Identification of 39 stripe rust resistance loci in a panel of 465 winter wheat entries presumabed to have high-temperature adult-plant resistance through genome-wide association mapping and marker-assisted detection

Authors: YAO, FANGJIE - Sichuan Academy Of Agricultural Science; WANG, MEINAN - Washington State University; See, Deven; YANG, ENNIAN - Sichuan Academy Of Agricultural Science; GUOYUE, CHEN - Sichuan University; Chen, Xianming

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/27/2024
Publication Date: 1/7/2025
Citation: Yao, F., Wang, M., See, D.R., Yang, E., Guoyue, C., Chen, X. 2025. Identification of 39 stripe rust resistance loci in a panel of 465 winter wheat entries presumabed to have high-temperature adult-plant resistance through genome-wide association mapping and marker-assisted detection. Frontiers in Plant Science. 15. Article 1514926. https://doi.org/10.3389/fpls.2024.1514926.
DOI: https://doi.org/10.3389/fpls.2024.1514926

Interpretive Summary: Stripe rust of wheat is a serious disease, and growing resistant varieties is the preferable strategy to control the disease. To identify wheat germplasms with quantitative trait loci (QTL) for stable resistance to stripe rust, 465 winter wheat entries presumably to have high-temperature adult-plant (HTAP) resistance based on previous tests were used in this study. In the greenhouse seedling tests with seven US races of the pathogen, 16 entries were found resistant to all races. The 465 entries were also tested at the adult-plant stage under natural infection of the stripe rust pathogen in multiple field environments in Washington state, and 345 accessions were found to have stable resistance. The 465 entries were genotyped through genotyping by multiplexed sequencing (GMS) of single-nucleotide polymorphism (SNP) markers. Combining the stripe rust response and SNP marker data, a genome-wide association study (GWAS) was conducted. The GWAS resulted in 143 marker-trait associations, and from which 28 QTL that were detected at least with two races or in two field environments were identified, including 7 for all-stage resistance (ASR) and 21 for HTAP resistance. These stable QTL explained 6.0% to 40.0% of the phenotypic variation. Compared with previously reported stripe rust resistance genes and QTL by the genetic or physical positions, two QTL for HTAP resistance were identified novel. Ten Kompetitive allele specific (KASP) PCR markers were developed for eight of HTAP resistance loci. In addition, molecular markers were used to detect 13 previously reported HTAP resistance genes/QTL including two detected in the GWAS analyses, and their frequencies ranged from 0.86% to 88.17%. The stable resistant germplasms, the genes/QTL identified, and the KASP markers developed in this study can be used for developing wheat varieties with durable resistance to stripe rust.

Technical Abstract: Stripe rust of wheat is a serious disease caused by Puccinia striiformis f. sp. tritici (Pst), and growing resistant cultivars is the preferable strategy to control the disease. To identify wheat germplasms with quantitative trait loci (QTL) for stable resistance to stripe rust, 465 winter wheat entries presumably to have high-temperature adult-plant (HTAP) resistance based on previous tests were used in this study. In the greenhouse seedling tests with seven US Pst races, 16 entries were found resistant to all races. The 465 entries were also tested at the adult-plant stage under natural infection of Pst in multiple field environments in Washington state, and 345 accessions were found to have stable resistance. The 465 entries were genotyped through genotyping by multiplexed sequencing (GMS) of single-nucleotide polymorphism (SNP) markers. Combining the stripe rust response and SNP marker data, a genome-wide association study (GWAS) was conducted. The GWAS resulted in 143 marker-trait associations, and from which 28 QTL that were detected at least with two races or in two field environments were identified, including 7 for all-stage resistance (ASR) and 21 for HTAP resistance. These stable QTL explained 6.0% to 40.0% of the phenotypic variation. Compared with previously reported Yr genes and QTL by the genetic or physical positions, two QTL for HTAP resistance were identified novel. Ten Kompetitive allele specific (KASP) PCR markers were developed for eight of HTAP resistance loci. In addition, molecular markers were used to detect 13 previously reported HTAP resistance genes/QTL including two detected in the GWAS analyses, and their frequencies ranged from 0.86% to 88.17%. The stable resistant germplasms, the genes/QTL identified, and the KASP markers developed in this study can be useful for developing wheat cultivars with durable resistance to stripe rust.