Large, Multi-Year Field Trials Identify Novel Barley Alleles

A genome wide panel of 3,072 SNPs representing the current allelic variation of US barley (Hordeum vulgare L.) breeding programs was genotyped on approximately 3,000 advanced generation lines as part of the US BarleyCAP. The trials were grown over a period of four years in a randomized complete block design replicated in rainfed and irrigated conditions in Bozeman, MT. 778 lines were evaluated each year with equal representation among the participants of the BarleyCAP. The data were used to conduct genome wide association studies in order to elucidate the alleles responsible for variation in six agronomic traits: yield, plant height, heading date, test weight, kernel plumpness, and grain protein content. The data were analyzed by year and environment to increase scope of the study. Mixed linear models were applied to the data using a Q + K approach in order to find single marker associations with the above phenotypic traits. Two programs, TASSEL (Bradbury et al 2001) and GAPIT (Lipka et al 2012) were used with the implementation of FDR p values to identify significant associations. The results of the studies give a comprehensive overview of the salient regions of the barley genome impacting the agronomic performance of this crop. Although a large number of identified associations were previously documented in biparental populations, a majority of those found were novel. These results will be used to construct a 384 SNP chip specific to the Montana production region for further use with genomic selection.