Genomic Regions Associated with Malt Quality Traits in Barley

Malting quality in barley is defined by a suite of traits that are expensive to measure. Enhanced knowledge of the genetic architecture of these traits in breeding germplasm would inform marker-based breeding efforts to improve quality.  We developed a panel of 479 6-rowed breeding lines from the University of Minnesota that were evaluated in 2-3 locations from 2006-2010 to conduct association mapping (AM) for malting quality. All lines were genotyped with 3,072 SNP markers which were filtered for maximum missing data of 20%. Nine check cultivars were consistently planted in all trials and a mixed model methodology was used to obtain best linear unbiased estimates (BLUEs) of each trait for all lines in the AM panel. Maximum likelihood estimation of marker effects was obtained via a likelihood ratio test of significance implemented by Efficient Mixed Model Association (EMMA) R package. A total of 2,115 SNP markers served as the genotypic matrix, of which 1,977 SNPs were mapped providing genetic linkage coverage of 1090 cM. SNP markers with a LOD > 6 identified QTL for β-glucan on Chr. 1H (LOD > 7.8) and 4H (LOD > 6.3); α-amylase on Chr. 5H (LOD > 10) and Chr. 6H (LOD > 12); diastatic power on Chr. 7H (LOD > 6.6); and kernel plumpness and malt extract on Chr. 7H (LOD > 21). The larger effect QTL will be suitable targets for marker assisted selection.