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作物学报 ›› 2009, Vol. 35 ›› Issue (6): 983-991.doi: 10.3724/SP.J.1006.2009.00983

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

玉米Gln1-4的gDNA序列、基因结构、保守功能域与等位变异

吴永升1,2，李新海1，郝转芳1，张世煌1，谢传晓1,*   

  1. 1中国农业科学院作物科学研究/国家农作物基因资源与基因改良生大科学工程，北京100081；2广西玉米研究所，广西南宁530227
  • 收稿日期:2008-10-30 修回日期:2009-03-23 出版日期:2009-06-12 网络出版日期:2009-04-16
  • 通讯作者: 谢传晓，E-mail:cxxie@caas.net.cn;Tel:010-82105853
  • 基金资助:

    本研究由国家高技术研究发展计划（863计划）项目（2006AA10Z191），国家自然科学基金项目（30871535），中央级公益性科研院所基本科研业务费专项资金（082060302-10）资助。

Genomic DNA Sequence,Gene Structure,Conserved Domains,and Natural Alleles of Gln1-4 Gene in Maize

WU Yong-Sheng12,LI Xin-Hai1,HAO Zhuan-Fang1,ZHANG Shi-Huang1,XIE Chuan-Xiao1*   

  1. 1Institute of Crop Sciences,Chinese Academy of Agricultural Sciences/Natiomal Key Facilities for Crop Gene Resource and Genetic Improvement,Beijing 100081,China;2Guangxi Maize Research Institute,Nanning 530227,China
  • Received:2008-10-30 Revised:2009-03-23 Published:2009-06-12 Published online:2009-04-16
  • Contact: XIE Chuan-Xiao，E-mail:cxxie@caas.net.cn;Tel:010-82105853

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被引次数

1

摘要：

本研究旨在分离玉米谷氨酰胺合成酶(GS)家族重要成员Gln1-4 gDNA序列全长，分析基因结构、保守功能域与自然等位变异，为氮利用效率功能位点关联性分析奠定基础。利用PCR步移(walking)方法分离Gln1-4基因区域基因组DNA序列，用生物信息学方法分析基因结构与保守功能域，测序与序列比对法分析重要区域自然等位变异。结果表明，分离得到自交系Mo17 Gln1-4区域gDNA 3 724 bp，起始密码子至终止密码子序列长2 858 bp，登录到GenBank (登录号为EU369651), 并注释。Gln1-4基因含10个外显子与9个内含子，18个剪接位点均为保守的5'供位GU与3'受位AG模式。编码的GS蛋白由356个氨基酸组成，分子量39.2 kD，等电点(pI)为5.202。氨基末端外显子2到外显子6为氨离子结合结构保守功能域；羧基末端外显子8与外显子9构成ATP酶活性保守功能域。Gln1-4与Gln1-3基因相比，在DNA序列、氨基酸序列、基因结构、保守功能域均很保守，氨基酸序列一致性达98.31%。52个玉米自交系的Gln1-4等位变异分析中，共鉴定出318个等位变异位点，其中242个SNP，45个Indels，占90%。该基因氮利用效率功能关联性分析区间应位于氨离子结合功能域与ATPase活性保守功能域中重要的变异位点，18个剪接位点。

关键词: 玉米, Glnl-4基因, 功能域, 自然等位变异, 氮利用效率

Abstract:

Maize (Zea mays L.) cultivars with improved nitrogen use efficiency would be beneficial for low-input production systems and for environment since it would reduce the surface water pollution and the nitrate leaching into underground water. Glutamine synthetase genes families are the core elements for nitrogen assimilation and metabolism in maize plants. The objectives of this study were to isolate the genomic DNA sequence of Gln1-4, which is one of the important members of glutamine synthetase gene family, to analyze the gene structure, conserved domains and natural allelic variations and so that was to found basis for association analysis of the functional sites related to nitrogen use efficiency in maize. PCR walking strategy was applied to isolate the gDNA sequence of Gln1-4 and its flanking sequence. The gene structure was analyzed by aligning gDNA sequence and its’ mature mRNA sequence. The conserved domains were obtained by searching Conserved Domain Database (CDD) at NCBI. The natural allelic variations were evaluated by resequencing and aligning DNA sequences among 52 inbreds. A total of 3 724 bp gDNA sequence of Gln1-4 of Mo17 was assembled. The full length of the coding region was 2 858 bp, which was comprised of ten exons separated by nine introns. All 18 splicing sites were the conserved sequence of GU at 5' donor sites and AG at 3' acceptor sites. The sequence has been submitted to GenBank (Accession No.: EU369651) and annotated in details. Gln1-4 encodes a GS protein with molecular weight of 39.2 kD, which was comprised of 356 amino acids. Its isoelectric point (pI) was 5.202. Conserved domain searching results showed that the region from exon 2 to exon 6 at amino-terminal was an ammonium ion binding domain, and exon 8 to exon 9 at carboxyl terminal consisted of an ATPase activity domain. As compared with Gln1-3, the DNA sequence, amino acid sequence, gene structure and conserved domains for Gln1-4 were highly conserved with a 98.31% identity of amino acid sequence. A total of 318 types of natural DNA variation at important and target region of Gln1-4 gene were identified among 52 maize inbred lines, of which 242 was SNPs and 45 was small indels, comprising 90% of the total allelic variations. The analysis of the functional sites gene associated with nitrogen use efficiency of Gln1-4 in maize should focus on binding and catalyzing domains and splicing sites.

Key words: Maize, Gln1-4, Conserved Functional domain, Natural allelic variation, Nitrogen use efficiency


[1] Cassman K G. Ecological intensification of cereal production systems: yield potential, soil quality, and precision agriculture. Proc Natl Acad Sci USA, 1999, 96: 5952-5959

[2] William R R, Gordon V J. Improving nitrogen use efficiency for cereal production. Agron J, 1999, 91: 357-363

[3] Zhang W-L(张维理), Wu S-X(武淑霞), Ji H-J(冀宏杰), Kolbe H. Estimation of agricultural non-point source pollution in China and the alleviating strategies: I. Estimation of agricultural non-point source pollution in China in early 21 century. Sci Agric Sin (中国农业科学), 2004, 37(7): 1008-1017 (in Chinese with English abstract)

[4] Sun Z-M(孙志梅), Wu Z-J(武志杰), Chen L-J(陈利军), Liu Y-G(刘永刚). Research advances in nitrogen fertilization and its environmental effects. Chin J Soil Sci (土壤通报), 2006, 37(4): 782-786(in Chinese with English abstract)

[5] Hirel B, Berlin P, Quillere I, Bourdoncle W, Attagnant C, Dellay C, Gouy A, Cadiou S, Retailliau C, Falque M, Gallais A. Towards a better understanding of the genetic and physiological basis for nitrogen use efficiency in Maize. Plant Physiol, 2001, 125: 1258-1270

[6] Gallais A, Hirel B. An approach of the genetics of nitrogen use efficiency in maize. J Exp Bot, 2004, 55: 295-306

[7] Coque M, Gallais A. Genomic regions involved in response to grain yield selection at high and low nitrogen fertilization in maize. Theor Appl Genet, 2006, 112: 1205-1220

[8] Li M G, Villemur R, Hussey P J, Silflow C D, Gantt J S, Snustad D P. Differential expression of six glutamine synthetase genes in Zea mays. Plant Mol Biol,1993, 23: 401-440

[9] Miflin B J, Habash D Z. The role of glutamine synthetase and glutamate dehydrogenase in nitrogen assimilation and possibilities for improvement in the nitrogen utilization of crops. J Exp Bot, 2002, 53: 979-987

[10] Gallais A, Coque M. Genetic variation and selection for nitrogen use efficiency in maize: A synthesis. Maydica, 2005, 50: 531-537

[11] Martin A, Lee J, Kichey T, Gerentes D, Zivy M, Tatout C, Dubois F, Balliau T, Valot B, Davanture M, Tercé-Laforgue T, Quilleré I, Coque M, Gallais A, Gonzalez-Moro M, Bethencourt L, Habash D Z, Lea P J, Charcosset A, Perez P, Murigneux A, Sakakibara H, Edwards K J, Hirel B. Two cytosolic glutamine synthetase isoforms of maize are specifically involved in the control of grain production. Plant Cell, 2006, 18: 3252-3274

[12] Wu Y-S(吴永升), Li X-H(李新海), Zhang Z(张征), Li M-S(李明顺), Hao Z-F(郝转芳), Zhang S-H(张世煌), Xie C-X(谢传晓).Genomic DNA sequence, gene structure, conserved domains, and natural alleles of gln1-3 gene in maize. Acta Agron Sin (作物学报), 2008, 34(7): 1114-1120 (in Chinese with English abstract)

[13] Saghai-Maroof M A, Soliman K, Jorgensen R A, Allard R W. Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA, 1984, 81: 8014-8018

[14] Jones D H, Winistorfer S C. Genome walking with 2 to 4 kb steps using panhandle PCR. PCR Methods Appl,1993, 2: 197-203

[15] Sambrook J, Fritsch E F, Maniatis T, eds. Huang P-T(黄培堂) trans. Molecular Cloning: A Laboratory Manual (分子克隆实验指南). Beijing: Science Press, 2002. pp 103-105 (in Chinese)

[16] Marchler-Bauer A, Anderson J B, Cherukuri P F, Deweese-Scott C, Geer L Y, Gwadz M, He S, Hurwitz D I, Jackson J D, Ke Z, Lanczycki C, Liebert C A, Liu C, Lu F, Marchler G H, Mullokandov M, Shoemaker B A, Simonyan V, Song J S, Thiessen P A, Yamashita R A, Yin J J, Zhang D, Bryant S H. CDD: a conserved domain database for protein classification. Nucl Acids Res, 2005, 33: 192-196

[17] Amanda C, Yang A P, Heather M, Rosalind C L, Nicola A. Ramsay. Identification of DNA sequences flanking T-DNA insertions by PCR-Walking. Plant Mol Biol Rep, 2001, 19: 321-327

[18] Peterman T K, Goodman H M. The glutamine synthetase gene family of Arabidopsis thaliana light-regulation and differential expression in leaves, roots and seeds. Mol Gen Genet, 1991, 230: 145-154

[19] Reddy A. Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu Rev Plant Biol, 2007, 58: 267-294

[20] Xie C X, Warburton M L, Li M S, Li X H, Xiao M J, Hao Z F, Zhao Q, Zhang S H. An analysis of population structure and linkage disequilibrium using multilocus data in 187 maize inbred lines. Mol Breed, 2008, 21: 407-418

[21] Thornsberry J M, Goodman M M, Doebley J, Kresovich S, Nielsen D, Buckler E S. Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet, 2001, 28: 286-289

[22] Jeppe R A, Tobias S, Albrecht E, M, Imad Z, Thomas L. Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.). Theor Appl Genet, 2005, 111: 206-217

[23] Camus-Kulandaivelu L, Veyrieras J B, Madur D, Combes V, Fourmann M, Barraud S, Dubreuil P, Gouesnard B, Manicacci D, Charcosset A. Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene. Genetics, 2006, 172: 2449-263

[24] Xie C-X(谢传晓), Wang Z-H(王振华), Yu L(於琍), Zhang W(张玮), Li M-S(李明顺), Li X-H(李新海), Cheng B-J(程备久), Zhang S-H(张世煌). Characterization of the sensitivity to photoperoid among 160 maize inbred lines. J Maize Sci (玉米科学), 2008, 16(3): 15-18 (in Chinese with English abstract)

[25] Carlos E H, Torbert R R, Bai L, Thomas P B, Catherine B K, Stephen G S, Ann E S, Ratnakar V, Mark W, Eleanore T W, Yan J B, Edward S B. Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science, 2008, 319: 330-333
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