Genome-wide identification, characterization, and expression profiling of bHLH genes under different development and abiotic stress conditions in Carya illinoinensis

Background: The basic helix-loop-helix (bHLH) transcription factors play pivotal roles in plant growth, development, and stress responses. While these factors have been extensively studied in model plants, the bHLH family in woody species, particularly in Carya illinoinensis, remains underexplored. As an economically important nut tree, C. illinoinensis encounters various abiotic stresses; thus, understanding the molecular mechanisms that govern its development and stress adaptation is essential for genetic improvement. Results: In this study, 165 bHLH genes (CibHLH01-CibHLH165) were identified in the C. illinoinensis genome and classified into 25 subfamilies. Significant diversity was observed in gene length and protein size, and promoter analysis revealed numerous cis-acting elements associated with abiotic stress responses. Expression profiling indicated that CibHLH genes were predominantly expressed in female and fruits, with some genes rapidly induced under stress conditions. The stress-responsive nature of 30 CibHLH genes was validated through qRT-PCR under low temperature, high temperature, drought, and salt stress treatments. Conclusions: This study presents the first comprehensive genome-wide analysis of the bHLH family in C. illinoinensis, elucidating its evolutionary dynamics, structural diversity, and functional roles in development and stress adaptation. The findings underscore the significance of CibHLH genes in mediating responses to abiotic stress, thereby providing potential targets for the genetic enhancement of C. illinoinensis and related species. (c) 2025 SAAB. Published by Elsevier B.V. All rights are reserved, including those for text and data mining, AI training, and similar technologies.