Genome-wide characterization and cold-responsive expression profile of Rab GTPases and their regulatory proteins in O. rufipogen.

The DXWR genome was found to contain 44 OrRabs. Most of the cold-activated OrRab genes belong to the RabA/Rab11 group, with OrRab11B3 the most strongly induced gene in DXWR. Dongxiang wild rice (Oryza rufipogon Griff., DXWR), the wild rice species distributed at the highest latitude, exhibits significantly greater cold tolerance than cultivated rice, making it a valuable genetic resource for enhancing cold resistance in domesticated varieties. While previous studies in Arabidopsis thaliana have shown that members of the Rab gene family-encoding small GTP-binding proteins-are regulated by cold acclimation, comparable regulatory mechanisms have yet to be elucidated in DXWR. In this study, 44 OrRabs were identified through whole-genome annotation and Hidden Markov Model (HMM)-based searches. Phylogenetic analysis classified the OrRabs into eight distinct groups. A novel member of the Rab family, OrRab18A1 (ORUFI04G32590), was identified and assigned to its respective subgroup. Dispersed duplication (DD) and whole-genome duplication/segmental duplication (WGD/SD) were the primary mechanisms contributing to the expansion of the total number of OrRabs. Expression profiling of OrRabs and their associated regulatory proteins-RabGAPs, RabGDIs, and RabGEFs-across different tissues and under cold stress conditions revealed diverse expression patterns. Five OrRabs, including three early cold-upregulated Rab genes and two late cold-upregulated Rab genes, were selected for further validation by quantitative RT-PCR under cold stress. Among these, transcripts of OrRab11B3 showed nearly a 15-fold change after 3 h of cold treatment, suggesting its potential role in the early response pathway to cold stress. Overall, these findings offer a foundational framework for understanding the functional roles of Rab GTPases in O. rufipogon.