Genome-wide association mapping for the identification of stripe rust resistance loci in U.S. hard winter wheat

Authors: SHARMA, RAJAT - Oklahoma State University; WANG, MEINAN - Washington State University; Chen, Xianming; LAKKAKULA, INDIRA PRIYADAR - Oklahoma State University; St Amand, Paul; Bernardo, Amy; Bai, Guihua; Bowden, Robert; CARVER, BRETT - University Of Oklahoma; Boehm Jr, Jeffrey; AOUN, MERIEM - Oklahoma State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/15/2025
Publication Date: 3/10/2025
Citation: Sharma, R., Wang, M., Chen, X., Lakkakula, I.S., St Amand, P.C., Bernardo, A.E., Bai, G., Bowden, R.L., Carver, B.F., Boehm Jr, J.D., Aoun, M. 2025. Genome-wide association mapping for the identification of stripe rust resistance loci in U.S. hard winter wheat. Theoretical and Applied Genetics. 2025(138). Article 67. https://doi.org/10.1007/s00122-025-04858-3.
DOI: https://doi.org/10.1007/s00122-025-04858-3

Interpretive Summary: Stripe rust is a destructive wheat disease. To identify sources of stripe rust resistance, a panel of 459 U.S. contemporary hard winter wheat genotypes were evaluated at the seedling stage against five U.S. races of the pathogen and at the adult plant stage in field environments in Oklahoma, Kansas, and Washington. The results showed that 7-14% of the genotypes were resistant to the races at the seedling stage, while 32-78% of genotypes were resistant at the adult plant stage across field environments, indicating the presence of adult plant resistance. Sixteen genotypes had a broad spectrum of resistance to all five races and across field environments. This panel was genotyped using multiplex restriction amplicon sequencing (MRA-Seq) and DNA markers linked to nine known stripe rust resistance genes. The genome-wide association study (GWAS) identified 113 SNP markers associated with stripe rust response, representing 112 loci including 40 novel loci. Markers linked to resistance genes Yr15 and Yr17 were also among significant GWAS associations. Based on diagnostic DNA markers, Yr5, Yr15, Yr17, Yr18, Yr29, and QYr.tamu-2B are present in this germplasm. The identified genes and their markers are useful for further breeding wheat varieties with adequate and durable resistance to stripe rust.

Technical Abstract: Stripe rust is a destructive wheat disease, caused by Puccinia striiformis f. sp. tritici (Pst). To identify sources of stripe rust resistance, a panel of 459 U.S. contemporary hard winter wheat genotypes were evaluated at the seedling stage against five U.S. Pst races and at the adult plant stage in field environments in Oklahoma, Kansas, and Washington. The results showed that 7-14% of the genotypes were resistant to Pst races at the seedling stage, while 32-78% of genotypes were resistant at the adult plant stage across field environments, indicating the presence of adult plant resistance. Sixteen genotypes had a broad spectrum of resistance to all five Pst races and across field environments. This panel was genotyped using multiplex restriction amplicon sequencing (MRA-Seq) and DNA markers linked to the known stripe rust resistance (Yr) genes Yr5, Yr15, Yr17, Yr18, Yr29, Yr36, Yr40, Yr46, and QYr.tamu-2B. A total of 9,858 single nucleotide polymorphism (SNP) markers generated from MRA-Seq, DNA markers linked to known Yr genes, and the phenotypic data were used for genome-wide association studies (GWAS). The GWAS identified 113 SNPs associated with stripe rust response, representing 112 loci. Markers linked to Yr15 and Yr17 were also among significant GWAS associations. Based on diagnostic DNA markers, the Yr genes Yr5, Yr15, Yr17, Yr18, Yr29, and QYr.tamu-2B are present in this germplasm. A total of 40 SNPs were located within genomic regions not known to carry characterized Yr genes/loci, thus likely associated with 40 novel stripe rust resistance loci.