A 191-bp insertion/deletion in GBSS1 region is responsible for the changes in grain amylose content in barley (Hordeum vulgare L.)

Amylose concentration in barley grain is one of the important quality traits. In this study, a major quantitative trait locus (QTL) for grain amylose content was identified from a doubled haploid (DH) population. This QTL was also detected from genome-wide association studies (GWAS) using 185 diverse barley germplasm. The waxy (GBSS1) gene was located in the QTL region and could be a candidate gene. Subsequent characterization of waxy alleles of two parents of the DH population revealed that a 191-bp insertion in the region from the transcription start site to start codon is responsible for the reduction of waxy transcript, leading to a lower expression level, thus, a lower amylose content. A genetic marker was designed for the waxy allele and can be effectively used in barley breeding programs.