Miscanthus lutarioriparius is a species of bioenergy crop unique to China. It is widely distributed in the south of China with high resistance to drought and salt stress. To date, the molecular mechanism of the adaption to drought stress in M. lutarioriparius is little known. In this study, RNA-seq technology was employed to analyze the transcriptome changes of diploid and tetraploid M. lutarioriparius after drought treatment. It was found that the number of differentially expressed genes in diploid M. lutarioriparius was much higher than tetraploid, whereas the tetraploid M. lutarioriparius may require fewer transcriptional changes. While the transcriptional changes in drought-tolerant tetraploid M. lutarioriparius are less than that of diploid, more known drought-tolerant pathways were significantly enriched than drought-sensitive diploid M. lutarioriparius. In addition, many drought-tolerance-related genes were constitutively and highly expressed in tetraploid under either normal condition or drought stress. These results together demonstrated that drought-tolerant tetraploid M. lutarioriparius, on the one hand, may preadapt to drought by constitutively overexpressing a series of drought-tolerant genes and, on the other hand, may adapt to drought by actively inducing other drought-tolerant-related pathways. Overall, this study could deepen our understanding of the molecular mechanism of drought-tolerance in bioenergy plants.

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.