Genetic gain, diversity, and marker-trait associations in Minnesota barley germplasm

Plant breeding aims to make genetic gains by accumulating favorable alleles through selection from populations exhibiting genetic diversity. Barley improvement relies on advanced cycle breeding, crossing elite by elite germplasm to improve adaptation and malting quality traits. The Minnesota six-rowed barley breeding program used 34 parental lines to develop malting barley varieties over a 40 year period. Significant genetic gains were documented for yield, plump grain percentage and malting quality traits including malt extract percentage and diastatic power. In parallel, there was reduction of phenotypic variation over time. The breeding process also led to a differentiation of the elite germplasm as revealed by principal component analysis, confirming the hypothesis of the formation of a core germplasm set. Based on the analysis of 71 molecular marker loci distributed across the genome, there was a significant reduction in allelic diversity with time. However, this reduction was not equal across the genome, suggesting specific genes were under selection. A correspondence analysis of the molecular marker data showed a differentiation of the germplasm similar to the results for phenotypic data. An examination of the allele correlations of mapped genetic markers in this population showed that linkage disequilibrium extended over distances higher than 20 cM. At total of six marker trait associations were identified using a mixed model that incorporated coancestry data to account for population structure. Four of the marker-trait associations detected corresponded to previously reported quantitative trait loci. We concluded that the plant breeding process affected the phenotypic variation available within the germplasm, although no signs of reduction in genetic gains could be observed for traits like yield. Association studies can be carried out within these types of populations, but validation of the association detected would be needed given the high risk of spurious associations.