Abstract

BackgroundThe basic helix-loop-helix transcription factors play important roles in diverse cellular and molecular processes. Comparative functional genomics can provide powerful approaches to draw inferences about gene function and evolution among species. The comprehensive comparison of bHLH gene family in different gramineous plants has not yet been reported.ResultsIn this study, a total of 183, 231 and 571 bHLHs were identified in rice, maize and wheat genomes respectively, and 1154 bHLH genes from the three species and Arabidopsis were classified into 36 subfamilies. Of the identified genes, 110 OsbHLHs, 188 ZmbHLHs and 209 TabHLHs with relatively high mRNA abundances were detected in one or more tissues during development, and some of them exhibited tissue-specific expression such as TabHLH454–459, ZmbHLH099–101 and OsbHLH037 in root, TabHLH559–562, − 046, − 047 and ZmbHLH010, − 072, − 226 in leaf, TabHLH216–221, − 333, − 335, − 340 and OsbHLH005, − 141 in inflorescence, TabHLH081, ZmbHLH139 and OsbHLH144 in seed. Forty five, twenty nine and thirty one differentially expressed bHLHs were respectively detected in wheat, maize and rice under drought stresses using RNA-seq technology. Among them, the expressions of TabHLH046, − 047, ZmbHLH097, − 098, OsbHLH006 and − 185 were strongly induced, whereas TabHLH303, − 562, ZmbHLH155, − 154, OsbHLH152 and − 113 showed significant down-regulation. Twenty two TabHLHs were induced after stripe rust infection at 24 h and nine of them were suppressed at 72 hpi, whereas 28 and 6 TabHLHs exhibited obviously down- and up-regulation after powdery mildew attack respectively. Forty one ZmbHLHs were differentially expressed in response to F. verticillioides infection. Twenty two co-expression modules were identified by the WGCNA, some of which were associated with particular tissue types. And GO enrichment analysis for the modules showed that some TabHLHs were involved in the control of several biological processes, such as tapetal PCD, lipid metabolism, iron absorption, stress responses and signal regulation.ConclusionThe present study identifies the bHLH family in rice, maize and wheat genomes, and detailedly discusses the evolutionary relationships, expression and function of bHLHs. This study provides some novel and detail information about bHLHs, and may facilitate understanding the molecular basis of the plant growth, development and stress physiology.

Highlights

  • The basic helix-loop-helix transcription factors play important roles in diverse cellular and molecular processes

  • Based on information of gene annotation, 176, 193 and 183 TabHLHs are non-randomly distributed in the A, B and D sub-genomes respectively, while 19 TabHLHs are located on scaffolds

  • Motifs 6 and 5 were detected in a great many proteins in subfamilies IIIf and III(d + e), such as TabHLH239, AtMYC2, TabHLH184 and ZmbHLH103, and we found they were significantly matched with an ACT domain that contributed to the recruitment of the C1 R2R3-MYB factor to the C1 binding sites located in the promoters of flavonoid biosynthetic genes [40]

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Summary

Introduction

The basic helix-loop-helix transcription factors play important roles in diverse cellular and molecular processes. The basic helix-loop-helix (bHLH) transcription factors constitute one of the largest transcription factor families in plants and are involved in a wide and diverse array of biological processes. Wei and Chen BMC Plant Biology (2018) 18:309 the expression of JA-responsive genes involved in salt stress tolerance in rice, such as OsHAK21 [14]. TabHLH1 can mediate tobacco adaptation to osmotic stress via ABA-dependent pathway [18], and improve tolerance to Pi and N deprivation through transcriptional regulation of phosphate transporter, nitrate transporter and antioxidant enzyme encoding genes [19]. Wheat bHLH060 overexpression negatively regulated plant resistance to Pseudomonas syringae through jasmonic acid (JA) and ethylene (ET) signaling in transgenic Arabidopsis [23]. Some functions of bHLHs have been characterized, the biological functions of most plant bHLHs remain unclear, especially in gramineous crops such as rice, maize and wheat

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