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

Plant Biotechnology Journal
Jianhui WuQingdong Zeng

Abstract

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...Continue Reading

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Citations

Mar 9, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Shengjie LiuDejun Han
Jan 21, 2021·Journal of Experimental Botany·Li TaiKun-Ming Chen
Jun 3, 2021·International Journal of Molecular Sciences·Antonia MoresDaniela Marone
Jun 3, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Yunlong PangShubing Liu

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Methods Mentioned

BETA
PCA
PCR
transgenic
genotyping
exome capture

Software Mentioned

BLAST
GEMMA
HAPLOVIEW
AgRenSeq
R
DNAMAN
CIMMYT
CC
Hmisc
lme4

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