Allelic variation and effects of 16 candidate genes on disease resistance in western Canadian spring wheat cultivars

Recently, we mapped genomic regions associated with resistance to wheat diseases and insensitivity to Pyrenophora tritici-repentis (Ptr) toxins using 81 historical and modern Canadian western spring wheat cultivars genotyped with genome-wide single nucleotide polymorphic (SNP) markers. Here, we investigate the frequency and effects of allelic variants of 50 markers associated with 16 candidate genes that regulate resistance to leaf rust (Puccinia triticina), yellow or stripe rust (P. striiformis f. sp. tritici), tan spot (P. tritici-repentis), and Ptr ToxA reaction in a subset of 70 of the 81 spring wheat cultivars. We evaluated the 70 cultivars in the field for all diseases except Ptr ToxA, which was evaluated in a greenhouse. Using Spearman rank correlation, stepwise discriminant analysis, and partial least squares regression, we identified between 4 and 11 markers as best predictors of each phenotypic trait. Overall, 23 of the 50 markers were associated with one or more of the phenotypic traits of which analysis of variance showed significant differences between allelic variants of 19 markers. In most analyses, markers for Lr34/Yr18 and Tsn1 loci were identified consistently as the best predictor of disease resistance and Ptr ToxA sensitivity, respectively. The same alleles from two Lr34/Yr18 diagnostic SNP markers (wMAS000003 and wMAS000004) not only decreased stripe rust scores up to 1.6 (on a 1 to 9 scale), but also increased grain yield up to 196 kg ha^?1 without affecting maturity. Results from this study could aid spring wheat breeders in selecting the best parental combinations and/or marker-assisted selection to integrate disease resistance with early maturity and short stature.