Comprehensive Characterization of PEBP Genes Reveals Their Roles in Tuber Development and Stress Responses in Yam

The phosphatidylethanolamine-binding protein (PEBP) family regulates flowering, seed development, and underground storage organ formation in plants, yet its functions in yam (Dioscorea rotundata) remain unclear. Here, we identified 17 PEBP genes in the yam genome and classified them into four clades (FTL, TFL1L, MFTL, and PEBPL). Dispersed duplication was the major driver of gene family expansion, while the limited tandem and segmental duplications evolved under strong purifying selection. Conserved motif and gene structure analyses confirmed the presence of core PEBP domains and indicated subfamily-specific divergence. Promoter analysis revealed abundant light- and hormone-responsive elements, implying complex regulatory inputs. Transcriptome profiling demonstrated distinct tissue-specific expression patterns: DrPEBP9 and DrPEBP10 were specifically expressed in flowers, whereas members such as DrPEBP3, DrPEBP15, DrPEBP16, and DrPEBP17 exhibited tuber-preferential expression. Several DrPEBP genes displayed dynamic transcriptional changes during tuber development, indicating potential involvement in tuber expansion and starch accumulation. Additionally, differential expression under scorch foot disease infection and mechanical wounding suggested roles in biotic and abiotic stress responses. Overall, this study provides the first systematic characterization of the PEBP gene family in yam, highlights candidate genes likely involved in flowering regulation, tuber development, and stress adaptation, and offers valuable resources for future functional studies and genetic improvement of tuber crops.