Genome-wide association studies reveal all-stage rust resistance loci in elite durum wheat genotypes

Authors: AOUN, MERIEM - NORTH DAKOTA STATE UNIVERSITY; ROUSE, MATTHEW; KOLMER, JAMES; KUMAR, AJAY - NORTH DAKOTA STATE UNIVERSITY; ELIAS, ELIAS - NORTH DAKOTA STATE UNIVERSITY

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/17/2021
Publication Date: 4/12/2021
Citation: Aoun, M., Rouse, M.N., Kolmer, J.A., Kumar, A., Elias, E.M. 2021. Genome-wide association studies reveal all-stage rust resistance loci in elite durum wheat genotypes. Frontiers in Plant Science. 12. Article e640739. https://doi.org/10.3389/fpls.2021.640739.
DOI: https://doi.org/10.3389/fpls.2021.640739

Interpretive Summary: Wheat leaf rust, wheat stripe rust, and wheat stem rust are major diseases to wheat production globally. Host resistance is the most desirable approach to manage these fungal diseases. Durum wheat is an important market class of wheat in the Upper Mid-West region of the United States. We investigated the phenotypic and genotypic structure of resistance to leaf rust, stem rust, and stripe rust pathogen races at the seedling stage in advanced durum wheat breeding lines and cultivars from the North Dakota State University durum wheat breeding program. Phenotypic evaluation showed that the majority of the durum wheat lines were susceptible to leaf rust pathogen isolates adapted to durum wheat, whereas all the genotypes were resistant to the more common leaf rust pathogen isolates adapted to bread wheat. The majority of lines were resistant to stripe rust and stem rust pathogen races. We also conducted genome-wide association mapping to identify genetic loci associated with resistance to the various isolates. The mapping revealed six leaf rust resistance loci. Two of these loci were identified at the positions of Lr52 and Lr64 genes, whereas the remaining loci are most likely novel. Four loci were identified that were associated with stripe rust response. None of these loci correspond to designated stripe rust resistance genes. For stem rust, a total of 22 loci were identified. Four of these loci were located at the positions of known genes/alleles (Sr7b, Sr8155B1, Sr13a, and Sr13b). The discovery of known and novel rust resistance genes and their linked SNPs will help diversify rust resistance in durum wheat. Molecular markers identified as associated with rust resistance genes in this study will be useful to track resistance genes in breeding programs. These results are useful for protecting U.S. durum wheat from rust disease yield losses.

Technical Abstract: Leaf rust, caused by Puccinia triticina (Pt), stripe rust caused by Puccinia striiformis f. sp. tritici (Pst), and stem rust caused by Puccinia graminis f. sp. tritici (Pgt) are major diseases to wheat production globally. Host resistance is the most suitable approach to manage these fungal pathogens. We investigated the phenotypic and genotypic structure of resistance to leaf rust, stem rust, and stripe rust pathogen races at the seedling stage in a collection of advanced durum wheat breeding lines and cultivars adapted to Upper Mid-West region of the United States. Phenotypic evaluation showed that the majority of the durum wheat genotypes were susceptible to Pt isolates adapted to durum wheat, whereas all the genotypes were resistant to common wheat type-Pt isolate. The majority of genotypes were resistant to stripe rust and stem rust pathogen races. The durum panel genotyped using Illumina iSelect 90 K wheat SNP assay was used for genome-wide association mapping (GWAS). The GWAS revealed 64 marker-trait associations (MTAs) representing six leaf rust resistance loci located on chromosome arms 2AS, 2AL, 5BS, 6AL, and 6BL. Two of these loci were identified at the positions of Lr52 and Lr64 genes, whereas the remaining loci are most likely novel. A total of 46 MTAs corresponding to four loci located on chromosome arms 1BS, 5BL, and 7BL were associated with stripe rust response. None of these loci correspond to designated stripe rust resistance genes. For stem rust, a total of 260 MTAs, representing 22 loci were identified on chromosome arms 1BL, 2BL, 3AL, 3BL, 4AL, 5AL, 5BL, 6AS, 6AL, 6BL, and 7BL. Four of these loci were located at the positions of known genes/alleles (Sr7b, Sr8155B1, Sr13, and Sr13b). The discovery of known and novel rust resistance genes and their linked SNPs will help diversify rust resistance in durum wheat.