Genome-wide association study for identification of marker-trait association conferring resistance to scald from globally collected barley germplasm.

Scald is one of the major economically important foliar diseases in barley, causing susceptible varieties up to 40% of yield loss. The identification of quantitative trait loci (QTL) and elite alleles that confer resistance to scald is imperative in reducing the threats to barley production. In this study, genome-wide association studies (GWAS) were conducted using a panel of 697 barley genotypes to identify QTL for scald resistance. Field experiments were conducted over three consecutive years. Among different models used for GWAS analysis, FarmCPU was shown to be the best-suited model. Nineteen significant marker-trait associations (MTAs) related to scald resistance were identified across six different chromosomes. Eleven of these MTAs correspond to previously reported scald resistance genes Rrs1, Rrs4, and Rrs2, respectively. Eight novel MTAs were identified in this study with the candidate genes encoding a diverse class of proteins including region leucine-rich repeats (LRR), AP2/ERF transcription factor, homeodomain-leucine zipper, and protein kinases family proteins. The combination of identified superior alleles significantly reduces disease severity scores. The results will be valuable for marker-assisted breeding for developing scald-resistant varieties.