Transcriptomic Insights into Grain Size Development in Qingke: Based on Weighted Gene Co-Expression Network Analysis

In this study, we explored the molecular mechanisms underlying seed size variation between two distinct qingke barley varieties through comprehensive phenotypic and transcriptomic analyses. Phenotypic observations revealed that seeds underwent rapid expansion post-filling, with significant differences in seed width and thickness across all three developmental stages, while seed length showed no notable variation by the end of the filling period. Transcriptome sequencing identified a peak in differentially expressed genes (DEGs) during the mid-filling stage, indicating that the regulation of grain size development predominantly occurs in the early and mid-filling phases. Weighted gene co-expression network analysis (WGCNA) highlighted a blue module strongly correlated with grain size, which was significantly enriched in key metabolic pathways such as starch and sucrose metabolism. Further investigation pinpointed seven hub genes, among which HvENO1 exhibited a remarkable upregulation in large-grain varieties during the mid-to-late filling stages, aligning closely with observed phenotypic traits. Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) validation confirmed the stage-specific and variety-specific expression patterns of these genes, corroborating the reliability of the transcriptomic data. These findings uncover critical genetic and metabolic regulators of qingke seed size, offering valuable insights and potential targets for future qingke breeding programs.