Identification of stripe rust resistance loci in U.S. spring wheat cultivars and breeding lines using genome-wide association mapping and Yr gene markers

Authors: LIU, L - Washington State University; WANG, M - Washington State University; ZHANG, Z - Washington State University; See, Deven; Chen, Xianming

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/21/2020
Publication Date: 8/1/2020
Citation: Liu, L., Wang, M.N., Zhang, Z.W., See, D.R., Chen, X. 2020. Identification of stripe rust resistance loci in U.S. spring wheat cultivars and breeding lines using genome-wide association mapping and Yr gene markers. Plant Disease. 104(8):2181-2192. https://doi.org/10.1094/PDIS-11-19-2402-RE.
DOI: https://doi.org/10.1094/PDIS-11-19-2402-RE

Interpretive Summary: Stripe rust poses a major threat to wheat production worldwide, especially the United States. To identify loci for effective stripe rust resistance in U.S. wheat, a genome-wide association study (GWAS) was conducted using a panel of 616 spring wheat varieties and breeding lines. The accessions in this panel were phenotyped for stripe rust response in the greenhouse at seedling stage with five predominant and highly virulent races of the pathogen and in different field environments at adult-plant stage in 2017 and 2018. In total, 2,029 single nucleotide polymorphism (SNP) markers that cover the whole genome were generated with genotyping by multiplexed sequencing (GMS) and used in GWAS. In addition, 23 markers of previously reported resistance genes or quantitative trait loci (QTL) were used to genotype the population. This spring panel was grouped into three sub-populations based on principal component analysis. A total of 37 genes or QTL for resistance to stripe rust were detected including 10 potentially new QTL. The frequencies of the resistance genes or QTL in various nurseries were determined, indicating different intensities of these genes or QTL used in breeding programs of different regions. The resistance loci and the information on their markers, effectiveness, and distributions should be useful for improving stripe rust resistance in wheat varieties.

Technical Abstract: Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a major threat to wheat production worldwide, especially the United States. To identify loci for effective stripe rust resistance in U.S. wheat, a genome-wide association study (GWAS) was conducted using a panel of 616 spring wheat cultivars and breeding lines. The accessions in this panel were phenotyped for stripe rust response in the greenhouse at seedling stage with five predominant and highly virulent races of Pst and in different field environments at adult-plant stage in 2017 and 2018. In total, 2,029 SNP markers that cover the whole genome were generated with genotyping by multiplexed sequencing (GMS) and used in GWAS. In addition, 23 markers of previously reported resistance genes or quantitative trait loci (QTL) were used to genotype the population. This spring panel was grouped into three sub-populations based on principal component (PC) analysis. A total of 37 genes or QTL for resistance to stripe rust were detected including 10 potentially new QTL. The frequencies of the resistance genes or QTL in various nurseries were determined, indicating different intensities of these genes or QTL used in breeding programs of different regions. The resistance loci and the information on their markers, effectiveness, and distributions should be useful for improving stripe rust resistance in wheat cultivars.