Transcriptomic insights into grain size development in naked barley (<i>Hordeum vulgare</i> L. var. <i>nudum</i> Hook. f): based on weighted gene co-expression network analysis

Phenotypic assessments revealed that grains underwent rapid expansion during the filling period, with significant differences in grain width (GW) and thickness (GT) across all three developmental periods. In contrast, grain length (GL) remained relatively consistent by the end of the filling period. Transcriptome sequencing identified a peak in differentially expressed genes (DEGs) during the mid-filling period, indicating that the regulation of grain size development is most active in the early and mid-filling phases. WGCNA identified a blue module strongly correlated with grain size, which was significantly enriched in key metabolic pathways, including starch and sucrose metabolism. Further analysis identified seven hub genes, among which <i>HvENO1</i> exhibited pronounced upregulation in large-grain varieties during the mid-to-late filling periods, closely aligning with the observed phenotypic traits. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) validation confirmed the period-specific and variety-specific expression patterns of these genes, further supporting the potential of these genes as targets for improving grain size in breeding.