Genome-Wide Identification and Expression Analysis of The BHLH Transcription Factor Family and Its Response to Abiotic Stress in Sorghum [Sorghum Bicolor (L.) Moench]

Abstract

Background: Basic helix-loop-helix (bHLH) is a superfamily of transcription factors that is widely found in plants and animals, and is the second largest transcription factor family in eukaryotes after MYB. They have been shown to be important regulatory components in tissue development and many different biological processes. However, no systemic analysis of the bHLH transcription factor family has yet been reported in Sorghum bicolor. Results: We conducted the first genome-wide analysis of the bHLH transcription factor family of Sorghum bicolor and identified 174 SbbHLH genes. Phylogenetic analysis of SbbHLH proteins and 158 Arabidopsis thaliana bHLH proteins was performed to determine their homology. In addition, conserved motifs, gene structure, chromosomal spread, and gene duplication of SbbHLH genes were studied in depth. To further infer the phylogenetic mechanisms in the SbbHLH family, we constructed six comparative syntenic maps of S. bicolor associated with six representative species. Finally, we analyzed the gene-expression response and tissue-development characteristics of 12 typical SbbHLH genes in plants subjected to six different abiotic stresses. Gene expression during flower and fruit development was also examined. Conclusions: This study is of great significance for functional identification and confirmation of the S. bicolor bHLH superfamily and for our understanding of the bHLH superfamily in higher plants.

Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

“…The cDNA was produced with a 1 mg RNA sample using a PrimeScript RT Reagent Kit with gDNA Eraser (TaKaRa) and SYBR Premix Ex Taq II (TaKaRa) [85]. Total RNA was extracted using the RNA out Kit (TaKaRa) and treated with RNase-free DNase I to remove trace amounts of DNA.…”

Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

“…The whole genomes of an increasing number of species have been sequenced, making it easy to identify gene families. In fact, many gene families in foxtail millet have been fully identified and analyzed, including bHLH [24], NAC [25], GRAS [26] and AP2/ ERF [27]. At present, the SPL gene families of several species have been extensively studied, including dicotyledons (Arabidopsis [18,28], tomato [22], Tartary buckwheat [23], grape [29], and cotton [30]), monocotyledons (rice [31,32], wheat [33], and barley [34]), and C4 crops (maize and Sorghum bicolor [35]).…”

Genome-wide identification and expression analysis of bHLH transcription factors reveal their putative regulatory effects on petal nectar spur development in Aquilegia

“…Compared with the conservative protein motif pattern, AqbHLH family has diverse intron/exon organizations in the same subfamily and among different subfamilies. The phenomenon also was found in the bHLH gene family in Chinese white pear (Dong et al, 2021), sorghum (Fan et al, 2021) and tobacco (Bano and Patal, 2021). The result suggested that the AqbHLH gene family may play diverse roles in many biological processes.…”