Comprehensive Characterization of the PEBP Gene Family in Osmanthus fragrans Reveals Genetic Diversity and Potential Roles in Floral Development

Abstract

The phosphatidylethanolamine-binding protein (PEBP) gene family plays essential roles in flowering regulation, plant development, and stress responses. However, its characteristics in Osmanthus fragrans remains largely unexplored. Here, a genome-wide analysis was conducted to comprehensively investigate the OfPEBP gene family. A total of 11 OfPEBP genes were identified and classified into three subgroups: FT-, TFL1-, and MFT-like. Genes within the same subgroup exhibited similar motif compositions and exon–intron structures. Promoter analysis revealed abundant light- and hormone-responsive cis-elements. Population genetic analyses identified significant differentiation in OfPEBP3, OfPEBP7, and OfPEBP8, with their single nucleotide polymorphisms (SNPs) and haplotypes closely associated with seasonal flowering phenotypes. DNA methylation profiling indicated that CpG and CHG methylation predominated across the OfPEBP family and remained relatively stable during flower development, whereas OfPEBP6, OfPEBP9, and OfPEBP10 displayed higher methylation levels. Segmental duplication was identified as the primary driver of family expansion, and duplicated gene pairs experienced strong purifying selection. Expression analyses revealed tissue-specific expression patterns and differential responses to temperature, ethylene, and DNA methylation inhibitor (Aza) treatments. These findings provide useful insights into the potential involvement of OfPEBP genes in seasonal flowering and offer candidate genetic resources for future functional studies and molecular breeding in O. fragrans.