Given the stringent requirements set by the malting and brewing industries and the complex nature of traits, marker based breeding will become increasingly important for the improvement of malting barley (Hordeum vulgare ssp. vulgare). Identification and exploitation of useful and novel alleles at quantitative trait loci (QTL) is crucial to improve genetic gains. We identified marker trait associations and assessed the prediction accuracy of genomic selection for agronomic and disease traits using a collection of 768 breeding lines from two closely related breeding programs in the Upper Midwest. Three hundred progeny lines derived from crosses among 14 parents from the two programs were used as a validation mapping panel in association mapping and to assess genomic prediction accuracy. In general, we found that different sets of QTL were segregating in the two breeding programs. The difference in QTL detected could be due to different genes segregating in the two programs, but could also be affected by differences in marker allele frequencies and linkage disequilibrium between adjacent markers. The genomic prediction accuracies of progeny for six traits were moderate to moderately high, indicating that genomic selection could be successfully implemented for agronomic, disease and quality traits with a range of heritabilities. Our results also indicated that the prediction accuracies were better when training and prediction panels were closely related. The information gained from this study will be valuable to design sound and cost-effective breeding strategies for malting barley whose genetic base has become narrower over time.
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