Genome-wide identification and expression analysis of the bHLH gene family in Lilium davidii var. unicolor and its response to abiotic stress

BACKGROUND: Basic helix-loop-helix (bHLH) transcription factors regulate plant growth, stress responses, and hormone signaling. Advances in bioinformatics, the bHLH transcription factor family has been comprehensively identified and characterized across a wide range of organisms. However, a genome-wide analysis of this family has not yet been performed in Lilium davidii var. unicolor, an economically important species in China valued for its nutritional and medicinal properties. RESULTS: Using whole-genome sequencing data, we identified 214 LdbHLH genes from the L. davidii var. unicolor genome and classified them into 23 subfamilies based on phylogenetic analysis. Gene structure was highly conserved within subfamilies. Collinearity analysis identified five syntenic gene pairs (LdbHLH3-LdbHLH9, LdbHLH17-LdbHLH61, LdbHLH176-LdbHLH125, LdbHLH181-LdbHLH197, and LdbHLH210-LdbHLH200), all derived from segmental duplication, indicating limited large-scale expansion. Promoter analysis showed that LdbHLH genes commonly contain cis-regulatory elements associated with development, abiotic stress, and hormone responses, suggesting their potential roles in signal crosstalk. Expression profiling demonstrated clear tissue specificity, with certain genes highly expressed in leaves, scales, stems, or tepals. Under hormone and stress treatments, most genes exhibited transient expression changes, while some genes, such as LdbHLH76 under salt stress and LdbHLH7 under ABA treatment, were strongly upregulated. Functional assays further confirmed that LdbHLH12, LdbHLH46, LdbHLH76, and LdbHLH189 positively contribute to salt tolerance. CONCLUSIONS: This study provides the first comprehensive functional and genomic characterization of the bHLH family in L. davidii var. unicolor, offering insights into their roles in stress adaptation and tissue development, and identifying candidate targets for molecular breeding aimed at enhancing stress resilience.