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Malting quality comprises one of the most economically relevant set of traits in barley ( L.). It is a complex phenotype, expensive and difficult to measure, that would benefit from a marker-assisted selection strategy. Malting quality is a target of the U.S. Barley Coordinated Agricultural Project (CAP) and development of winter habit malting barley varieties is a key objective of the U.S. barley research community. The objective of this work was to detect quantitative trait loci (QTL) for malting quality traits in a winter breeding program that is a component of the U.S. Barley CAP. We studied the association between five malting quality traits and 3072 single nucleotide polymorphisms (SNPs) from the barley oligonucleotide pool assay (BOPA) 1 and 2, assayed in advanced inbred lines from the Oregon State University (OSU) breeding program from three germplasm arrays (CAP I, CAP II, and CAP III). After comparing 16 models we selected a structured association model with posterior probabilities inferred from software STRUCTURE (QK) approach to use on all germplasm arrays. Most of the marker-trait associations are germplasm- and environment-specific and close to previously mapped genes and QTL relevant for malt and beer quality. We found alleles fixed by random genetic drift, novel unmasked alleles, and genetic-background interaction. In a relatively small population size study we provide strong evidence for detecting true QTL.

Winterhardiness is a complex trait that involves low temperature tolerance (LTT), vernalization sensitivity, and photoperiod sensitivity. Quantitative trait loci (QTL) for these traits were first identified using biparental mapping populations; candidate genes for all loci have since been identified and characterized. In this research we used a set of 148 accessions consisting of advanced breeding lines from the Oregon barley ( L. subsp ) breeding program and selected cultivars that were extensively phenotyped and genotyped with single nucleotide polymorphisms. Using these data for genome-wide association mapping we detected the same QTL and genes that have been systematically characterized using biparental populations over nearly two decades of intensive research. In this sample of germplasm, maximum LTT can be achieved with facultative growth habit, which can be predicted using a three-locus haplotype involving , , and . The and LTT QTL explained 25% of the phenotypic variation, offering the prospect that additional gains from selection can be achieved once favorable alleles are fixed at these loci.