Association Mapping of Malting Quality Quantitative Trait Loci in Winter Barley: Positive Signals from Small Germplasm Arrays

Abstract

Malting quality comprises one of the most economically relevant set of traits in barley (Hordeum vulgare L.). It is a complex phenotype, expensive and diffi cult to measure, that would benefi t 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 fi ve 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 markertrait associations are germplasm- and environment-specifi c and close to previously mapped genes and QTL relevant for malt and beer quality. We found alleles fi xed 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.