Genome-wide survey of the bHLH super gene family in Brassica napus

Abstract

Background: The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus. Results: We identified 602 potential bHLHs in the B. napus genome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs. Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA 3 , gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function. Conclusion: The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus. Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research.

Genome-wide Identification, Evolution and Expression Analysis of Basic Helix-loop-helix (bHLH) Gene Family in Barley (Hordeum vulgare L.)

“…Except for HvbHLH55 , other HvbHLHs displayed the negative gravity values, representing the hydrophilic characteristics of barley bHLH genes. Subcellular location prediction showed that most (90.07%) of the HvbHLHs were localized in the nucleus, which was similar to the previous study on Brassica napus [ 11 ]. To further validate the existence of these HvbHLHs , we performed BLAST search against the barley ESTs.…”

“…Up to now, the bHLH gene family has been extensively identified in many plant species. It is reported that 167 bHLH genes were identified in Arabidopsis thaliana [ 2 ], 167 in rice ( Oryza sativa) [ 7 ], 146 in Brachypodium distachyon [ 8 ], 571 in wheat ( Triticum aestivum ) [ 9 ], 208 in maize ( Zea mays ) [ 10 ] and 602 in Brassica napus [ 11 ]. The bHLH genes are widely involved in diverse signal transductions and metabolic pathways.…”

Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response

“…A group of transcription factors contains a highly conserved amino acid motif known as basic helix-loop-helix (bHLH) domain. These bHLH proteins perform a myriad of regulatory function in eukaryotic lineages and have been studied in several plants [ 6 , 11 ]. The bHLH transcription factors have been previously studied in several plant species, including maize and potato [ 3 , 4 , 11 , 26 – 28 ].…”

“…The gene expression patterns during different growth stages and conditions could also be an indicator of gene function [ 11 ].…”

“…Comprehensive characterization and functional analysis of bHLH TFs have been performed in several important crop plants, including Chinese cabbage and Brassica [ 5 , 7 , 11 ]. However, no study of this essential TF family is reported in pineapple, an economically crucial perennial fruit crop belonging to Bromeliaceae .…”