Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis

Shivreet Kaur; Harsimardeep S Gill; Matthew Breiland; James A Kolmer; Rajeev Gupta; Sunish K Sehgal; Upinder Gill

doi:10.3389/fpls.2023.1090163

Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis

Front Plant Sci. 2023 Feb 1:14:1090163. doi: 10.3389/fpls.2023.1090163. eCollection 2023.

Authors

Shivreet Kaur¹, Harsimardeep S Gill², Matthew Breiland¹, James A Kolmer³, Rajeev Gupta⁴, Sunish K Sehgal², Upinder Gill¹

Affiliations

¹ Department of Plant Pathology, North Dakota State University, Fargo, ND, United States.
² Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States.
³ Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN, United States.
⁴ Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Fargo, ND, United States.

Abstract

Leaf rust, caused by Puccinia triticina (Pt) is among the most devastating diseases posing a significant threat to global wheat production. The continuously evolving virulent Pt races in North America calls for exploring new sources of leaf rust resistance. A diversity panel of 365 bread wheat accessions selected from a worldwide population of landraces and cultivars was evaluated at the seedling stage against four Pt races (TDBJQ, TBBGS, MNPSD and, TNBJS). A wide distribution of seedling responses against the four Pt races was observed. Majority of the genotypes displayed a susceptible response with only 28 (9.8%), 59 (13.5%), 45 (12.5%), and 29 (8.1%) wheat accessions exhibiting a highly resistant response to TDBJQ, TBBGS, MNPSD and, TNBJS, respectively. Further, we conducted a high-resolution multi-locus genome-wide association study (GWAS) using a set of 302,524 high-quality single nucleotide polymorphisms (SNPs). The GWAS analysis identified 27 marker-trait associations (MTAs) for leaf rust resistance on different wheat chromosomes of which 20 MTAs were found in the vicinity of known Lr genes, MTAs, or quantitative traits loci (QTLs) identified in previous studies. The remaining seven significant MTAs identified represent genomic regions that harbor potentially novel genes for leaf rust resistance. Furthermore, the candidate gene analysis for the significant MTAs identified various genes of interest that may be involved in disease resistance. The identified resistant lines and SNPs linked to the QTLs in this study will serve as valuable resources in wheat rust resistance breeding programs.

Keywords: GWAS - genome-wide association study; Puccinia triticana; QTL; SNP; leaf rust; marker assisted selection (MAS); seedling resistance; wheat.

Grants and funding

This project was collectively supported by the USDA National Institute of Food and Agriculture, Hatch project number ND02243, North Dakota Wheat Commission, and the USDA Agriculture and Food Research Initiative Competitive Grants 2022-68013-36439 (Wheat-CAP) from the USDA National Institute of Food and Agriculture. The funders had no role in the study design, data collection, analysis, decision to publish, or manuscript preparation.