [Indexed: 11/22/2022] Open
Abstract
Rice (Oryza sativa L) is a most important staple food crop of the world because more than half of the World’s population is dependent on it for their livelihood. Global rice production must be doubled by 2050 to cope up with the situation of population growth. Narrow genetic base in the released varieties has made the improvement in plateaus. Widening the genetic base is necessary to overcome the yield barrier. Hybridization and pre-breeding has been carried out to broaden the genetic base. Heritability and genetic advances were measured in the F5 lines (Tulaipanji × IR64), F3 lines (Tulaipanji × IR64 × PB1460), and F3 lines (Badshabhog × Swarna sub1). Some of the breeding lines were showing promising field performance with high yield potentiality. Wide crosses were performed to widen the genetic base between (Ranjit × O. rufipogon) and (Badshabhog × O. rufipogon) and the heritability pattern of the morphological characteristics in the progeny lines was evaluated. Nutritional quality of the rice grain is totally dependent on the morphology and histological characteristics of the caryopsis which are genetically determined. Caryopses ultrastructural analyses were carried out in seventeen different rice breeding lines through SEM. SEM analysis showed distinguishing ultrastructure in respect to pericarp, testa, aleurone layer, protein bodies and starchy endosperm in the breeding lines with distinctive inheritance pattern. This study provides information about the cross compatibility of the wide hybridization and heritability measures of the morphological traits which may supplement the breeding program to break the yield plateaus.
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17
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Kamboj R, Singh B, Mondal TK, Bisht DS. Current status of genomic resources on wild relatives of rice. BREEDING SCIENCE 2020; 70:135-144. [PMID: 32523396 PMCID: PMC7272243 DOI: 10.1270/jsbbs.19064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/26/2019] [Indexed: 06/02/2023]
Abstract
Rice is a food crop of global importance, cultivated in diverse agro-climatic zones of the world. However, in the process of domestication many beneficial alleles have been eroded from the gene pool of the rice cultivated globally and eventually has made it vulnerable to a plethora of stresses. In contrast, the wild relatives of rice, despite being agronomically inferior, have inherited a potential of surviving in a range of geographical habitats. These adaptations enrich them with novel traits that upon introgression to modern cultivated varieties offer tremendous potential of increasing yield and adaptability. But, due to the unavailability of their genetic as well as genomic resources, identification and characterisation of these novel beneficial alleles has been a challenging task. Nevertheless, with the unprecedented surge in the area of conservation genomics, researchers have now shifted their focus towards these natural repositories of beneficial traits. Presently, there are several generic and specialized databases harboring genome-wide information on wild species of rice, and are acting as a useful resource for identification of novel genes and alleles, designing of molecular markers, comparative analysis and evolutionary biology studies. In this review, we introduce the key features of these databases focusing on their utility in rice breeding programs.
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Affiliation(s)
- Richa Kamboj
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Balwant Singh
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Tapan Kumar Mondal
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Deepak Singh Bisht
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
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18
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Andorf C, Beavis WD, Hufford M, Smith S, Suza WP, Wang K, Woodhouse M, Yu J, Lübberstedt T. Technological advances in maize breeding: past, present and future. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:817-849. [PMID: 30798332 DOI: 10.1007/s00122-019-03306-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 02/05/2019] [Indexed: 05/18/2023]
Abstract
Maize has for many decades been both one of the most important crops worldwide and one of the primary genetic model organisms. More recently, maize breeding has been impacted by rapid technological advances in sequencing and genotyping technology, transformation including genome editing, doubled haploid technology, parallelled by progress in data sciences and the development of novel breeding approaches utilizing genomic information. Herein, we report on past, current and future developments relevant for maize breeding with regard to (1) genome analysis, (2) germplasm diversity characterization and utilization, (3) manipulation of genetic diversity by transformation and genome editing, (4) inbred line development and hybrid seed production, (5) understanding and prediction of hybrid performance, (6) breeding methodology and (7) synthesis of opportunities and challenges for future maize breeding.
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Affiliation(s)
| | - William D Beavis
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Matthew Hufford
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011-1010, USA
| | - Stephen Smith
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Walter P Suza
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | | | - Jianming Yu
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA.
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19
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Nguyen KL, Grondin A, Courtois B, Gantet P. Next-Generation Sequencing Accelerates Crop Gene Discovery. TRENDS IN PLANT SCIENCE 2019; 24:263-274. [PMID: 30573308 DOI: 10.1016/j.tplants.2018.11.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 05/22/2023]
Abstract
The identification and isolation of genes underlying quantitative trait loci (QTLs) associated with agronomic traits in crops have been recently accelerated thanks to next-generation sequencing (NGS)-based technologies combined with plant genetics. With NGS, various revisited genetic approaches, which benefited from higher marker density, have been elaborated. These approaches improved resolution in QTL position and assisted in determining functional causative variations in genes. Examples of QTLs/genes associated with agronomic traits in crops and identified using different strategies based on whole-genome sequencing (WGS)/whole-genome resequencing (WGR) or RNA-seq are presented and discussed in this review. More specifically, we summarize and illustrate how NGS boosted bulk-segregant analysis (BSA), expression profiling, and the construction of polymorphism databases to facilitate the detection of QTLs and causative genes.
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Affiliation(s)
- Khanh Le Nguyen
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France; LMI RICE 2, AGI, Km2 Pham Van Dong, Tu Liem, Hanoi, Vietnam
| | - Alexandre Grondin
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France
| | - Brigitte Courtois
- CIRAD, UMR AGAP, F-34398 Montpellier, France; Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Pascal Gantet
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France; Centre of the Region Haná for Biotechnological and Agricultural Research, Dept. of Molecular Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic.
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20
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Mou S, Gao F, Shen L, Yang S, He W, Cheng W, Wu Y, He S. CaLRR-RLK1, a novel RD receptor-like kinase from Capsicum annuum and transcriptionally activated by CaHDZ27, act as positive regulator in Ralstonia solanacearum resistance. BMC PLANT BIOLOGY 2019; 19:28. [PMID: 30654746 PMCID: PMC6337819 DOI: 10.1186/s12870-018-1609-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/19/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Bacterial wilt caused by Ralstonia solanacearum is one of the most important diseases in pepper worldwide, however, the molecular mechanism underlying pepper resistance to bacterial wilt remains poorly understood. RESULTS Herein, a novel RD leucine-rich repeat receptor-like kinase, CaLRR-RLK1, was functionally characterized in immunity against R. solanacearum. CaLRR-RLK1 was targeted exclusively to plasma membrane and was up-regulated by R. solanacearum inoculation (RSI) as well as by the exogenous application of salicylic acid (SA), methyl jasmonate (MeJA) or ethephon (ETH). The silencing of CaLRR-RLK1 led to enhanced susceptibility of pepper plants to RSI, accompanied by down-regulation of immunity-related genes including CaACO1, CaHIR1, CaPR4 and CaPO2. In contrast, transient overexpression of CaLRR-RLK1 triggered hypersensitive response (HR)-like cell death and H2O2 accumulation in pepper leaves, manifested by darker trypan blue and DAB staining respectively. In addition, the ectopic overexpression of CaLRR-RLK1 in tobacco plants enhanced resistance R. solanacearum, accompanied with the immunity associated marker genes including NtPR2, NtPR2, NtHSR203 and NtHSR515. Furthermore, it was found that CaHDZ27, a positive regulator in pepper response to RSI in our previous study, transcriptionally activated CaLRR-RLK1 by direct targeting its promoter probably in a CAATTATTG dependent manner. CONCLUSION The study revealed that CaLRR-RLK1 confers pepper resistance to R. solanacearum as the direct targeting of CaHDZ27.
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Affiliation(s)
- Shaoliang Mou
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
| | - Feng Gao
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
| | - Lei Shen
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
| | - Sheng Yang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
| | - Weihong He
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
| | - Wei Cheng
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
| | - Yang Wu
- College of Life Science, Jinggangshan University, Ji’an, Jiangxi 343000 People’s Republic of China
| | - Shuilin He
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
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21
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Tyagi S, Mazumdar PA, Mayee P, Shivaraj SM, Anand S, Singh A, Madhurantakam C, Sharma P, Das S, Kumar A, Singh A. Natural variation in Brassica FT homeologs influences multiple agronomic traits including flowering time, silique shape, oil profile, stomatal morphology and plant height in B. juncea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:251-266. [PMID: 30466591 DOI: 10.1016/j.plantsci.2018.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/17/2018] [Accepted: 09/21/2018] [Indexed: 06/09/2023]
Abstract
Natural structural variants of regulatory proteins causing quantitative phenotypic consequences have not been reported in plants. Herein, we show that 28 natural structural variants of FT homeologs, isolated from 6 species of Brassica, differ with respect to amino-acid substitutions in regions critical for interactions with FD and represent two evolutionarily distinct categories. Analysis of structural models of selected candidates from Brassica juncea (BjuFT_AAMF1) and Brassica napus (BnaFT_CCLF) predicted stronger binding between BjuFT and Arabidopsis thaliana FD. Over-expression of BjuFT and BnaFT in wild type and ft-10 mutant backgrounds of Arabidopsis validated higher potency of BjuFT in triggering floral transition. Analysis of gain-of-function and artificial miRNA mediated silenced lines of B. juncea implicated Brassica FT in multiple agronomic traits beyond flowering, consistent with a pleiotropic effect. Several dependent and independent traits such as lateral branching, silique shape, seed size, oil-profile, stomatal morphology and plant height were found altered in mutant lines. Enhanced FT levels caused early flowering, which in turn was positively correlated to a higher proportion of desirable fatty acids (PUFA). However, higher FT levels also resulted in altered silique shape and reduced seed size, suggesting trait trade-offs. Modulation of FT levels for achieving optimal balance of trait values and parsing pair-wise interactions among a reportoire of regulatory protein homeologs in polyploid genomes are indeed future areas of crop research.
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Affiliation(s)
- Shikha Tyagi
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | | | - Pratiksha Mayee
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India; Department of Research, Ankur Seeds Pvt. Ltd., 27, Nagpur, Maharashtra, 440018, India
| | - S M Shivaraj
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India; Departement de Phytologie, Université Laval, Quebec City, Quebec, G1V 0A6, Canada
| | - Saurabh Anand
- Department of Botany, University of Delhi, New Delhi, 110007, India
| | - Anupama Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Chaithanya Madhurantakam
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Prateek Sharma
- Department of Energy and Environment, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Sandip Das
- Department of Botany, University of Delhi, New Delhi, 110007, India
| | - Arun Kumar
- National Phytotron Facility, IARI, New Delhi, 110012, India
| | - Anandita Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India.
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22
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Macovei A, Sevilla NR, Cantos C, Jonson GB, Slamet‐Loedin I, Čermák T, Voytas DF, Choi I, Chadha‐Mohanty P. Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to Rice tungro spherical virus. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1918-1927. [PMID: 29604159 PMCID: PMC6181218 DOI: 10.1111/pbi.12927] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/27/2018] [Accepted: 03/18/2018] [Indexed: 05/03/2023]
Abstract
Rice tungro disease (RTD) is a serious constraint in rice production across tropical Asia. RTD is caused by the interaction between Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. RTSV resistance found in traditional cultivars has contributed to a reduction in the incidence of RTD in the field. Natural RTSV resistance is a recessive trait controlled by the translation initiation factor 4 gamma gene (eIF4G). The Y1059 V1060 V1061 residues of eIF4G are known to be associated with the reactions to RTSV. To develop new sources of resistance to RTD, mutations in eIF4G were generated using the CRISPR/Cas9 system in the RTSV-susceptible variety IR64, widely grown across tropical Asia. The mutation rates ranged from 36.0% to 86.6%, depending on the target site, and the mutations were successfully transmitted to the next generations. Among various mutated eIF4G alleles examined, only those resulting in in-frame mutations in SVLFPNLAGKS residues (mainly NL), adjacent to the YVV residues, conferred resistance. Furthermore, our data suggest that eIF4G is essential for normal development, as alleles resulting in truncated eIF4G could not be maintained in homozygous state. The final products with RTSV resistance and enhanced yield under glasshouse conditions were found to no longer contain the Cas9 sequence. Hence, the RTSV-resistant plants with the novel eIF4G alleles represent a valuable material to develop more diverse RTSV-resistant varieties.
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Affiliation(s)
- Anca Macovei
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
- Present address:
Department of Biology and Biotechnology ‘L. Spallanzani’University of PaviaPaviaItaly
| | - Neah R. Sevilla
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Christian Cantos
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
- Present address:
Huck Institute of the Life SciencesPennsylvania State UniversityUniversity ParkPAUSA
| | - Gilda B. Jonson
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Inez Slamet‐Loedin
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Tomáš Čermák
- Department of GeneticsCell Biology & Development and Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Daniel F. Voytas
- Department of GeneticsCell Biology & Development and Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Il‐Ryong Choi
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Prabhjit Chadha‐Mohanty
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
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Gene diagnosis and targeted breeding for blast-resistant Kongyu 131 without changing regional adaptability. J Genet Genomics 2018; 45:539-547. [PMID: 30391410 DOI: 10.1016/j.jgg.2018.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/17/2018] [Accepted: 08/28/2018] [Indexed: 12/11/2022]
Abstract
The fungus Magnaporthe oryzae threatens the rice production of Kongyu 131 (KY131), a leading japonica variety in Northeast China. In this study, two rice lines, KP1 and KP2-Hd1, were obtained by introgressing the blast resistance genes Pi1 and Pi2 into KY131, respectively. However, both lines headed later than KY131. RICE60K SNP array analysis showed that Hd1 closely linked to Pi2 was introgressed into KP2-Hd1, and the linkage drag of Hd1 was broken by recombination. On the other hand, no known flowering genes were introgressed into KP1. Gene diagnosis by resequencing six flowering genes showed that KP1 carried functional Hd16 and Ghd8 alleles. Due to its suppression role in heading under long-day conditions, Ghd8 was chosen as the target for gene editing to disrupt its function. Four sgRNAs targeting different sites within Ghd8 were utilized to induce large-deletion mutations, which were easy to detect via agarose gel electrophoresis. All the ghd8-mutated KP1 lines were resistant to rice blast disease and headed earlier than the control KP1, even than KY131, under natural long-day conditions, which ensures its growth in Northeast China. This study confirmed that a combination of gene diagnosis and targeted gene editing is a highly efficient way to quickly eliminate undesired traits in a breeding line.
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Stacking of blast resistance orthologue genes in susceptible indica rice line improves resistance against Magnaporthe oryzae. 3 Biotech 2018; 8:37. [PMID: 29291150 DOI: 10.1007/s13205-017-1062-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/21/2017] [Indexed: 02/06/2023] Open
Abstract
The emergence of new strains of Magnaporthe oryzae (M. oryzae) is associated with recurrent failure of resistance response mediated by single resistance (R) gene in rice. Therefore, stacking or combining of multiple R genes could improve the durability of resistance against multiple strains of M. oryzae. To achieve this, in the present study, intragenic stacking of rice blast resistance orthologue genes Pi54 and Pi54rh was performed through co-transformation approach. Both these genes were expressed under the control of independent promoters and blast susceptible indica rice line IET17021 was used for transformation. The highly virulent M. oryzae strain Mo-ei-ger1 that could knock down most of the major single blast R genes including Pi54 and exhibiting 89% virulence spectrum was used for phenotypic analysis. The stacked transgenic IET17021 lines (Pi54 + Pi54rh) have shown complete resistance to Mo-ei-ger1 strain in comparison to non-transgenic lines. These two R gene stacked indica transgenic lines could serves as a novel germplasm for rice blast resistance breeding programmes.
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25
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Advances in Sequencing and Resequencing in Crop Plants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018. [PMID: 29516115 DOI: 10.1007/10_2017_46] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA sequencing technologies have changed the face of biological research over the last 20 years. From reference genomes to population level resequencing studies, these technologies have made significant contributions to our understanding of plant biology and evolution. As the technologies have increased in power, the breadth and complexity of the questions that can be asked has increased. Along with this, the challenges of managing unprecedented quantities of sequence data are mounting. This chapter describes a few aspects of the journey so far and looks forward to what may lie ahead. Graphical Abstract.
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Tang M, Ning Y, Shu X, Dong B, Zhang H, Wu D, Wang H, Wang GL, Zhou B. The Nup98 Homolog APIP12 Targeted by the Effector AvrPiz-t is Involved in Rice Basal Resistance Against Magnaporthe oryzae. RICE (NEW YORK, N.Y.) 2017; 10:5. [PMID: 28205154 PMCID: PMC5311014 DOI: 10.1186/s12284-017-0144-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/10/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND The effector AvrPiz-t of Magnaporthe oryzae has virulence function in rice. However, the mechanism underlying its virulence in host is not fully understood. RESULTS In this study, we analyzed the function of AvrPiz-t interacting protein 12 (APIP12) in rice immunity. APIP12 significantly bound to AvrPiz-t and APIP6 in its middle portion and N-terminus, respectively, in yeast two-hybrid assay. Glutathione S-transferase (GST) pull-down assay further verified the interactions of APIP12 with AvrPiz-t and APIP6. APIP12 encodes a homologue of nucleoporin protein Nup98 without the conserved domain of Phe-Gly repeats and has no orthologue in other plants. Both knockout and knockdown of APIP12 caused enhanced susceptibility of rice plants to virulent isolates of M. oryzae. The expression of some pathogenesis-related (PR) genes was reduced in both knockout and knockdown mutants, suggesting that APIP12 is required for the accumulation of transcripts of PR genes upon the infection. It is worth noting that neither knockout/knockdown nor overexpression of APIP12 attenuates Piz-t resistance. CONCLUSIONS Taken together, our results demonstrate that APIP12 is a virulence target of AvrPiz-t and is involved in the basal resistance against M. oryzae in rice.
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Affiliation(s)
- Mingzhi Tang
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuese Ning
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoli Shu
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Bo Dong
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongyan Zhang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Dianxing Wu
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Hua Wang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guo-Liang Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Plant Pathology, the Ohio State University, Columbus, 43210, USA
| | - Bo Zhou
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
- The Division of Genetics and Biotechnology, International Rice Research Institute, Los Baños, 4031, Philippines.
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Xiao G, Borja FN, Mauleon R, Padilla J, Telebanco-Yanoria MJ, Yang J, Lu G, Dionisio-Sese M, Zhou B. Identification of resistant germplasm containing novel resistance genes at or tightly linked to the Pi2/9 locus conferring broad-spectrum resistance against rice blast. RICE (NEW YORK, N.Y.) 2017; 10:37. [PMID: 28779340 PMCID: PMC5544663 DOI: 10.1186/s12284-017-0176-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/31/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND The rice Pi2/9 locus harbors multiple resistance (R) genes each controlling broad-spectrum resistance against diverse isolates of Magnaporthe oryzae, a fungal pathogen causing devastating blast disease to rice. Identification of more resistance germplasm containing novel R genes at or tightly linked to the Pi2/9 locus would promote breeding of resistance rice cultivars. RESULTS In this study, we aim to identify resistant germplasm containing novel R genes at or tightly linked to the Pi2/9 locus using a molecular marker, designated as Pi2/9-RH (Pi2/9 resistant haplotype), developed from the 5' portion of the Pi2 sequence which was conserved only in the rice lines containing functional Pi2/9 alleles. DNA analysis using Pi2/9-RH identified 24 positive lines in 55 shortlisted landraces which showed resistance to 4 rice blast isolates. Analysis of partial sequences of the full-length cDNAs of Pi2/9 homologues resulted in the clustering of these 24 lines into 5 haplotypes each containing different Pi2/9 homologues which were designated as Pi2/9-A5, -A15, -A42, -A53, and -A54. Interestingly, Pi2/9-A5 and Pi2/9-A54 are identical to Piz-t and Pi2, respectively. To validate the association of other three novel Pi2/9 homologues with the blast resistance, monogenic lines at BC3F3 generation were generated by marker assisted backcrossing (MABC). Resistance assessment of the derived monogenic lines in both the greenhouse and the field hotspot indicated that they all controlled broad-spectrum resistance against rice blast. Moreover, genetic analysis revealed that the blast resistance of these three monogenic lines was co-segregated with Pi2/9-RH, suggesting that the Pi2/9 locus or tightly linked loci could be responsible for the resistance. CONCLUSION The newly developed marker Pi2/9-RH could be used as a potentially diagnostic marker for the quick identification of resistant donors containing functional Pi2/9 alleles or unknown linked R genes. The three new monogenic lines containing the Pi2/9 introgression segment could be used as valuable materials for disease assessment and resistance donors in breeding program.
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Affiliation(s)
- Gui Xiao
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Institute of Biological Sciences, University of the Philippines Los Baños, 4031 Laguna, Philippines
| | - Frances Nikki Borja
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Ramil Mauleon
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Jonas Padilla
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Mary Jeanie Telebanco-Yanoria
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Jianxia Yang
- Fujian Agriculture and Forest University, Fuzhou, 350002 China
| | - Guodong Lu
- Fujian Agriculture and Forest University, Fuzhou, 350002 China
| | - Maribel Dionisio-Sese
- Institute of Biological Sciences, University of the Philippines Los Baños, 4031 Laguna, Philippines
| | - Bo Zhou
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Cameron JN, Han Y, Wang L, Beavis WD. Systematic design for trait introgression projects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1993-2004. [PMID: 28647895 PMCID: PMC5606951 DOI: 10.1007/s00122-017-2938-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/15/2017] [Indexed: 05/18/2023]
Abstract
Using an Operations Research approach, we demonstrate design of optimal trait introgression projects with respect to competing objectives. We demonstrate an innovative approach for designing Trait Introgression (TI) projects based on optimization principles from Operations Research. If the designs of TI projects are based on clear and measurable objectives, they can be translated into mathematical models with decision variables and constraints that can be translated into Pareto optimality plots associated with any arbitrary selection strategy. The Pareto plots can be used to make rational decisions concerning the trade-offs between maximizing the probability of success while minimizing costs and time. The systematic rigor associated with a cost, time and probability of success (CTP) framework is well suited to designing TI projects that require dynamic decision making. The CTP framework also revealed that previously identified 'best' strategies can be improved to be at least twice as effective without increasing time or expenses.
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Affiliation(s)
- John N. Cameron
- Department of Agronomy, Iowa State University, Ames, IA 50010 USA
| | - Ye Han
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, IA 50010 USA
| | - Lizhi Wang
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, IA 50010 USA
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29
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Garrett KA, Andersen KF, Asche F, Bowden RL, Forbes GA, Kulakow PA, Zhou B. Resistance Genes in Global Crop Breeding Networks. PHYTOPATHOLOGY 2017; 107:1268-1278. [PMID: 28742460 DOI: 10.1094/phyto-03-17-0082-fi] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Resistance genes are a major tool for managing crop diseases. The networks of crop breeders who exchange resistance genes and deploy them in varieties help to determine the global landscape of resistance and epidemics, an important system for maintaining food security. These networks function as a complex adaptive system, with associated strengths and vulnerabilities, and implications for policies to support resistance gene deployment strategies. Extensions of epidemic network analysis can be used to evaluate the multilayer agricultural networks that support and influence crop breeding networks. Here, we evaluate the general structure of crop breeding networks for cassava, potato, rice, and wheat. All four are clustered due to phytosanitary and intellectual property regulations, and linked through CGIAR hubs. Cassava networks primarily include public breeding groups, whereas others are more mixed. These systems must adapt to global change in climate and land use, the emergence of new diseases, and disruptive breeding technologies. Research priorities to support policy include how best to maintain both diversity and redundancy in the roles played by individual crop breeding groups (public versus private and global versus local), and how best to manage connectivity to optimize resistance gene deployment while avoiding risks to the useful life of resistance genes. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
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Affiliation(s)
- K A Garrett
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - K F Andersen
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - F Asche
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - R L Bowden
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - G A Forbes
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - P A Kulakow
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - B Zhou
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
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Lv Q, Huang Z, Xu X, Tang L, Liu H, Wang C, Zhou Z, Xin Y, Xing J, Peng Z, Li X, Zheng T, Zhu L. Allelic variation of the rice blast resistance gene Pid3 in cultivated rice worldwide. Sci Rep 2017; 7:10362. [PMID: 28871108 PMCID: PMC5583387 DOI: 10.1038/s41598-017-10617-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 08/11/2017] [Indexed: 11/12/2022] Open
Abstract
In this study, the re-sequencing data from 3,000 rice genomes project (3 K RGP) was used to analyze the allelic variation at the rice blast resistance (R) Pid3 locus. A total of 40 haplotypes were identified based on 71 nucleotide polymorphic sites among 2621 Pid3 homozygous alleles in the 3k genomes. Pid3 alleles in most japonica rice accessions were pseudogenes due to premature stop mutations, while those in most indica rice accessions were identical to the functional haplotype Hap_6, which had a similar resistance spectrum as the previously reported Pid3 gene. By sequencing and CAPS marker analyzing the Pid3 alleles in widespread cultivars in China, we verified that Hap_6 had been widely deployed in indica rice breeding of China. Thus, we suggest that the priority for utilization of the Pid3 locus in rice breeding should be on introducing the functional Pid3 alleles into japonica rice cultivars and the functional alleles of non-Hap_6 haplotypes into indica rice cultivars for increasing genetic diversity.
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Affiliation(s)
- Qiming Lv
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhiyuan Huang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Xiao Xu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Tang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Hai Liu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Chunchao Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhuangzhi Zhou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yeyun Xin
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Junjie Xing
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Zhirong Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Xiaobing Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tianqing Zheng
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Lihuang Zhu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China. .,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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31
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Oliva R, Quibod IL. Immunity and starvation: new opportunities to elevate disease resistance in crops. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:84-91. [PMID: 28505583 DOI: 10.1016/j.pbi.2017.04.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/27/2017] [Accepted: 04/30/2017] [Indexed: 05/18/2023]
Abstract
Plants use multiple mechanisms to defend themselves against invading microbes. Besides using their immune system to surveil and eliminate pathogens, plants actively block the pathogens' access to nutrients as an alternative way to prevent colonization. In this review, we focus on immunity and starvation as major obstacles for pathogens' adaptation. We summarize the key mechanisms employed by pathogens to modulate host immunity and to guarantee sugar uptake. In contrast to genes that deal with the immune system and show high levels of plasticity, pathogen genes involved in sugar acquisition are highly conserved, and may not have adapted to co-evolving interactions with the host. We propose a model to assess the durability of different control strategies based on the ability of pathogens to deal with host immunity or starvation. This analysis opens new opportunities to elevate disease resistance in crops by reducing the likelihood of pathogen adaptation.
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Affiliation(s)
- Ricardo Oliva
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines.
| | - Ian Lorenzo Quibod
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
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32
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Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population. G3-GENES GENOMES GENETICS 2017; 7:1721-1730. [PMID: 28592653 PMCID: PMC5473752 DOI: 10.1534/g3.117.042101] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Multi-parent Advanced Generation Intercross (MAGIC) populations are fast becoming mainstream tools for research and breeding, along with the technology and tools for analysis. This paper demonstrates the analysis of a rice MAGIC population from data filtering to imputation and processing of genetic data to characterizing genomic structure, and finally quantitative trait loci (QTL) mapping. In this study, 1316 S6:8 indica MAGIC (MI) lines and the eight founders were sequenced using Genotyping by Sequencing (GBS). As the GBS approach often includes missing data, the first step was to impute the missing SNPs. The observable number of recombinations in the population was then explored. Based on this case study, a general outline of procedures for a MAGIC analysis workflow is provided, as well as for QTL mapping of agronomic traits and biotic and abiotic stress, using the results from both association and interval mapping approaches. QTL for agronomic traits (yield, flowering time, and plant height), physical (grain length and grain width) and cooking properties (amylose content) of the rice grain, abiotic stress (submergence tolerance), and biotic stress (brown spot disease) were mapped. Through presenting this extensive analysis in the MI population in rice, we highlight important considerations when choosing analytical approaches. The methods and results reported in this paper will provide a guide to future genetic analysis methods applied to multi-parent populations.
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33
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Han Y, Cameron JN, Wang L, Beavis WD. The Predicted Cross Value for Genetic Introgression of Multiple Alleles. Genetics 2017; 205:1409-1423. [PMID: 28122824 PMCID: PMC5378103 DOI: 10.1534/genetics.116.197095] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 01/19/2016] [Indexed: 11/18/2022] Open
Abstract
We consider the plant genetic improvement challenge of introgressing multiple alleles from a homozygous donor to a recipient. First, we frame the project as an algorithmic process that can be mathematically formulated. We then introduce a novel metric for selecting breeding parents that we refer to as the predicted cross value (PCV). Unlike estimated breeding values, which represent predictions of general combining ability, the PCV predicts specific combining ability. The PCV takes estimates of recombination frequencies as an input vector and calculates the probability that a pair of parents will produce a gamete with desirable alleles at all specified loci. We compared the PCV approach with existing estimated-breeding-value approaches in two simulation experiments, in which 7 and 20 desirable alleles were to be introgressed from a donor line into a recipient line. Results suggest that the PCV is more efficient and effective for multi-allelic trait introgression. We also discuss how operations research can be used for other crop genetic improvement projects and suggest several future research directions.
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Affiliation(s)
- Ye Han
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa 50011
| | - John N Cameron
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Lizhi Wang
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa 50011
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Guan H, Ali F, Pan Q. Dissection of Recombination Attributes for Multiple Maize Populations Using a Common SNP Assay. FRONTIERS IN PLANT SCIENCE 2017; 8:2063. [PMID: 29250099 PMCID: PMC5714861 DOI: 10.3389/fpls.2017.02063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 11/17/2017] [Indexed: 05/16/2023]
Abstract
Recombination is a vital characteristic for quantitative trait loci mapping and breeding to enhance the yield potential of maize. However, recombination characteristics in globally used segregating populations have never been evaluated at similar genetic marker densities. This study aimed to divulge the characteristics of recombination events, recombinant chromosomal segments, and recombination frequency for four dissimilar populations. These populations were doubled haploid (DH), recombination inbred line (RIL), intermated B73xMo17 (IBM), and multi-parent advanced generation inter-cross (MAGIC), using the Illumina MaizeSNP50 BeadChip to provide markers. Our results revealed that the average number of recombination events was 16, 41, 72, and 86 per line in DH, RIL, IBM, and MAGIC populations, respectively. Accordingly, the average length of recombinant chromosomal segments was 84.8, 47.3, 29.2, and 20.4 Mb in DH, RIL, IBM, and MAGIC populations, respectively. Furtherly, the recombination frequency varied in different genomic regions and population types [DH (0-12.7 cM/Mb), RIL (0-15.5 cM/Mb), IBM (0-24.1 cM/Mb), MAGIC (0-42.3 cM/Mb)]. Utilizing different sub-sets of lines, the recombination bin number and size were analyzed in each population. Additionally, different sub-sets of markers and lines were employed to estimate the recombination bin number and size via formulas for relationship in these populations. The relationship between recombination events and recombination bin length was also examined. Our results contribute to determining the most suitable number of genetic markers, lines in each population, and population type for successful mapping and breeding.
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Affiliation(s)
- Haiying Guan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- National Engineering Laboratory of Wheat and Maize, Jinan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, China
| | - Farhan Ali
- Cereal Crops Research Institute, Nowshera, Pakistan
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Qingchun Pan,
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Mizobuchi R, Fukuoka S, Tsushima S, Yano M, Sato H. QTLs for Resistance to Major Rice Diseases Exacerbated by Global Warming: Brown Spot, Bacterial Seedling Rot, and Bacterial Grain Rot. RICE (NEW YORK, N.Y.) 2016; 9:23. [PMID: 27178300 PMCID: PMC4870548 DOI: 10.1186/s12284-016-0095-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 05/04/2016] [Indexed: 05/04/2023]
Abstract
In rice (Oryza sativa L.), damage from diseases such as brown spot, caused by Bipolaris oryzae, and bacterial seedling rot and bacterial grain rot, caused by Burkholderia glumae, has increased under global warming because the optimal temperature ranges for growth of these pathogens are relatively high (around 30 °C). Therefore, the need for cultivars carrying genes for resistance to these diseases is increasing to ensure sustainable rice production. In contrast to the situation for other important rice diseases such as blast and bacterial blight, no genes for complete resistance to brown spot, bacterial seedling rot or bacterial grain rot have yet been discovered. Thus, rice breeders have to use partial resistance, which is largely influenced by environmental conditions. Recent progress in molecular genetics and improvement of evaluation methods for disease resistance have facilitated detection of quantitative trait loci (QTLs) associated with resistance. In this review, we summarize the results of worldwide screening for cultivars with resistance to brown spot, bacterial seedling rot and bacterial grain rot and we discuss the identification of QTLs conferring resistance to these diseases in order to provide useful information for rice breeding programs.
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Affiliation(s)
- Ritsuko Mizobuchi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Shuichi Fukuoka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Seiya Tsushima
- National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Ibaraki, 305-8604, Japan
| | - Masahiro Yano
- NARO Institute of Crop Science (NICS), 2-1-18 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Hiroyuki Sato
- National Agriculture and Food Research Organization, Kyushu Okinawa Agricultural Research Center (NARO/KARC), 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan.
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Mansueto L, Fuentes RR, Borja FN, Detras J, Abriol-Santos JM, Chebotarov D, Sanciangco M, Palis K, Copetti D, Poliakov A, Dubchak I, Solovyev V, Wing RA, Hamilton RS, Mauleon R, McNally KL, Alexandrov N. Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic Acids Res 2016; 45:D1075-D1081. [PMID: 27899667 PMCID: PMC5210592 DOI: 10.1093/nar/gkw1135] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/14/2016] [Accepted: 11/04/2016] [Indexed: 11/16/2022] Open
Abstract
We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Web-service calls were implemented to access most data. These features enable seamless querying of SNP-Seek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org.
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Affiliation(s)
- Locedie Mansueto
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Roven Rommel Fuentes
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Frances Nikki Borja
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Jeffery Detras
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | | | - Dmytro Chebotarov
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Millicent Sanciangco
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Kevin Palis
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.,Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85750, USA
| | - Alexandre Poliakov
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Inna Dubchak
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | | | - Rod A Wing
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.,Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85750, USA
| | | | - Ramil Mauleon
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Kenneth L McNally
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Nickolai Alexandrov
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
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37
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Zhang Q, Zheng T, Hoang L, Wang C, Nafisah, Joseph C, Zhang W, Xu J, Li Z. Joint Mapping and Allele Mining of the Rolled Leaf Trait in Rice (Oryza sativa L.). PLoS One 2016; 11:e0158246. [PMID: 27441398 PMCID: PMC4956317 DOI: 10.1371/journal.pone.0158246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/12/2016] [Indexed: 01/01/2023] Open
Abstract
The rolled leaf trait, long considered to be a key component of plant architecture, represents an important target trait for improving plant architecture at the population level. We therefore performed linkage mapping using a set of 262 highly variable RILs from two rice cultivars (Minghui 63 and 02428) with minor differences in leaf rolling index (LRI) in conjunction with GWAS mapping of a random subset of the 1127 germplasms from the 3K Rice Genomes Project (3K Rice). A total of seven main-effect loci were found to underlie the transgressive segregation of progenies from parents with minor differences in LRI. Five of these loci were previously identified and two (qRl7b and qRl9b) are newly reported with additional evidence from GWAS mapping for qRl7b. A total of 18 QTLs were identified by GWAS, including four newly identified QTLs. Six QTLs were confirmed by linkage mapping with the above RIL population, and 83.3% were found to be consistent with previously reported loci based on comparative mapping. We also performed allele mining with representative SNPs and identified the elite germplasms for the improvement of rolled leaf trait. Most favorable alleles at the detected loci were contributed by various 3K Rice germplasms. By a re-scanning of the candidate region with more saturated SNP markers, we dissected the region harboring gRl4-2 into three subregions, in which the average effect on LRI was 3.5% with a range from 2.4 to 4.1% in the third subregion, suggesting the presence of a new locus or loci within this region. The representative SNPs for favorable alleles in the reliable QTLs which were consistently identified in both bi-parental mapping and GWAS, such as qRl4, qRl5, qRl6, qRl7a, and qRl7b will be useful for future molecular breeding programs for ideal plant type in rice.
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Affiliation(s)
- Qiang Zhang
- Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Tianqing Zheng
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Long Hoang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Chunchao Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Nafisah
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Charles Joseph
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Wenzhong Zhang
- Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Shenzhen Institute of Breeding & Innovation, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
- Shenzhen Institute of Breeding & Innovation, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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