Transcriptome and Co-expression Network Analysis Reveals Key Modules and Hub Genes Controlling Husk Number in Maize

<title>Abstract</title> <p>Background Husk number is a key agronomic trait in maize that affects grain dehydration rate and yield, yet its regulatory mechanisms remain largely unknown. This study aimed to systematically identify the gene modules and hub genes controlling husk number using an integrated transcriptome approach. Results RNA-seq was performed on ear tissues from two maize inbred lines with extreme husk numbers (LJ311, ~ 20 husks; PHG35, ~ 5 husks) at four developmental stages (V7–V10). A total of 12,605 husk-specific genes were identified. Hierarchical clustering combined with differential expression analysis revealed a late-stage-specific gene cluster (Cluster 3, 44 genes) that was strongly upregulated at V8–V10 in the high-husk line. WGCNA identified three co-expression modules significantly correlated with husk number: MEblue and MEbrown (positively) and MEturquoise (negatively). Cluster 3 shared only seven genes with MEblue and was enriched in the TCA cycle, DNA replication, and glycerophospholipid metabolism. By intersecting hub genes (|kME| &gt; 0.9) with high-confidence differentially expressed genes (|log2FC| &gt; 2), two final candidate gene sets were obtained. The upregulated candidates were enriched in cell cycle, brassinosteroid signaling, and phospholipid metabolism, whereas the downregulated candidates were enriched in MAPK signaling, glycolysis, and cell wall polysaccharide degradation. Conclusion The results suggest that increased husk number is driven by a BR–MAPK–cell cycle regulatory program, with an opposing mechanism in the low-husk line. This study provides an integrated regulatory network and valuable candidate genes for future functional validation and molecular breeding.</p>