Genome-wide association mapping of agronomic traits and grain characteristics in spring wheat under conventional and organic management systems

Previous genome-wide association studies in Canadian spring wheat (Triticum aestivum L.) cultivars were based on consensus linkage maps of small population sizes. Here, we used a panel of 192 spring wheat cultivars widely used in western Canada to (a) explore the allelic variation and effects of six known genes and (b) identify genomic regions associated with eight agronomic traits and grain characteristics using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 map. The panel was evaluated for heading, maturity, plant height, lodging, grain yield, grain protein content, test weight, and kernel weight under four conventionally (high N) and three organically (low N) managed environments and genotyped with the wheat 90K single-nucleotide polymorphism (SNP) array of which 23,342 SNPs were polymorphic. Using gene-specific functional markers, the proportion of homozygous genotypes with favorable alleles was low for Fhb1 (7-8%), Rht-D1 (14%), and Rht-B1 (18%); moderate for Lr34/Yr18 (28-39%); and high for Glu-A1 (78%) and Glu-D1 (85%). We identified a total of 172 SNPs located at 94 genomic regions across 19 chromosomes of which 82 regions were associated with a single trait and 12 regions coincided with two to three traits. Twenty-seven of the 94 regions (28%) were common between the conventional and organic managements systems; the remaining were management specific. Two of the identified regions on chromosome 5A (586.5-588.6 Mb) and 5B (575.8 Mb) coincided with the vernalization response Vrn-A1 and Vrn-B1 genes, respectively. The IWGSC RefSeq v2.0 physical positions presented here would serve as the basis for easily comparing independent discovery studies in the future.