Dusheng Lu

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 identify gene modules and hub genes associated with husk number by integrating transcriptome profiling, hierarchical clustering, and weighted gene co-expression network analysis (WGCNA). Methods: 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 putative husk-associated genes were identified. Differential expression analysis, hierarchical clustering, and WGCNA were combined to prioritize candidate genes. Results: Hierarchical clustering revealed a late-stage-specific gene cluster (Cluster 3, 44 genes) strongly up-regulated at V8–V10 in the high-husk line. WGCNA identified three modules significantly correlated with husk number: MEblue and MEbrown (positively) and MEturquoise (negatively). Cluster 3 was enriched in the tricarboxylic acid (TCA) cycle, DNA replication, and glycerophospholipid metabolism. Intersecting hub genes (|kME| > 0.9) with high-confidence differentially expressed genes (DEGs) (|log2FoldChange| > 2) yielded two prioritized candidate gene sets: up-regulated genes enriched in cell cycle, brassinosteroid (BR) signaling, and phospholipid metabolism; down-regulated genes enriched in mitogen-activated protein kinase (MAPK) signaling, glycolysis, and cell wall degradation. Conclusions: These results suggest that husk number may be regulated by a potential BR–MAPK–cell cycle regulatory axis, providing a regulatory network and candidate genes for future validation and molecular breeding.

Husk number (HN) trait is an important factor affecting maize kernel dehydration rate after the physiological maturity stage. In general, a reasonable reduction in HN is a key target sought for breeding maize varieties that are suitable for mechanized harvesting. In this study, the HN of a maize natural population panel containing 232 inbred lines was analyzed, and the results showed a broad-sense heritability of 0.89, along with a wide range of phenotypic variation. With the best linear unbiased prediction (BLUP) values across the three environments, a genome-wide association study (GWAS) was conducted using 995,106 single-nucleotide polymorphism (SNP) markers. A total of 16 SNPs significantly associated with HN were identified by the mixed linear model and general linear model using the TASSEL 5.0 software program. A local linkage disequilibrium (LD) study was performed to infer the candidate interval around the lead SNPs. A total of 19 functionally annotated genes were identified. The candidate genes were divided into multiple functional types, including transcriptional regulation, signal transduction, and metabolic and cellular transport. These results provide hints for the understanding of the genetic basis of the HN trait and for the breeding of maize varieties with fewer HN and faster dehydration rate.