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A large-scale genomic association analysis identifies the candidate causal genes conferring stripe rust resistance under multiple field environments

Creator: Jianhui Wu
Creator: Rui Yu
Creator: Haiying Wang
Creator: Cai'e Zhou
Creator: Huang, S.
Creator: Hanxuan Jiao
Creator: Shizhou Yu
Creator: Xiaojun Nie
Creator: Qilin Wang
Creator: Shengjie Liu
Creator: Song Weining
Creator: Singh, R.P.
Creator: Bhavani, S.
Creator: Zhensheng Kang
Creator: Dejun Han
Creator: Qingdong Zeng
Year: 2021
Language: English
Publisher: Wiley
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose
Type: Article
Place of Publication: Oxford (United Kingdom)
Pages: 177-191
Issue: 1
Volume: 19
DOI: 10.1111/pbi.13452
Keywords: Common Wheat
Keywords: Stripe Rust
Keywords: 660 K SNP Array
Keywords: Genome-Wide Association Study
Keywords: Candidate Region Association Analysis
Keywords: Serine/Threonine Protein Kinase
Keywords: Marker-Assisted Breeding
Description: The incorporation of resistance genes into wheat commercial varieties is the ideal strategy to combat stripe or yellow rust (YR). In a search for novel resistance genes, we performed a large-scale genomic association analysis with high-density 660K single nucleotide polymorphism (SNP) arrays to determine the genetic components of YR resistance in 411 spring wheat lines. Following quality control, 371 972 SNPs were screened, covering over 50% of the high-confidence annotated gene space. Nineteen stable genomic regions harbouring 292 significant SNPs were associated with adult-plant YR resistance across nine environments. Of these, 14 SNPs were localized in the proximity of known loci widely used in breeding. Obvious candidate SNP variants were identified in certain confidence intervals, such as the cloned gene Yr18 and the major locus on chromosome 2BL, despite a large extent of linkage disequilibrium. The number of causal SNP variants was refined using an independent validation panel and consideration of the estimated functional importance of each nucleotide polymorphism. Interestingly, four natural polymorphisms causing amino acid changes in the gene TraesCS2B01G513100 that encodes a serine/threonine protein kinase (STPK) were significantly involved in YR responses. Gene expression and mutation analysis confirmed that STPK played an important role in YR resistance. PCR markers were developed to identify the favourable TraesCS2B01G513100 haplotype for marker-assisted breeding. These results demonstrate that high-resolution SNP-based GWAS enables the rapid identification of putative resistance genes and can be used to improve the efficiency of marker-assisted selection in wheat disease resistance breeding.
Agrovoc: RUSTS
Related Datasets:
ISSN: 1467-7644
Journal: Plant Biotechnology Journal

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  • Wheat
    Wheat - breeding, phytopathology, physiology, quality, biotech

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