Genome-wide identification and expression analysis of salt-responsive bHLH transcription factors in the wheat (Triticum aestivum) genome

Soil salinity is an increasing environmental constraint affecting agriculture worldwide, with major impacts on wheat ( Triticum aestivum ) productivity. Understanding the transcriptional regulatory mechanisms underlying salt tolerance is therefore essential for crop improvement. The basic helix–loop–helix (bHLH) transcription factor family plays important roles in plant stress responses. In this study, a genome-wide analysis of the Chinese Spring wheat reference genome identified five salt-responsive bHLH transcription factors: TaMYC2-B, TaMYC2-D, FIT1 , and two ORG2 /bHLH38-like paralogs. Using in silico promoter analysis, transcription factor enrichment analysis, and co-expression network analysis, we identified twelve predicted downstream target genes regulated by these transcription factors, including RLK, CLC , and TaAPY . RT-qPCR-based expression profiling of shoots and roots from the moderately salt-tolerant cultivar BARI Gom-25 exposed to 100 mM NaCl revealed tissue-specific regulation of several transcription factors and their putative target genes. TaMYC2-B and TaMYC2-D , along with their putative downstream targets FOMT and CCoAOMT , were downregulated in both tissues under salt stress. In contrast, a predicted FIT1 -associated CLC gene was upregulated in roots despite reduced expression of the FIT1 transcription factor. The apyrase gene TaAPY showed strong induction, particularly in roots, suggesting a role in extracellular ATP (eATP) turnover during stress. These expression patterns suggest transcriptional regulation potentially influencing ion homeostasis and stress signalling during salinity responses. Although functional validation is required to confirm these regulatory relationships, this study identifies candidate regulators and target genes that provide a foundation for future mechanistic studies and potential wheat improvement strategies.