Population Structure and Genomewide Association Analysis of Resistance to Disease and Insensitivity to Ptr Toxins in Canadian Spring Wheat Using 90K SNP Array

Abstract

Leaf rust, yellow (stripe) rust, common bunt, and tan spot are economically significant diseases affecting wheat (Triticum aestivum L.) production in Canada. In this study, we investigated the genetic relationship and population structure of 81 Canadian western spring wheat cultivars released primarily between 1963 and 2011 and identified genomic regions associated with resistance to the above four diseases and insensitivity to three Pyrenophora tritici‐repentis (Ptr) toxins (Ptr ToxA, Ptr ToxB and Ptr ToxC). The cultivars were evaluated for field reaction to the four diseases and for reaction to the three Ptr toxins in a greenhouse and were genotyped with a subset of 19,919 of the wheat 90K single‐nucleotide polymorphic array and 11 gene‐specific markers. There were large genetic differences among pairwise comparisons of cultivars, except six pairs that showed <0.05 genetic distance. The cultivars exhibited clear population structure, generally in agreement with the major western Canada spring wheat classes. Using a threshold of p ≤ 5 × 10−5 and a weighted mixed linear model, we identified 94 markers from seven chromosomes associated with all traits except Ptr ToxC. Two major‐effect genomic regions on chromosomes 5B (71–74 cM) and 1A (52–53 cM) were associated with Ptr ToxA, of which the former coincided with the Tsn1 gene. For Ptr ToxB, we identified two other major‐effect regions on chromosomes 2B and 5B. The genomic regions associated with common bunt mapped on 2B, 4B, and 7A, whereas those associated with leaf rust mapped at two positions on 2B. We were only able to uncover a single marker‐trait association for tan spot on 7B and for yellow rust on 2A.