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

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 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 from the Illumina iSelect 90K SNP assay. Ten of the twenty-one SNP markers are closely linked (<2.2 cM, or co-segregating) with Sr42. We converted five of the closely linked SNP markers 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), codominant, sequence-based SNP assays will aid marker-assisted selection and map-based cloning of Sr42.