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 revealed that CiBAHD genes were mainly expressed in female and male tissues, with some genes showing rapid induction under stress conditions. The stress responsive behavior of 20 CiBAHD genes was further confirmed by qRT-PCR under drought, salt, low temperature, and high temperature stress treatments. Conclusions This study provides the first genome-wide characterization of the BAHD gene family in C. illinoinensis , revealing its evolutionary patterns, structural variations, and functional significance in growth and stress response. The systematic analysis of CiBAHD genes provides fundamental insights for further gene functional assays and potential applications in genetic improvement of C. illinoinensis cultivars.