Identification of E2F/DP gene family and their expression analysis under cold stress in rice

The rice E2F/DP gene family plays a crucial role in regulating the cell cycle and responses to environmental stresses. In this study, we identified and analyzed eight members of the rice E2F/DP gene family (OsE2F1 to OsE2F8) using the RiceSuperPIRdb database. Each protein contains the conserved E2F_TDP domain. Phylogenetic analysis classified the E2F/DP proteins into three groups. Physicochemical property analysis revealed that the E2F/DP proteins are hydrophilic, with varying amino acid lengths, isoelectric points, and molecular weights, and are primarily localized in the nucleus and chloroplast. Chromosomal localization indicated that these genes are distributed across six rice chromosomes. Gene structure analysis revealed diverse exon-intron arrangements, while motif analysis identified 10 conserved motifs. Collinearity analysis showed gene duplication events, suggesting purifying selection. Cis-regulatory element analysis indicated their involvement in abiotic stress responses. The protein-protein interaction analysis revealed that most OsE2F/DP proteins are associated with cell cycle regulation and transcriptional control. Expression analysis revealed tissue-specific expression patterns and differential expression under various stress conditions. Specifically, qRT-PCR validation under cold stress showed that some E2F/DP genes were upregulated at 12 hours and downregulated at 24 hours, indicating their potential role in cold tolerance. These findings provide a foundation for further investigation of the roles of the rice E2F/DP gene family in development and stress responses.