Implementing Association Mapping and Genomic Selection to Advance Breeding for Complex Traits in Barley

Abstract

To efficiently respond to challenges presented by global climate change, plant breeders can implement methods that utilize genome-wide marker data to discover and deploy useful genes. We investigated the use of genome-wide association mapping and genomic selection to improve two traits related to protecting natural resources: nitrogen use efficiency (NUE) and winter hardiness. In our first study, we identified quantitative trait loci (QTL) for improved NUE using phenotypic data and calculated stress indices in conjunction with genome-wide marker data for 250 six-row and 250 two-row barley breeding lines. We identified a QTL for grain protein concentration (GPC) on chromosome 6H that has been mapped previously in barley and is collinear with the well-characterized Gpc-B1 locus in wheat. Groups of lines defined by marker haplotypes at this locus exhibited significant differences in GPC but not in grain yield. Overall, our results indicated that potentially effective breeding strategies for NUE include selection based on stress indices, marker assisted selection for desirable alleles, and genomic selection to capture small effect loci. In a second study, we assessed the utility of genomic selection to initiate a breeding program for winter barley based on observed gains from selection, changes in phenotypic variation, and changes in marker allele frequencies. After conducting two cycles of genomic selection for a selection index that combined predictions for low temperature tolerance, malt extract, grain yield, heading date, and plant height, we assessed the selected sets of lines in field trials. Between cycles 0 and 2, genomic selection improved low temperature tolerance and malt extract while maintaining the other selection index traits. Phenotypic variance fluctuated but did not change significantly. Three markers previously shown to be linked to winter hardiness traits shifted in genotypic frequency over the cycles of selection. Based on all marker data, the population shifted toward similarity with the winter growth-type parent lines after two cycles of genomic selection. Overall, this study demonstrated that genomic selection is an effective method for improving trait values in a population at the initiation of a breeding program. Together, these studies support the use of marker-based breeding strategies to improve genetically complex traits that contribute to sustainable agricultural systems that will address climate change.