Transcriptome and WGCNA analysis revealed the molecular mechanism of drought resistance in new sugarcane varieties

Drought is a key constraint to sugarcane production, yet the molecular mechanisms underlying sugarcane drought resistance remain poorly understood. In this study, three experimental sugarcane varieties were subjected to drought stress using PEG6000, followed by transcriptome sequencing on Illumina and PacBio platforms. Sequencing generated a total transcript length of 77,930,985 bp and identified 40,359 unique genes, of which 38,791 were annotated across seven databases. Differential expression analysis revealed significant enrichment and upregulation of metabolic pathways related to photosynthesis, plant hormones, polysaccharide synthesis, and amino acid metabolism in the variety ZZ9 under drought. Transcription factor families including bHLH, bZIP, ERF, NAC, MYB, and GRAS were drought-inducibly expressed. Weighted gene co-expression network analysis (WGCNA) identified 22 co-expression modules, from which key genes were selected in the most correlated module (MEten), including NACA1, ABA-related genes, ERA1, PER70, ATX, two SOD genes (SODF1 and SODF2), two LEA genes, and two LOX genes. Additionally, Cytoscape-based analysis identified the novel gene PSY1 and two post-selection genes potentially linked to photosynthetic regulation under drought. Integrating second- and third-generation transcriptomics with WGCNA, this study provides potential molecular regulatory mechanisms and candidate hub genes for sugarcane drought resistance, offering critical insights for drought-tolerant variety breeding and functional genomics research.