Genome-Wide Identification and Expression Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Factor Family in Gastrodia elata

The basic helix-loop-helix (bHLH) transcription factor family is the second largest transcription factor family in plants, regulating various biological processes. However, a comprehensive genome-wide analysis of bHLH proteins in Gastrodia elata has not been yet reported. This study conducted a genome-wide analysis of 160 putative bHLH family genes (GebHLH) in G. elata, exploring their physiochemical features and constructing phylogenetic trees. The 160 GebHLH genes were unevenly distributed across 17 of 18 chromosomes and possessed typical bHLH domains. Distinct expression patterns emerged between healthy and fungal-infected G. elata tubers, with more genes upregulated in infected tubers, suggesting their involvement in fungal infection response. From the MAPK signaling and plant-pathogen interaction pathways, 37 genes were identified as responding to fungal diseases, with 17 genes (e.g., Ge4CL1, GeNPR1, GePR4, and GeCDPK9) significantly upregulated in infected tubers. Quantitative real-time reverse transcription polymerase chain reaction revealed varying expression profiles of disease-resistant genes in mature tubers between different G. elata varieties. Protein-protein interaction analysis showed most GebHLH proteins interacted with multiple bHLH proteins, indicating cooperative roles in plant growth and development. GebHLH89 was predicted to be a common transcription factor in light, abscisic acid, and jasmonic acid signaling pathways. GebHLH34 can bind to GeTTG1, essential for anthocyanin accumulation, suggesting it may regulate flavonoid biosynthesis. This study provides insights into the potential functions of bHLH transcription factors in G. elata, laying a foundation for future genetic breeding efforts.