Genome-wide association mapping of loci for resistance to stripe rust in North American elite spring wheat germplasm

Authors: GODOY, JAYFRED - Washington State University; RYNEARSON, SHERI - Washington State University; Chen, Xianming; PUMPHREY, MICHAEL - Washington State University

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/22/2017
Publication Date: 2/20/2018
Citation: Godoy, J., Rynearson, S., Chen, X., Pumphrey, M. 2018. Genome-wide association mapping of loci for resistance to stripe rust in North American elite spring wheat germplasm. Phytopathology. 108(2):234-245.

Interpretive Summary: Stripe rust, also known as yellow rust, is a major yield-limiting foliar disease of wheat worldwide. In this study, a genome-wide association study (GWAS) was conducted using a set of 237 elite spring wheat lines from 10 North American breeding programs and genotyped with the Illumina Infinium 90K SNP assay. All-stage resistance was evaluated in seedling stage using stripe rust races PSTv-4 and PSTv-14 in controlled conditions and field evaluations were conducted under natural disease pressure in eight environments across Washington State. High heritability estimates and correlation between infection type (IT) and severity (SEV) data were observed among the wheat genotypes. Population structure coincided with the two (western and eastern US) major geographic locations of the breeding programs. Ten loci for race-specific all-stage resistance were confirmed from previous mapping studies. Three potentially new loci associated with race-specific all-stage resistance were identified on chromosomes 1D, 2A, and 5A. For adult plant resistance (APR), 11 highly significant quantitative trait loci (QTL) were identified, of which three QTL on chromosomes 3A, 5D, and 7A are potentially novel. The effect of pyramiding more resistance alleles reduced both IT and SEV. Most of the resistance alleles associated with APR are present in cultivars from breeding programs in the western US and CIMMYT. The QTL identified in this study can be very useful to enrich the current gene pool and improve the diversity of resistance to stripe rust infection.

Technical Abstract: Stripe rust, also known as yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), is a major yield-limiting foliar disease of wheat (Triticum aestivum L.) worldwide. Varieties with resistance based on one or few race-specific resistance genes are constantly challenged and often defeated by new virulent races in the Pst population. In this study, the genetic variability of elite wheat germplasm from North America was investigated to characterize the genetic basis of effective all-stage and adult plant resistance. A genome-wide association study (GWAS) was conducted using a set of 237 elite spring wheat lines from 10 North American breeding programs and genotyped with the Illumina Infinium 90K SNP assay. All-stage resistance was evaluated in seedling stage using Pst races PSTv-4 and PSTv-14 in controlled conditions and field evaluations were conducted under natural disease pressure in eight environments across Washington State, USA. High heritability estimates and correlation between infection type (IT) and severity (SEV) were observed among the genotypes. Population structure coincided with the two (western and eastern US) major geographic locations of the breeding programs. Ten loci for race-specific all-stage resistance were confirmed from previous mapping studies. Three potentially new loci associated with race-specific all-stage resistance were identified on chromosomes 1D, 2A, and 5A. For adult plant resistance (APR), 11 highly significant quantitative trait loci (QTL) (FDR < 0.01) were identified, of which three QTL on chromosomes 3A, 5D, and 7A are potentially novel. The effect of pyramiding more resistance alleles reduced both IT and SEV. Most of the resistance alleles associated with APR are present in cultivars from breeding programs in the western US and CIMMYT. The QTL identified in this study can be very useful to enrich the current gene pool and improve the diversity of resistance to stripe rust infection.