Genome-wide association studies reveal genetic control of nutritional quality, milling traits, and agronomic characteristics in oat (Avena sativa L.).

Marker-trait associations (MTAs) are invaluable to the understanding of biological processes and implementation of marker-assisted selection (MAS) to increase genetic gain in modern breeding programs. In this study, a genome-wide association study (GWAS) was performed to identify MTAs that influence oat nutritional quality, as well as agronomic and milling traits, in advanced breeding spring oat (Avena sativa L.) germplasm from North Dakota State University. High-density sequence-based molecular markers (15,037) were identified in a population of 1,092 unique lines evaluated in 11 field conditions over three years. Linkage disequilibrium analysis confirmed that decay metrics of 5, 11.5, and 2.2 Mb for the A, C, and D sub-genomes, respectively, matched the 1.25 Mb/single nucleotide polymorphism marker density used in this study. We identified 160 MTAs and 44 durable quantitative trait loci (QTL) for nine traits that individually explained 3.7%-43.9% of the variation in the data. Haplotypes assembled from the three most predictive QTL for each trait increased the variation explained to 16%-46%. The haplotype effects are substantial, with their presence resulting in predicted mean percentage increases-greater than 20% for many of the investigated traits. These results confirm that significant MTAs for oat can be identified directly within breeding germplasm using GWAS. These markers are excellent candidates for the implementation of MAS to increase the selection efficiency and genetic gain.