Identification of mixed linkage beta-glucan quantitative trait loci and evaluation of AsCslF6 homoeologs in hexaploid oat

Hexaploid oat (Avena sativa L.) is a commercially important cereal crop due in part to (1-3,1-4)-beta-D-glucan (beta-glucan), a hemicellulose important to human health. Cellulose synthase-like (Csl) genes have been shown to contribute to beta-glucan production, with CslF6 likely being of major importance. Here, we report a genome-wide association study (GWAS) to identify quantitative trait loci (QTLs) controlling beta-glucan production in oat. Three panels of elite accessions (Spring, Winter, and World Diversity) of oat were grown in multiple North American locations and genotyped using the Oat 6K Custom Infinium iSelect BeadChip. Independent GWAS were performed on each set of accessions and locations, with a meta-analysis identifying 58 significantly associated markers. Synteny with the barley (Hordeum vulgare L.) genome identified four major regions of interest revealing the CslF and CslH gene families along with UGPase and AGPase as candidate genes. Subgenome-specific expression of the A, C, and D AsCslF6 homoeologs revealed that AsCslF6_C is the least expressed in all tissue types and time points, with low-beta-glucan varieties recording the highest proportion of AsCslF6_C expression. Linkage mapping of the homoeologs placed AsCslF6_D on consensus linkage group Mrg02 overlapping with QTL 2.2 and AsCslF6_A on Mrg12 flanked by markers associated with QTL 12.2. Many QTLs identified in this study were homoeologous, representing different gene copies duplicated in ancestral genomes, suggesting that multiple homoeologous copies of beta-glucan biosynthesis genes are contributing to the overall phenotype.