The use of oats for human consumption is increasing every day due to the health benefits of oat products. With the objective to study relationships among factors affecting oat grain quality, two Recombinant Inbred Lines (RIL) mapping populations (`ND030299' x `ND991151' and `ND030299' x `Souris') have been used in this study. The two populations with their parents and three check cultivars were evaluated in a square lattice design in 2008 and 2009 at two North Dakota locations. Data were recorded on the following agronomic traits: grain yield, test weight, 1000 kernel weight, thin kernels, heading date, and plant height. Chemical and grain physical analysis were performed for â-glucan, oil, and groat percentage. A total of 4975 SNP markers were assessed on the two populations using a 32-bead chip platform developed by Illumina. QTLs for agronomic and grain physical traits were mapped and characterized in the two populations using Windows QTL Cartographer. Grain yield was positively correlated with test weight, thin kernels, plant height, â-glucan content, and associated negatively with 1000 kernel weight. Thirty linkage groups using 1168 polymorphic markers were formed for population 05021, whereas population 05026 comprised 33 linkage groups using 1024 polymorphic markers. The 30 linkage groups of population 05021 contained from 3 to 62 markers, and varied in size from 15.8 to 225.3 cM for a total map size of 2601.7 cM. The 33 linkage groups of population 05026 comprised from 2 to 42 markers, and varied in size from 2.3 to 143.2 cM for a total map size of 1174.2 cM. Nineteen genomic regions on 14 linkage groups were significantly associated with agronomic and grain chemical traits in the population 05021. Fourteen genomic regions on 12 linkage groups were identified for agronomic traits in the population 05026. The same genomic region on LG 05021-16 was associated with thin kernels, test weight, 1000 kernel weight, and oil content. LG 05026-19 loci, from position 23.7 to 47 cM, had strong effects on heading date, plant height, and grain yield. The QTLs consistently detected across environments and between the two populations could serve as starting points for marker-assisted selection.