Genome-wide identification and expression profiling of the bHLH transcription factor family under salt stress and hormonal treatments in cowpea (Vigna unguiculata).

The basic helix-loop-helix (bHLH) gene family, a major class of transcription factors in plants, plays critical role in growth, development, and responses to environmental stresses. Despite its importance, knowledge of bHLH gene functions in cowpea remains limited. Here, we conducted a comprehensive genome-wide in silico analysis of the cowpea bHLH family. A total of 60 VubHLH genes were identified and found to be non-uniformly distributed across the 11 chromosomes. Phylogenetic analysis grouped 60 VubHLH and 127 AtbHLH genes into six distinct subgroups. Gene structural characteristics were conserved within subgroups but diversed among subgroups. Synteny analysis indicated that segmental duplication, rather than tandem duplication, was the primary driver of VubHLH family expansion. Promoter analysis revealed diverse cis-acting elements associated with plant growth, developmental processes, phytohormone regulation, and stress responses. Tissue-specific expression suggested functional diversification of VubHLH genes during evolution. qRT-PCR analysis showed that VubHLH1.1 and VubHLH11.1 genes were significantly upregulated under ABA, MeJA, and salt treatments, whereas VubHLH3.7, VubHLH5.1, and VubHLH6.3 were downregulated. Collectively, these results provide valuable insights into the evolutionary relationships and functional characteristics of the bHLH gene family and lay a foundation for future studies of bHLH gene function and improving the cowpea salt tolerance.