Cold stress significantly constrains the growth, development, productivity, and distribution of rice, particularly the indica cultivar, known for its susceptibility to cold, limiting its cultivation to specific regions. This study investigated the genes associated with cold responsiveness in the roots of two indica cultivars, SQSL (cold-tolerant) and XZX45 (cold-susceptible), through transcriptome dynamics analysis during the seedling stage. The analysis identified 8144 and 6427 differentially expressed genes (DEGs) in XZX45 and SQSL, respectively. Among these DEGs, 4672 (G2) were shared by both cultivars, while 3472 DEGs (G1) were specific to XZX45, and 1755 DEGs (G3) were specific to SQSL. Additionally, 572 differentially expressed transcription factors (TFs) from 48 TF families, including WRKY, NAC, bHLH, ERF, bZIP, MYB, C2H2, and GRAS, were identified. Gene Ontology (GO) enrichment analysis revealed significant enrichment of DEGs in the G3 group, particularly in the “response to cold” category, highlighting the crucial role of these specific genes in response to cold stress in SQSL. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated pronounced enrichment of DEGs in the G3 group in metabolic pathways such as “Pyruvate metabolism”, “Glycolysis/Gluconeogenesis”, and “Starch and sucrose metabolism”, contributing to cold tolerance mechanisms in SQSL. Overall, this study provides comprehensive insights into the molecular mechanisms underlying cold responses in the indica cultivar, informing future genetic improvement strategies to enhance cold tolerance in susceptible indica rice cultivars.

Background: Rapeseed ( Brassica napus L.) is a globally important oil crop whose productivity is increasingly threatened by drought stress. Although DNA methylation is recognized as a key regulator of plant stress responses, the integrated epigenetic and transcriptional landscapes underlying divergent drought tolerance in rapeseed remain poorly understood. Results: Here we performed whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) on extreme drought-tolerant and drought-sensitive rapeseed genotypes. Drought stress triggered extensive DNA methylation reprogramming, with differentially methylated regions (DMRs) in the CHH context accounting for over 68% of all significant DMRs, highlighting the prominent role of non-CG methylation. The drought-sensitive genotypes exhibited an “over-defense” strategy, characterized by pervasive hyper-methylation, a larger number of DMRs and differentially expressed genes (DEGs), and widespread activation of stress-response pathways. In contrast, the tolerant genotypes displayed a “precision-regulation” strategy, featuring balanced methylation dynamics, fewer but highly specific DMRs and DEGs, and enrichment of pathways associated with carbohydrate transport and resource allocation. Integrated multi-omics analysis identified 19 core pathways consistently altered at both epigenetic and transcriptional levels. Furthermore, we identified 106 high-confidence candidate genes exhibiting negative correlations between DNA methylation and gene expression, among which 12 hub genes were located within the core pathways, including pivotal regulators such as BnBBX21 and BnTAT7 . Conclusions: Our results reveal two contrasting molecular strategies underlying drought adaptation in rapeseed: an extensive but energetically costly “over-defense” response in sensitive genotypes and a more efficient “precision-regulation” strategy in tolerant genotypes. These strategies are mediated by genotype-specific coordination between epigenetic remodeling and transcriptional reprogramming. This study provides mechanistic insights into drought adaptation and highlights valuable epigenetic and genetics targets for improving drought resilience in rapeseed.