Discovering leaf and stripe rust resistance in soft red winter wheat through genome-wide association studies

Leaf rust (LR) and stripe rust (YR), which are caused by Puccinia triticina and Puccinia striiformis, respectively, are among the most devastating wheat rusts worldwide. These diseases can be managed by using genetically resistant cultivars, an economical and environmentally safer alternative to fungicides. Over 100 and 80 Lr and Yr resistance genes have been discovered, respectively; however, rust pathogens are overcoming introduced resistance genes in the southeastern United States. Genome-wide association study has emerged as a valuable tool to identify new LR and YR resistance loci. In this study, a panel of 263 soft red winter wheat genotypes was evaluated for LR and YR severity in Plains, GA, and Williamson, GA, in a randomized complete block design of two replicates during 2019 and 2021-2023. Also, LR and YR infection types were assessed on seedlings at the three leaf stage in three greenhouse trials. A total of 26 significant quantitative trait loci (QTL) explaining 0.6%-30.8% phenotypic variance (PV) was detected by at least two of the five GAPIT models (BLINK, CMLM, FarmCPU, GLM, and MLM) tested. Nine major QTL included QLrYr-2A.1 linked to single-nucleotide polymorphism S2A_20855466, which had the highest overall PV (30.8%) for response to both rust pathogens in the field. Using the Chinese Spring Reference Genome Version 1.0, we detected 16 candidate genes, and four known R genes and QTL overlapped two major QTL. Of these QTL, 16 are likely novel genetic loci with potential for marker-assisted selection.