研究报告

高粱SBP-box基因家族全基因组鉴定及表达分析

展开
  • 1. 山西省农业科学院旱地农业研究中心,农业部黄土高原作物基因资源和种质创制重点实验室,太原030031;
    2. 山西省农业科学院高粱研究所,高粱遗传与种质创新山西省重点实验室,晋中 030600;
    3. 山西省农业科学院作物科学研究所,太原030031
常建忠,博士,助理研究员,研究方向:作物逆境分子生物学。E-mail: cjzyfx@163.com 闫凤霞,硕士,助理研究员,研究方向:高粱种质资源创新。E-mail: yfxcjz@126.com常建忠和闫凤霞为并列第一作者。

收稿日期: 2016-01-17

  修回日期: 2016-03-28

  网络出版日期: 2016-04-19

基金资助

现代农业产业技术体系建设专项(编号:CARS-06-01-01),山西省财政支农项目(编号:2014ZYFZ-09),山西省农业科学院重点项目(编号:YZD1401)和山西省农业科学院博士研究基金项目(编号:YBSJJ1407)资助

Genome-wide identification and expression analysis of SBP-box gene family in Sorghum bicolor L.

Expand
  • 1. Dryland Agriculture Research Center, Shanxi Academy of Agricultural Sciences/Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan 030031, China;
    2. Sorghum Institute of Shanxi Academy of Agricultural Sciences/Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Jinzhong 030600, China;
    3. Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan 030031, China

Received date: 2016-01-17

  Revised date: 2016-03-28

  Online published: 2016-04-19

Supported by

Supported by the Earmarked Fund for Modern Agro-industry Technology Research System (No; CARS-06-01-01), Financial Supporting Agriculture Project in Shanxi Province (No; 2014ZYFZ-09), Key Project of Shanxi Academy of Agricultural Science (No; YZD1401), and Doctoral Science Foundation of Shanxi Academy of Agricultural Science (No; YBSJJ1407)

摘要

SQUAMOSA PROMOTER BINDING PROTEIN box (SBP-box)基因家族编码一类绿色植物特有的转录因子,其功能涉及作物遗传改良的许多方面,如产量、株型、抗逆性等,具有重要的实际应用价值。本研究通过生物信息学方法从高粱(Sorghum bicolor L.)全基因组中鉴定出18个SBP-box基因,分布于9条染色体上,其中8个基因位于基因组重复区域。系统发育分析表明高粱SBP-box基因家族可分为6个亚家族,其中SbSBP12SbSBP3SbSBP15分别与玉米ZmLG1ZmTGA1ZmUB2/3直系同源。基于RNA-seq数据的表达分析发现高粱SBP-box基因在花序原基中表达量最高,SbSBP9SbSBP17为花序原基特异表达基因,SbSBP5SbSBP8SbSBP18等基因受外源ABA和PEG胁迫上调表达,表明SBP-box基因可能参与高粱对非生物逆境的响应。本研究为高粱SBP-box家族重要基因的克隆提供了参考,相关基因可作为高粱遗传改良的候选基因。

本文引用格式

常建忠, 闫凤霞, 乔麟轶, 郑军, 张福耀, 柳青山 . 高粱SBP-box基因家族全基因组鉴定及表达分析[J]. 遗传, 2016 , 38(6) : 569 -580 . DOI: 10.16288/j.yczz.16-008

Abstract

SQUAMOSA PROMOTER BINDING PROTEIN-box (SBP-box) family genes encoding plant-specific transcription factors are involved in many aspects of crop genetic improvement such as yield, plant-type and stress-resistance. The SBP-box gene family have important practical applications. In this study, 18 SBP-box genes were identified from the reference genome of sorghum (Sorghum bicolor L.) using bioinformatics. These genes distributed on nine chromosomes while eight of them located in the segmental duplication region. Phylogenetic reconstruction resulted in six subfamilies of SBP-box genes, among which SbSBP12, SbSBP3 and SbSBP15 are orthologous to ZmLG1, ZmTGA1 and ZmUB2/3 in corn, respectively. RNA-seq data analysis indicated that SbSBP-box genes show the highest expression level in primordial inflorescences. Moreover, SbSBP9 and SbSBP17 exhibited a tissue specific expression in primordial inflorescences. The expression levels of SbSBP5, SbSBP8 and SbSBP18 were increased in response to exogenous ABA and PEG,indicating that SbSBP-box genes are involved in the defense response against abiotic stresses in sorghum. This research provides references for cloning important genes in SbSBP-box gene family. Genes identified in this study could be considered as candidate genes for genetic improvement of sorghum.

参考文献

[1] Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, Gingeras TR. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell , 2004, 116(4): 499-509.
[2] Yang ZR, Wang XC, Li XM, Yang CD. Advance on the study of transcription factors in higher plants. Hereditas (Beijing) , 2004, 26(3): 403-408. 杨致荣, 王兴春, 李西明, 杨长登. 高等植物转录因子的研究进展. 遗传, 2004, 26(3): 403-408.
[3] Klein J, Saedler H, Huijser P. A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA . Mol Gen Genet , 1996, 250(1): 7-16.
[4] 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(1): 49-63.
[5] Birkenbihl RP, 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(3): 585-596.
[6] Cardon GH, 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(2): 367-377.
[7] Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M. OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet , 2010, 42(6): 545-549.
[8] Hultquist JF, Dorweiler JE. Feminized tassels of maize mop1 and ts1 mutants exhibit altered levels of miR156 and specific SBP-box genes. Planta , 2008, 229(1): 99-113.
[9] Liu X, Zhang B, Mao XG, Li A, Sun MR, Jing RL. Cloning of tae-MIR156 precursor gene and sequence polymorphisms of tae-miR156 targeted TaSPL17 . Hereditas (Beijing) , 2014, 36(6): 592-602. 刘霞, 张斌, 毛新国, 李昂, 孙美荣, 景蕊莲. 小麦tae-MIR156前体基因的克隆及其靶基因 TaSPL17 多态性分析. 遗传, 2014, 36(6): 592-602.
[10] Salinas M, Xing SP, Höhmann S, Berndtgen R, Huijser P. Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato. Planta , 2012, 235(6): 1171-1184.
[11] Nodine MD, Bartel DP. MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. Genes Dev , 2010, 24(23): 2678-2692.
[12] Usami T, Horiguchi G, Yano S, Tsukaya H. The more and smaller cells mutants of Arabidopsis thaliana identify novel roles for SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes in the control of heteroblasty. Development , 2009, 136(6): 955-964.
[13] Moreno MA, Harper LC, Krueger RW, Dellaporta SL, Freeling M. Liguleless1 encodes a nuclear-localized protein required for induction of ligules and auricles during maize leaf organogenesis. Genes Dev , 1997, 11(5): 616-628.
[14] Kawakatsu T, Itoh J, Miyoshi K, Kurata N, Alvarez N, Veit B, Nagato Y. PLASTOCHRON2 regulates leaf initiation and maturation in rice. Plant Cell , 2006, 18(3): 612-625.
[15] Wahl V, Ponnu J, Schlereth A, Arrivault S, Langenecker T, Franke A, Feil R, Lunn JE, Stitt M, Schmid M. Regulation of flowering by trehalose-6-phosphate signaling in Arabidopsis thaliana . Science , 2013, 339(6120): 704-707.
[16] Huijser P, Schmid M. The control of developmental phase transitions in plants. Development , 2011, 138(19): 4117-4129.
[17] Xing SP, Salinas M, Garcia-Molina A, Höhmann S, Berndtgen R, Huijser P. SPL8 and miR156-targeted SPL genes redundantly regulate Arabidopsis gynoecium differential patterning. Plant J , 2013, 75(4): 566-577.
[18] Gou JY, Felippes FF, Liu CJ, Weigel D
文章导航

/