Multi-locus mixed model analysis of stem rust resistance in a worldwide collection of winter wheat

Authors: MIHALYOV, PAUL - WASHINGTON STATE UNIVERSITY; NICHOLS, VIRGINIA - WASHINGTON STATE UNIVERSITY; BULLI, PETER - WASHINGTON STATE UNIVERSITY; ROUSE, MATTHEW; PUMPHREY, MICHAEL - WASHINGTON STATE UNIVERSITY

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/18/2017
Publication Date: 6/27/2017
Citation: Mihalyov, P.D., Nichols, V.A., Bulli, P., Rouse, M.N., Pumphrey, M.O. 2017. Multi-locus mixed model analysis of stem rust resistance in a worldwide collection of winter wheat. The Plant Genome. 10(2):1-12.

Interpretive Summary: Wheat stem rust is a devastating fungal disease of wheat. A strain of the wheat stem rust fungus known as Ug99 emerged in Uganda in 1999 and threatens global wheat production because it is able to infect nearly all wheat varieties. We assessed 1411 winter wheat lines for response to stem rust pathogen strains including Ug99. In addition, 5390 molecular markers were evaluated on the lines. Genome-wide association mapping identified 11 high-confidence significant associations between the markers and resistance to stem rust. The 11 regions include previously characterized resistance genes and at least four new resistance genes. The resistance genes and associated markers that we identified could be used by wheat breeding programs to select for Ug99 resistance to develop resistant wheat varieties that would protect United States wheat production from yield losses caused by foreign and domestic strains of the stem rust pathogen.

Technical Abstract: Genome-wide association mapping is a powerful tool for dissecting the relationship between phenotypes and genetic variants in diverse populations. With improved cost efficiency of high-throughput genotyping platforms, association mapping is a desirable method to mine populations for favorable alleles that hold value for crop improvement. Stem rust, caused by the fungus Puccinia graminis f. sp. tritici, is a devastating disease that threatens wheat (Triticum aestivum L.) production worldwide. Here, we explored the genetic basis of stem rust resistance in a global collection of 1,411 hexaploid winter wheat accessions genotyped with 5,390 SNP markers. To facilitate the development of resistant varieties, we characterized marker-trait associations underlying field resistance to North American races and seedling resistance to the races TTKSK (Ug99), TRTTF, TTTTF, and BCCBC. After evaluating several commonly used linear models, a multi-locus mixed model provided maximum statistical power and improved identification of loci with direct breeding application. At least 11 high-confidence resistance loci were identified, including SNP markers linked to Sr8a, Sr9h, Sr28, and Sr31, and at least four newly discovered resistance loci that are strong candidates for introgression into modern cultivars. Additionally, we report the first known iSelect 9K wheat SNP marker (IWA435) that can be used to reliably detect the 1BL.1RS rye translocation in diverse germplasm. In the present study, we assessed the power of multi-locus association mapping while providing an in-depth analysis for its practical ability to assist breeders with the introgression of rare alleles into elite varieties.