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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #323589

Title: Development of genotyping by sequencing (GBS) and array derived SNP markers for stem rust resistance gene Sr42

item GAO, LIANGLIANG - University Of Minnesota
item KIELSMEIRER-COOK, JOSH - University Of Minnesota
item BAJGAIN, PRABIN - University Of Minnesota
item ZHANG, XIAOFEI - University Of Minnesota
item Chao, Shiaoman
item Rouse, Matthew
item ANDERSON, JAMES - University Of Minnesota

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/23/2015
Publication Date: 11/5/2015
Publication URL:
Citation: Gao, L., Kielsmeirer-Cook, J., Bajgain, P., Zhang, X., Chao, S., Rouse, M.N., Anderson, J.A. 2015. Development of genotyping by sequencing (GBS)- and array-derived SNP markers for stem rust resistance gene Sr42. Molecular Breeding. 35:207.

Interpretive Summary: Wheat stem rust is a fungal disease of wheat that decreases yield. 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. In order to find moleular markers associated with resistance to Ug99, two biparental populations of wheat were assessed at the seedling stage to Ug99 at the USDA-ARS Cereal Disease Laboratory. The lines in each population were genotyped by both a custom chip and sequencing to identify single nucleotide polymorphsims (SNPs). Markers were identified that were linked to Ug99 resistance in both populations. The resistance-liniked markers identified were validated on a panel of wheat lines with and without Ug99 resistance. These markers can be utlized in wheat breeding for Ug99 resistant wheat varieties. Ug99 resistant wheat cultivars will protect United States wheat production from yield loss if a Ug99 epidemic were to occur in the United States.

Technical Abstract: The stem rust fungus, particularly race TTKSK (Ug99), poses a serious threat to world wheat production. Gene Sr42 or SrCad (which could be the same gene or an allele of Sr42) is effective against race TTKSK. However, known genetic markers for Sr42 are mostly SSR markers which are generally labor intensive to use. In this study, we mapped a race TTKSK resistance gene derived from PI 595667 at the same locus as Sr42 on chromosome 6DS. Based on position, pedigree and infection type information, we propose that this gene, derived from PI 595667, is SrCad (Sr42). We enriched the genetic map for the Sr42 region using genotyping by sequencing (GBS) and array-derived SNP markers. In total, 21 SNP markers were discovered, spanning a genetic distance of 27.2 cM. Nine of them are derived from GBS and twelve of them are derived from Illumina iSelect 90K SNPs. Ten of the twenty-one SNP markers are closely linked (<2.2cM, or co-segregating) with Sr42. We converted five of the closely linked SNPs into uniplex KASP assays which will better facilitate marker assisted selection. We validated the KASP assay in a doubled haploid wheat population derived from a three way cross between accessions PI 410954, RB07, and Faller that shared an uncharacterized resistance gene mapped at approximately the same locus as PI 595667. The development of closely linked (co-segregating), co-dominant, sequence-based SNP assays will aid marker assisted selection and map-based cloning of Sr42.