Genome-Wide Association Study of Agronomic Traits in European Spring Barley from Polish Gene Bank

Abstract

The barley old cultivars can be used as a source of genetic diversity to breed new varieties well adapted to different environmental conditions. In this study, 431 European barley accessions were evaluated phenotypically across 2 years under field conditions and genotypically using DArTseq to gain insight into the genetic architecture of phenology, biomass, yield components, and seed yield traits. Accessions were grouped into sub-collections by cultivation period (group A—cultivated prior to 1985, B—cultivated after 1985, and C—Polish landraces), and by European country of origin or European region, to compare their phenological and agronomic value for 16 traits such as: days to heading (DH), days to milk-waxy stage (DMW), days to maturity (DM), days to harvest (DPH), plant height (PH), lodging (LT), row number (RN), spike density (SD), spike length (SL), grain per spike (NGS), glume colour (GC1), grain awn type (GAT), grain covering (GT), grain pericarp colour (GPC), and 1000—grain weight (TGW), and to indicate marker-trait associations (MTAs) with these traits. Based on the results, phenotypic plants per se under field conditions and spikes, or seeds under laboratory conditions it was possible to cluster the collection. DH negatively correlated with PH and important yield components, such TGW. Overall, the genome-wide association study (GWAS) analysis identified 143 MTAs associated with these traits. Twenty-three MTAs were associated with plant phenological stages: 5 MTAs with DH, 6 MTAs with DMW, 5 MTAs with DM, and 9 MTAs with DPH. Eighty-nine SMTAs for plant phenotypic traits were identified: 1 for LT and 88 MTAs for PH. Thirty-one markers were identified for agronomic yield traits: 16 MTAs for SD, 11 MTAs for NGS, and 4 for TGW. One association result, 7241263-17 on chromosome 2H, corresponded to the genomic region mapped for DM, DPH, and SD. Marker 3258999-37-C/T on chromosome 2H, significant for NGS, was closely located to results 3263044-31-G/T for SD and 3263989-64-A/C for DMW. On chromosome 6H, closely located were markers significant for SD (3255466-35-C/G) and for NGS (3259102-57-C/A). Moreover, on chromosome 6H, closely located were markers significant for SD (3918801-14-G/A), for NGS (3666407-49-T/G), and for DMW (3663162-62-A/C). The well-characterized barley collection and identified MTAs markers will be used to create a Polish Genebank platform and will serve as a valuable resource for precise breeding programs.