Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat

The 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.
Nội dung trích xuất từ tài liệu:
Comparative functional genomics analysis of bHLH gene family in rice, maize and wheatWei and Chen BMC Plant Biology (2018) 18:309https://doi.org/10.1186/s12870-018-1529-5 RESEARCH ARTICLE Open AccessComparative functional genomics analysisof bHLH gene family in rice, maizeand wheatKaifa Wei1* and Huiqin Chen2 Abstract Background: The 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. Results: In 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. Conclusion: The 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. Keywords: bHLHs, Gramineous crops, Expression regulation, Growth and development, Stress responsesBackground homeostasis [4], root vascular cell proliferation [5], shootThe basic helix-loop-helix (bHLH) transcription factors branching [6], stomatal initiation [7], flowering time [8],constitute one of the largest transcription factor families pollen, gynoecium and fruit development [9, 10], andin plants and are involved in a wide and diverse array of grain yield [11]. Previous studies revealed that bHLHsbiological processes. A series of evidences showed that played very important roles in response of plants to abi-bHLHs participated in the regulation of plant growth otic stresses such as drought, salt and cold. AtbHLH068and development including morphogenesis [1–3], iron and OsbHLH148 overexpressing in transgenic Arabidop- sis and rice respectively conferred plant tolerance to* Correspondence: kaifa-wei@163.com drought stress via ABA- and JA-mediated signaling path-1 School of Biological Sciences and Biotechnology, Minnan Normal University,36 Xian-Qian-Zhi Street, Zhangzhou 363000, Fujian, China way [12, 13]. OsbHLH062, OsJAZ9 and OsNINJAFull list of author information is available at the end of the article formed a transcriptional regulation complex to fine tune © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits u ...