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Genome-wide analysis of the AP2/ERF gene family in maize waterlogging stress response

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Abstract

Members of the APETALA2/ethylene response factor (AP2/ERF) transcription factor superfamily are widely present in plants and play important roles in the plant cell cycle, growth and development, as well as the response to biotic and abiotic stresses. The maize genome project has been completed; therefore, it is possible to identify all of the AP2/ERF genes in the maize genome. In this study, 184 AP2/ERF genes were identified by an in silico cloning method, and were compared with AP2/ERF genes from Arabidopsis, rice, grape and poplar. The 184 AP2/ERF maize genes were classified into four subfamilies: DREB (51), ERF (107), AP2 (22) and RAV (3), as well as one soloist. The amino acid sequence composition, physical and chemical characteristics, phylogenetic trees, conserved domain sequences, functional domains, and chromosomal location of the genes were predicted and analyzed. The 184 AP2/ERF genes are distributed on maize chromosomes 1–10 (31, 21, 13, 19, 22, 18, 21, 16, 11 and 12 genes, respectively). Under 0, 1, 2, 4 h waterlogging stress, the expression of 184 AP2/ERF genes in root of Hz32 inbred line (tolerance to waterlogging) were performed using RNA-sequence, and the result showed that 38 genes were responsive to waterlogging stress. This study lays the foundation for subsequent cloning and investigation of the function of the AP2/ERF genes responding to waterlogging stress in maize.

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References

  • Aharoni A, Dixit S, Jetter R, Thoenes E, Arkel GV, Pereira A (2004) The SHINE of AP2 domain transcription factors activates wax biosynthesis, alters cuticle properties, and confers drought tolerance when overexpressed in Arabidopsis. Plant Cell 16:2463–2480

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34:369–373

    Article  Google Scholar 

  • Boyer JS (1982) Plant productivity and environment. Science 218:443–448

    Article  CAS  PubMed  Google Scholar 

  • Bray EA, Bailey-Serres J, Weretilnyk E (2000) Response to abiotic stresses. In: Gruissem W, Buchannan B, Jones R (eds) Biochemistry and molecular biology of plants. American Society of Plant Physiologists, Rochville, pp 1158–1249

    Google Scholar 

  • Broun P, Poindexter P, Osborne E, Jiang CZ, Riechmann JL (2004) WIN1, a transcriptional activator of epidermal wax accumulation in Arabidopsis. Proc Nati Acad Sci USA 101:4706–4711

    Article  CAS  Google Scholar 

  • Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the clustal series of programs. Nucleic Acids Res 31:3497–3500

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • DMR (2001). Research achievements. In: Azad CS (ed) Proceedings of 49th annual maize workshop. Directorate of maize research (DMR), University of Agriculture and Technology, Kanpur (UP)

  • Du DL, Hao RJ, Cheng TR, Pan HT, Yang WR, Wang J, Zhang QX (2012) Genome-wide analysis of the AP2/ERF gene family in prunus mume. Plant Mol Biol Rep. doi:10.1007/s11105-012-0531-6

    Google Scholar 

  • Fukao T, Xu KN, Ronald PC, Bailey-Serres J (2006) A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell 18:2021–2034

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Guo A, He K, Liu D, Bai S, Gu X (2005) DATF: a database of Arabidopsis transcription factors. Bioinformatics 21:2568–2569

    Article  CAS  PubMed  Google Scholar 

  • Hattori Y, Nagai K, Furukawa S, Song XJ, Kawano R, Sakakibara H, Wu J, Matsumoto T, Yoshimura A, Kitano H, Matsuoka M, Mori H, Ashikari M (2009) The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 460:1026–1031

    Article  CAS  PubMed  Google Scholar 

  • Hinz M, Wilson IW, Yang J, Buerstenbinder K, Llewellyn D, Dennis ES, Sauter M, Dolferus R (2010) Arabidopsis RAP2.2: an ethylene response transcription factor that is important for hypoxia survival. Plant Physiol 153:757–772

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Jofuku KD, den Boer BG, Van Montagu M, Okamuro JK (1994) Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 6:1211–1225

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kizis D, Lumbreras V, Pagès M (2001) Role of AP2/EREBP transcription factors in gene regulation during abiotic stress. FEBS Lett 498:187–189

    Article  CAS  PubMed  Google Scholar 

  • Licausi F, Dongen JTV, Giuntoli B, Novi G, Santaniello A, Geigenberger P, Perata P (2010) HER1 and HER2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana. Plant J 62:302–315

    Article  CAS  PubMed  Google Scholar 

  • Licausi F, Kosmacz M, Weits DA, Giuntoli B, Giorgi FM, Voesenek LACJ, Perata P, Dongen TV (2011) Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization. Nature 479:419–422

    Article  CAS  PubMed  Google Scholar 

  • Meng XP, Li FG, Liu CL, Zhang CJ, Wu ZX, Chen YJ (2010) Isolation and characterization of an ERF transcription factor gene from cotton (Gossypium barbadense L.). Plant Mol Biol Rep 28:176–183

    Article  CAS  Google Scholar 

  • Nakano T, Suzuki K, Fujimura T, Shinshi H (2006) Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol 140:411–432

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ohme-Takagi M, Shinshi H (1995) Ethylene inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7(2):173–182

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Rathore TR, Warsi MZK, Zaidi PH, Singh NN (1997) Waterlogging problem for maize production in Asian region. TAMNET News Lett 4:13–14

    Google Scholar 

  • Riaño-Pachón DM, Ruzicic S, Dreyer I, Mueller RB (2007) PlnTFDB: an integrative plant transcription factor database. MBC Bioinform 8:42

    Google Scholar 

  • Sakuma Y, Liu Q, Dubouzet JG, Abe H, Shinozaki K, Yamaguchi-Shinozaki K (2002) DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration and cold-inducible gene expression. Biochem Biophys Res Cummun 290:998–1009

    Article  CAS  Google Scholar 

  • Seki M, Kamei A, Yamaguchi-Shinozaki K, Shinozaki K (2003) Molecular responses to drought, salinity and frost: common and different paths for plant protection. Curr Opin Biotechnol 14(2):194–199

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  CAS  PubMed  Google Scholar 

  • Xu KN, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708

    Article  CAS  PubMed  Google Scholar 

  • Zhang JZ, Creelman RA, Zhu JK (2004) From laboratory to field: using information from Arabidopsis to engineer salt, cold, and drought tolerance in crops. Plant Physiol 135:615–621

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zhuang J, Cai B, Peng RH, Zhu B, Jin XF, Xue Y, Gao F, Fu XY, Tian YS, Zhao W, Qiao YS, Zhang Z, Xiong AS, Yao QH (2008) Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa. Biochem Biophys Res Commun 371:468–474

    Article  CAS  PubMed  Google Scholar 

  • Zhuang J, Cai B, Peng RH, Zhu B, Jin XF, Xue Y, Gao F, Fu XF, Tian YS, Zhao W, Qiao YS, Zhang Z, Xiong AS, Yao QH (2009) Genome-wide analysis of the AP2/ERF gene family in Vitis vinifera. Sci Hortic 123:73–81

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The work was supported by National Natural Science Foundation (31271741), the Hubei Province Natural Science Foundation (2011CDB006 and 2012FFA051), Youth Foundation of Hubei Province Department of Education (Q20111313), Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization (2011BLKF242), and Hubei Provincial Key Discipline, the Crop Science in Yangtze University.

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Correspondence to Hewei Du or Shuiyuan Cheng.

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Hewei Du and Min Huang have contributed equally to this study.

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Du, H., Huang, M., Zhang, Z. et al. Genome-wide analysis of the AP2/ERF gene family in maize waterlogging stress response. Euphytica 198, 115–126 (2014). https://doi.org/10.1007/s10681-014-1088-2

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