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Acta Agron Sin ›› 2016, Vol. 42 ›› Issue (02): 201-211.doi: 10.3724/SP.J.1006.2016.00201

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-wide Identification and Function Analysis of SBP Gene Family in Maize

PENG Hua1,**,HE Xiu-Jing2,**,GAO Jian4,LUO Mao3,PAN Guang-Tang2,*,ZHANG Zhi-Ming2,*   

  1. 1 SiChuan Tourism College, Chengdu 610100, China; Maize Research Institute of Sichuan Agricultural University, Wenjiang 611130, China; 3 Research Center for Drug Discovery of Luzhou Medical College, Luzhou 646000, China, 4 Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, and Key Laboratory of Tumor Immunopathology, Ministry of Education, Chongqing 400038, China
  • Received:2015-05-12 Revised:2015-11-20 Online:2016-02-12 Published:2015-12-07
  • Contact: 潘光堂, 张志明, E-mail: panlab605@gmail.com, Tel: 86-28-86290917
  • Supported by:

    This study was supported by the National High Technology Research and Development Program of China (863 Program) (2012AA10A307) and Youth Science Fund Project from Technological Office of Sichuan Province (2015JQO021).

Abstract:

SBP gene family, as a plant special transcription factors is involved in plant growth and development, as well as many physiological and biochemical processes. Recently, SBP transcription factor family has been identified in model plants, such as Arabidopsis and Oryza sativa; however, systematic analysis of SBP transcription factor family in maize (Zea mays L.) is scarcely. In this study, based on homology alignment technology, we aligned all known SBP TFs from Arabidopsis and Oryza sativa with those from maize genome sequence to mine novel SBP TFs in maize. A total of 37 SBP TFs distributed in eight chromosomes were identified. Phylogenetic analysis indicated that SBP transcription factor genes have stronger homology, especially between Zea mays and Oryza sativa. Moreover, Promoters-cis Elements analysis of those SBP TFs demonstrated that they might be involved in plant growth and development, morphogenesis, adversity response, the development of flower organs and photosynthesis. It is probable that SBP TFs regulate plant growth and development through the multiple hormone of signaling transduction pathway, such as gibberellin, auxin, abscisic acid, and salicylic acid.

Key words: Maize, SBP TFs gene family, Bioinformatics

[1] Huijser P, Klein J, Lönnig W E, Meijer H, Saedler H, Sommer H. Bracteomania, an inflorescence anomaly, is caused by the loss of function of the MADS-box gene squamosa in Antirrhinum majus. EMBO J, 1992, 11: 1239–1249



[2] Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Nunokawa E, Ishizuka Y, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S. A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. J Mol Biol, 2004, 337: 49–63



[3] Birkenbihl R P, Jach G, Saedler H, Huijser P. Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains. J Mol Biol, 2005, 352: 585–596



[4] Schmid M, Uhlenhaut N H, Godard F, Demar M, Bressan R, Weigel D, Lohmann J U. Dissection of floral induction pathways using global expression analysis. Development, 2003, 130: 6001–6012



[5] Cardon G H, Höhmann S, Nettesheim K, Saedler H, Huijser P. Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition. Plant J, 1997, 12: 367–377



[6] Yang Z, Wang X, Gu S, Hu Z, Xu H, Xu C. Comparative study of SBP-box gene family in Arabidopsis and rice. Gene, 2008, 407: 1–11



[7] Manning K, Tör M, Poole M, Hong Y, Thompson A J, King G J, Giovannoni J J, Seymour G B. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet, 2006, 38: 948–952



[8] Liu H, Yang X, Liao X, Zuo T, Qin C, Cao S, Dong L, Zhou H, Zhang Y, Liu S, Shen Y, Lin H, Lübberstedt T, Zhang Z, Pan G. Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development. Genomics, 2015, 106: 52–60



[9] Moreno M A, Harper L C, Krueger R W, Dellaporta S L, Freeling M. liguleless1 encodes a nuclear-localized protein required for induction of ligules and auricles during maize leaf organogenesis. Genes Dev, 1997, 11: 616–628



[10] Chuck G, Whipple C, Jackson D, Hake S. The maize SBP-box transcription factor encoded by tasselsheath4 regulates bract development and the establishment of meristem boundaries. Development, 2010, 137: 1243–1250



[11] Eveland A L, Goldshmidt A, Pautler M, Morohashi K, Liseron-Monfils C, Lewis M W, Kumari S, Hiraga S, Yang F, Unger-Wallace E, Olson A, Hake S, Vollbrecht E, Grotewold E, Ware D, Jackson D. Regulatory modules controlling maize inflorescence architecture. Genome Res, 2014, 24: 431–443



[12] Lännenpää M, Jänönen I, Hölttä-Vuori M, Gardemeister M, Porali I, Sopanen T. A new SBP-box gene BpSPL1 in silver birch (Betula pendula). Physiol Plant, 2004, 120: 491–500



[13] Chuck G S, Brown P J, Meeley R, Hake S. Maize SBP-box transcription factors unbranched2 and unbranched3 affect yield traits by regulating the rate of lateral primordia initiation. Proc Natl Acad Sci USA, 2014, 111: 18775–18780



[14] Chuck G, Cigan A M, Saeteurn K, Hake S. The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA. Nat Genet, 2007, 39: 544–549



[15] 曹雪, 上官凌飞, 于华平, 杨光等, 王晨, 谭洪花, 房经贵. 葡萄SBP基因家族生物信息学分析. 基因组学与应用生物学, 2010, 29: 791–798



Cao X, Shang-Guan L F, Yu H P, Yang G, Wang C, Tan H H, Fang J G. Bioinformatics analysis of the SBP gene family in grapevine. Genomics Appl Biol, 2010, 29: 791–798 (in Chinese with English abstract)



[16] 刘更森, 慕茜, 戴洪义, 上官凌飞, 张玉刚. 苹果SBP基因家族生物信息学分析. 江西农业学报, 2011, 23(12): 23–27



Liu G S, Mu Q, Dai H Y, Shang-Guan L F, Zhang Y G. Bioinformatics analysis of SBP gene family in apple. Acta Agric Jiangxi, 2011, 23(12): 23–27 (in Chinese with English abstract)



[17] 朱命喜, 刘洋, 吴琼, 刘春燕, 徐晶, 陈庆山, 胡国华. 大豆SBP转录因子家族的预测分析. 大豆科学, 2011, 30: 177–183



Zhu M X, Liu Y, Wu Q, Liu C Y, Xu J, Chen Q S, Hu G H. Forecasting analysis of SBP transcription factor families in soybean. Soybean Sci, 2011, 30: 177–183 (in Chinese with English abstract)



[18] 葛安静, 张春华, 董清华, 赵密珍, 宋长年, 张希. 草莓SBP基因家族生物信息学初步分析. 中国农学通报, 2012, 28(13): 215–220



Ge A J, Zhang C H, Dong Q H, Zhao M Z, Song C N, Zhang X. Primary bioinformatics analysis of the SBP gene family in strawberry. Chin Agric Sci Bull, 2012, 28(13): 215–220 (in Chinese with English abstract)



[19] 万红建, 袁伟, 俞锞, 刘云飞, 李志邈, 叶青静, 王荣青, 阮美颖, 周国治, 姚祝平, 杨悦俭. 番茄SBP基因家族的全基因组鉴定、结构特征及表达分析. 分子植物育种, 2013, 11: 299–306



Wan H J, Yuan W, Yu K, Liu Y F, Li Z M, Ye Q J, Wang R Q, Ruan M Y, Zhou G Z, Yao Z P, Yang Y J. Genome-wide identification, structure characterization and expression analysis of SBP gene family in tomato. Mol Plant Breed, 2013, 11: 299–306 (in Chinese with English abstract)



[20] Wang L, Cao C, Ma Q, Zeng Q, Wang H, Cheng Z, Zhu G, Qi J, Ma H, Nian H, Wang Y. RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications. BMC Plant Biol, 2014, 14: 169



[21] Huang L, Zhao X, Yu Q, Cui W Z, Liu Q X. Evidence for the coevolution of axon guidance molecule Netrin and its receptor Frazzled. Gene, 2014, 544: 25–31



[22] Li P S, Yu T F, He G H, Chen M, Zhou Y B, Chai S C, Xu Z S, Ma Y Z. Guan-Hua HeGenome-wide analysis of the Hsf family in soybean and functional identification of GmHsf-34 involvement in drought and heat stresses. BMC Genomics, 2014, 15: 1009



[23] Haag J R, Brower-Toland B, Krieger E K, Sidorenko L, Nicora C D, Norbeck A D, Irsigler A, LaRue H, Brzeski J, McGinnis K, Ivashuta S, Pasa-Tolic L, Chandler V L, Pikaard C S. Functional diversification of maize RNA Polymerase IV and V subtypes via alternative catalytic subunits. Cell Rep, 2014, 9: 378–390



[24] Chen X, Zhang Z, Liu D, Zhang K, Li A, Mao L. SQUAMOSA promoter-binding protein-like transcription factors: Star players for plant growth and development. J Integr Plant Biol, 2010, 52: 946–951



[25] Martin R C, Asahina, M, Liu P P, Kristof J R, Coppersmith J L, Pluskota W E, Bassel G W, Goloviznina N A, Nguyen T T, Pupel P, Nonogaki H. The microRNA156 and microRNA172 gene regulation cascades at post-germinative stages in Arabidopsis. Seed Sci Res, 2010, 20: 79–87

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