Identification of malting quality QTLs in advanced generation breeding germplasm

Malting quality has been one of the primary foci in barley (Hordeum vulgare L.) breeding programs but has been difficult for breeders to manipulate due to the quantitative nature of the traits involved and the cost of trait measurement. To assist in breeding for malt quality traits, identifying the genomic regions that affect these traits is essential. Two populations were used to conduct genome-wide association studies in order to elucidate the alleles responsible for variation in malting traits. The first population, composed of 367 lines genotyped with 3,072 single-nucleotide polymorphism (SNP) markers, was a representative sample of the entire germplasm of the Montana State University barley breeding program, including feed, food, and malt lines. The second population, with 650 lines genotyped with 384 SNPs, consisted of 11 biparental families whose parents were cultivars and elite experimental lines developed strictly for malting purposes. Lines were phenotyped at the United States Department of Agriculture-Agricultural Research Service Cereal Crops Research Unit in Madison, WI. Mixed linear models were applied to the data using a Q+K approach in order to identify single marker-trait associations accounting for population structure and relatedness among lines. Fifty-four significant marker-trait associations were found. The results of this work give a comprehensive overview of the salient regions of the barley genome affecting malting traits that vary within a modern malting barley breeding program.