Comparative investigation of tomato bHLH transcription factors and their roles in flower and fruit development

The bHLH transcription factor (TF) family, known as key regulators in plants, was systematically identified in tomato to explore genes related to flower and fruit development and to gain deeper insight into their genomic features and potential functions. A total of 177 bHLH TFs were identified, with 18.6 % forming gene clusters and 47.5 % exhibiting collinearity. Based on phylogenetic relationships, the tomato bHLHs were categorized into 21 clades, with 70.1 % of clades 1–4 and 11–21 consisting of G-box-binding proteins, and 72.1 % of clades 5–10 comprising of non-E-box-binding proteins. About 49.7 % of the bHLHs formed 59 pairs of homologs, with all Ka/Ks values <1. Additionally, 38.2 % of the bHLHs were preferentially expressed in flowers and fruits, with 13 genes likely involved in fruit development and ripening. Their promoters mainly contained key response elements for light, ethylene, MeJA, and ABA. Furthermore, 58.8 % of the bHLHs formed 153 pairs of interactions, particularly Solyc01g102300.3 interacting with Solyc07g043580.4, which may play a significant role in flower and fruit development. RT-qPCR analysis revealed that 5 genes were expressed predominantly in stamens. The CRISPR/Cas9 editing of Solyc01g102300.3 generated 9 mutants, with base deletions being the primary mutation type, including 2 homozygous mutants. These plants showed no significant changes in vegetative growth, but pollen viability was significantly reduced. In conclusion, a comprehensive identification of tomato bHLHs revealed several potential regulatory genes in flower and fruit development.