Identification of genomic loci and candidate genes underlying preharvest sprouting-induced alpha-amylase activity in barley through genome-wide association study

Alpha-Amylase activity is the primary underlying factor for starch degradation and therefore yield and quality losses induced by preharvest sprouting (PHS) in barley. The present study identified genomic regions/candidate causal genes associated with PHS-induced α-amylase (AMY) activity through genome-wide association study (GWAS) of highly diverse barley genotypes over four environments. The genotypes studied exhibited a wide variation in Rapid Visco Analysis (RVA) results, which served as indicators of differing AMY activity levels. Marker-trait association analysis detected six markers significantly associated with AMY activity based on false discovery rate (FDR) threshold of α = 0.05. The six markers explained 7.41% to 16.95% of the phenotypic variation and represented five quantitative trait loci (QTLs) on chromosomes 1H (QAmy.umb-1H.1), 4H (QAmy.umb-4H.1), 5H (QAmy.umb-5H.1 and QAmy.umb-5H.2) and 7H (QAmy.umb-7H.1). Expression analysis of genes that harbour the significant single-nucleotide polymorphism (SNP) markers revealed their potential role in regulating PHS-induced AMY activity. Haplotype analysis of SNP markers within QAmy.umb-5H.2 identified a haplotype for low AMY activity or enhanced PHS resistance. Overall, this study identified genetic loci, SNP markers and novel candidate genes that control AMY activity and therefore have the potential to be applied for marker-assisted selection of low AMY activity and PHS resistant barley cultivars.