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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #414798
Research Project: Enhancing Barley and Oat Productivity, Quality, and Stress Resistance

Location: Small Grains and Potato Germplasm Research

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

Author
item BAGWELL, JOHN - University Of Georgia
item MERGOUM, MOHAMED - University Of Georgia
item SUBEDI, MADHAV - University Of Georgia
item Sapkota, Suraj
item GHIMIRE, BIKASH - University Of Georgia
item LOPEZ, BENJAMIN - University Of Georgia
item BUCK, JAMES - University Of Georgia
item BAHRI, BOCHRA - University Of Georgia

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/1/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: Wheat is a major food crop and it supplies about 20% of calories to the human population worldwide. Soft red winter wheat (SRWW) is the largest class of wheat grown in the US southeast region, contributing about 17% of total US wheat production and up to 20% wheat area. Wheat production is impacted by several diseases including leaf and stripe rusts which can cause up to US $5 billion in losses annually worldwide. In this study, we evaluated a set of 266 SRWW lines for resistance to leaf and stripe rusts under field and greenhouse conditions, and employed genome-wide association study (statistical method to identify the association of genotype with phenotype) to discover regions of wheat genome (complete set of DNA) associated with rusts resistance. The findings of this research will be used by plant breeders to more efficiently select rusts resistance SRWW lines, and to speed up the development of SRWW cultivars suited for growing in the US southeast region.

Technical Abstract: 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 US. 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 variation (PV) was detected by at least two of the five GAPIT models (BLINK, CMLM, FarmCPU, GLM, MLM) tested. Nine major QTL included QLrYr-2A.1 linked to SNP 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.