Integrating Genome-wide association and whole transcriptome analysis to reveal genetic control of grain quality traits in barley

Abstract Barley (Hordeum vulgare L.) is an important cereal crop used in animal feed, beer brewing, and food production. Quality traits of barley grain, such as starch and protein contents, have specific requirements depending on the intended end-use product. In this study, 250 barley accessions were evaluated for key grain quality traits, including protein content (GPC), starch content (GSC) and fibre content (GFC) across a two-year period. Through genome-wide association study (GWAS) analysis, we identified 96 significant SNPs associated with grain quality traits. Additionally, two materials showed significant differences in grain quality were further selected for transcriptome analysis. A total of 4636 differentially expressed genes (DEGs) and 3684 DEGs were identified in different development stage. These DEGs mainly participate in carbon fixation in photosynthetic organisms, starch and sucrose metabolism, and so on. By integrating GWAS and RNA-Seq data analysis approaches, we identified 15 candidate genes primarily involved in hydrolysis of starch, glycosyltransferase and post-translational modification. These findings provide valuable insights for gene cloning related to grain quality and server as a reference for high-quality barley cultivars.