Comprehensive genomic analysis of BAHD gene family: expression patterns during development and stress responses in pecan (Carya illinoinensis)

BACKGROUND: The BAHD acyltransferase gene family performs diverse and essential biological functions in plants, mediating the biosynthesis of terpenoids, phenolic compounds, and esters that contribute to stress response mechanisms, cellular homeostasis, and fruit quality regulation. However, systematic characterization of this gene family in Carya illinoinensis remains largely unexplored. RESULTS: In this study, 88 BAHD genes (CiBAHD1-CiBAHD88) were characterized in the C. illinoinensis genome, with phylogenetic analysis categorizing them into five distinct evolutionary clades. The analysis showed significant diversity in gene length and protein size, while promoter examination identified numerous cis-acting elements linked to abiotic stress responses. Expression profiling across six tissues revealed a predominant expression of most CiBAHD genes in reproductive organs, particularly in female tissues, with 10 genes (e.g., CiBAHD8, 16, 34) showing fruit-specific expression. Under stress conditions, qRT-PCR analysis of 20 selected CiBAHD genes demonstrated diverse induction patterns: key genes like CiBAHD50 were rapidly and strongly induced by low temperature, CiBAHD54 and CiBAHD55 were significantly upregulated under high temperature, CiBAHD26 responded transiently to drought, and CiBAHD32 showed early induction under salt stress. CONCLUSIONS: This study presents the first genome-wide characterization of the BAHD acyltransferase family in pecan. The analysis identifies clade-specific conservation in gene structure and motif composition, and demonstrates enrichment of stress and hormone-related regulatory elements in promoter regions. Expression profiling establishes functional roles for CiBAHD members in reproductive processes and fruit development, while delineating specific genes with rapid and sustained transcriptional responses to abiotic stresses. These findings establish a foundational resource for future functional characterization and highlight potential targets for genetic improvement of stress resilience in C. illinoinensis.