Open AccessA large‐scale genomic association analysis identifies the candidate causal genes conferring stripe rust resistance under multiple field environments
Author(s) -
Wu Jianhui,
Yu Rui,
Wang Haiying,
Zhou Cai'e,
Huang Shuo,
Jiao Hanxuan,
Yu Shizhou,
Nie Xiaojun,
Wang Qilin,
Liu Shengjie,
Weining Song,
Singh Ravi Prakash,
Bhavani Sridhar,
Kang Zhensheng,
Han Dejun,
Zeng Qingdong
Publication year - 2021
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.13452
Subject(s) - biology , single nucleotide polymorphism , genetics , linkage disequilibrium , snp , candidate gene , locus (genetics) , haplotype , gene , snp array , quantitative trait locus , marker assisted selection , genetic association , tag snp , genome wide association study , association mapping , allele , genotype
Summary 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.