Genome-wide association study and gene specific markers identified 51 genes or QTL for resistance to stripe rust in U.S. winter wheat cultivars and breeding lines

Authors: MU, JINGMEI - Washington State University; LIU, LU - Washington State University; LIU, YAN - Washington State University; WANG, M - Washington State University; See, Deven; HAN, DEJUN - Northwest A&f University; Chen, Xianming

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/17/2020
Publication Date: 7/3/2020
Citation: Mu, J., Liu, L., Liu, Y., Wang, M.N., See, D.R., Han, D., Chen, X. 2020. Genome-wide association study and gene specific markers identified 51 genes or QTL for resistance to stripe rust in U.S. winter wheat cultivars and breeding lines. Frontiers in Plant Science. 11:998. https://doi.org/10.3389/fpls.2020.00998.
DOI: https://doi.org/10.3389/fpls.2020.00998

Interpretive Summary: Stripe rust is a destructive disease of wheat worldwide, especially in the United States. Growing resistant cultivars is the most effective, economical, and environmentally friendly approach to control the disease. To determine stripe rust resistance genes in U.S. winter wheat cultivars and breeding lines, we analyzed a winter wheat panel of 857 cultivars and breeding lines in a genome-wide association study (GWAS) using genotyping by multiplexed sequencing (GMS) and by genotyping with molecular markers of 18 important stripe rust resistance genes. The accessions were phenotyped for stripe rust response at adult-plant stage under natural infection in Pullman and Mount Vernon, Washington in 2018 and 2019, and in the seedling stage with six predominant or most virulent races of the pathogen. The GMS-GWAS analysis identified 36 loci on 15 chromosomes significantly associated with stripe rust resistance, including 16 loci for race-specific all-stage resistance identified only in the seedling tests and 20 loci only in the field tests. Among these 36 loci, at least four genes are new. Of the 18 previously reported genes tested with markers, 16 were present in this winter wheat panel at various frequencies in different nurseries from different regions. This study provides useful information on stripe rust resistance genes in U.S. winter wheat cultivars and breeding lines. The identified genes/QTL and their markers are useful in breeding programs to improve the overall level and durability of resistance to stripe rust.

Technical Abstract: Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a destructive disease of wheat worldwide, especially in the United States. Growing resistant cultivars is the most effective, economical, and environmentally friendly approach to control the disease. To determine stripe rust resistance genes in U.S. winter wheat cultivars and breeding lines, we analyzed a winter wheat panel of 857 cultivars and breeding lines in a genome-wide association study (GWAS) using genotyping by multiplexed sequencing (GMS) and by genotyping with molecular markers of 18 important stripe rust resistance genes or quantitative trait loci (QTL). The accessions were phenotyped for stripe rust response at adult-plant stage under natural infection in Pullman and Mount Vernon, Washington in 2018 and 2019, and in the seedling stage with six predominant or most virulent races of Pst. The GMS-GWAS analysis identified 36 loci on 15 chromosomes (1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 5A, 5B, 5D, 6A, 6B, 7A, and 7B) significantly associated with stripe rust resistance, including 16 loci for race-specific all-stage resistance identified only in the seedling tests and 20 loci only in the field tests. Among these 36 loci, at least four of them were new based on comparison with previously reported genes or QTL for stripe rust resistance. Of the 18 previously reported genes/QTL tested with markers, 16 were present in this winter wheat panel at various frequencies in different nurseries from different regions. This study provides useful information on stripe rust resistance genes in U.S. winter wheat cultivars and breeding lines. The identified genes/QTL and their markers are useful in breeding programs to improve the overall level and durability of resistance to stripe rust.