Identification of candidate genes for grain size in barley through combined GWAS and transcriptome analysis

Barley (Hordeum vulgare L.) is an important cereal crop with diverse uses, including animal feed, beer brewing, and food production. Grain size plays a crucial role in determining grain weight and quality, which is one of the key breeding objectives in response to market and industry demands. However, the molecular mechanisms of grain size in barley are still poorly understood. In this study, 250 barley accessions were evaluated for key grain size traits, including thousand grain weight (TGW), grain length (GL), grain width (GW), grain length to width ratio (GLWR), grain area (GA) and grain perimeter (GP) across a two-year period. A total of 369 significant Single Nucleotide Polymorphisms (SNPs) significantly associated with the six grain traits were detected. Among these SNPs, 30 were continuously detected in different years. Additionally, two accessions (ZQ25 and GK5) whose grain size significantly differed were selected for transcriptome analysis. Differentially expressed genes (DEGs) were identified at two time points: 3,733 at 21 days post anthesis (DPA) and 4,396 at 28 DPA. These DEGs were enriched mainly in photosynthesis-antenna proteins, phenylpropanoid biosynthesis and flavonoid biosynthesis. Furthermore, by integrating a genome-wide association study (GWAS) and RNA-seq, we identified 25 candidate genes involved primarily in various transcription factors, phytohormones, and sugar metabolism pathways. These results provide valuable information for grain size-related gene cloning and abundant molecular data for the breeding of new high yield varieties of barley in the future.