Genome- and transcriptome-wide systematic identification of bHLH transcription factor family and characterization of promising members that respond to abiotic stress in tomato

Abstract

Background The bHLH (basic helix-loop-helix) transcription factors function as crucial regulators in numerous biological processes including abiotic stress responses and plant growth and development. Although SlbHLH gene family in tomato has been studied and the functions of some members have been explored, there are still many tomato SlbHLH genes that have not been identified and numbered, which will hinder the later study of SlbHLH genes. A genome-wide systematical identification and characterization is necessary for tomato SlbHLH genes. Results In the study, numerous genes were identified to be the potential and significant candidates that response to salt stress through RNA-seq analysis. 195 bHLH genes that unevenly distributed onto 12 chromosomes were identified from tomato genome. Phylogenetic relationships showed that SlbHLHs were classified into 26 subfamilies based on their conserved domain, motif compositions and gene structures. The collinearity between SlbHLHs and interrelated orthologs from ten plants further revealed evolutionary insights into SlbHLHs. Cis-elements investigations of SlbHLH gene promotors futhrer suggested the potential roles of SlbHLHs in tomato development and stress responses. The qRT-PCR analysis displayed that the expression of 12 selected SlbHLHs were varyingly and markedly induced by multiple abiotic stresses (salt, cold, heat and drought) and hormone treatments (SA, ABA, IAA, ACC and MeJA). Conclusions These results provide valuable foundations for further exploring possible regulatory mechanisms and functional characterizations of SlbHLHs, and numerous members may function as the potential regulators to enhance plant tolerance to abiotic stress.