Genome-Wide Identification and Expression Profiling of the bHLH Transcription Factor Gene Family in Saccharum spontaneum Under Bacterial Pathogen Stimuli

The basic helix-loop-helix (bHLH) families that act as transcription factors play a central role in regulating a wide range of physiological, metabolic, and developmental processes in higher organisms. Systematic identification and characterization of bHLH gene families has not yet been performed in sugarcane. In the present study, 37 SsbHLH genes (101 total alleles) were identified in Saccharum spontaneum (Ss), with 1–4 alleles each. Phylogenetic analysis indicated that these SsbHLH could be classified into 17 subfamilies according to bHLH domains. All of the SsbHLHs were localized on 20 chromosomes, and the SsbHLH member’s likely arose through gene duplication. Based on a sugarcane transcriptome dataset trigged by Acidovorax avenae subsp. avenae (Aaa) causing red stripe, SsbHLH27 and SsbHLH36 were significantly upregulated by 1.12- to 5.96-fold [log2(Fold Change)] in cultivar ROC22 (red stripe resistant), while both genes were significantly depressed in cultivar MT11-610 (red stripe susceptible) under Aaa infection. Based on another sugarcane transcriptome dataset trigged by Xanthomonas albilineans (Xa) causing leaf scald, four genes (SsbHLH03/04/36/37) were highly upregulated by 1.23- to 5.11-fold [log2(Fold Change)] in LCP85-384 (leaf scald-resistant), but downregulated or non-significantly changed in cultivar ROC20 (leaf scald-susceptible) under Xa infection. SsbHLH15/17 were positively induced by both Aaa and Xa stimuli, whereas SsbHLH30/33 were negatively regulated by both pathogens. Some genes, such as SsbHLH06/11, had different expression profiles under the two pathogens infections, showing increased expression after Aaa infection but reduced expression with Xa. These findings provide important candidate genes for further functional analyses in sugarcane in response to bacterial stress.