Genetic structure and genome-wide association study of a genomic panel of two-row, spring barley (Hordeum vulgare L.) with differential reaction to Fusarium head blight (Fusarium graminearum Schwabe) and deoxynivalenol production

Abstract Fusarium head blight (FHB), primarily incited by Fusarium graminearum Schwabe, is the most devastating disease of barley (Hordeum vulgare L.) in Canada. Contaminated grains are unsuitable for use as livestock feed or by the malting industry, primarily due to contamination by mycotoxins such as deoxynivalenol (DON). Reducing DON content has been a long-term goal of barley breeders; however, the complex genetics of resistance and laborious testing required have made it difficult to develop resistant cultivars. An Illumina 50 K SNP beadchip was used to genotype a diverse collection (n = 400) of two-row barley genotypes, selected primarily from North American-breeding programs. This genomic panel was phenotyped in three environments in Manitoba, Canada, over two growing seasons. Genotypes were evaluated for heading date, height, FHB score, and DON content. A genome-wide association study (GWAS) was carried out using a mixed linear model (MLM: Q + K) accounting for population structure (Q) and kinship (K) as covariates. This study characterized the population structure of two-row barley germplasm important to North American-breeding programs. Significant marker-trait associations were identified on all chromosomes for FHB, and on all chromosomesexcept 1 H and 6 H for DON content. Individual marker effects were small, explaining only up to 5% of the phenotypic variation. Genes within genomic regions that were associated with FHB-related traits displayed multiple functions linked with disease resistance. While numerous minor, marker-trait associations were identified, phenotypic evaluations are still the best predictors of these traits, despite their time-consuming nature and dependenceon environmental conditions.