大豆全基因组分枝相关基因发掘及与QTL共定位

doi:10.3724/SP.J.1005.2013.00793

遗传 ›› 2013, Vol. 35 ›› Issue (6): 793-804.doi: 10.3724/SP.J.1005.2013.00793

大豆全基因组分枝相关基因发掘及与QTL共定位

谭冰^1,2, 郭勇², 邱丽娟²

1. 东北农业大学大豆研究所, 哈尔滨150030 2. 中国农业科学院作物科学研究所, 国家农作物基因资源与遗传改良重大科学工程, 北京100081

收稿日期:2012-11-14 修回日期:2012-12-17 出版日期:2013-06-20 发布日期:2013-06-25
通讯作者: 邱丽娟 E-mail:qiulijuan@caas.cn
基金资助:
国家高技术研究发展计划(863计划)项目(编号：2012AA101106)和国家自然科学基金项目(编号：30490251)资助

Whole genome discovery of genes related to branching and co-localization with QTLs in soybean

TAN Bing^1,2, GUO Yong², QIU Li-Juan²

1. Soybean Research Institute, Northeast Agricultural University, Harbin 150030, China 2. The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China

Received:2012-11-14 Revised:2012-12-17 Online:2013-06-20 Published:2013-06-25

摘要/Abstract

摘要： 大豆(Glycine max)分枝在个体和群体水平上均与大豆产量关系密切, 因此大豆分枝相关基因的发掘及利用对大豆高产分子育种具有重要意义。文章通过GO(Gene ontology)分类和文献检索共获得植物分枝发育相关基因183个。基于序列相似和结构域相同的原则, 从大豆基因组中发掘出大豆分枝相关的候选基因406个。通过收集已发表的大豆分枝相关QTL, 利用BioMercator2.1软件, 将符合映射条件的35个QTL映射到公共图谱的12个染色体。通过共定位分析发现, 在20个分枝相关的QTL区间内存在大豆分枝相关候选基因57个。本文发掘的分枝发育相关基因信息为大豆分枝相关QTL的精细定位和克隆以及大豆分枝发育的分子生物学基础研究提供了参考。

关键词: 共定位, 大豆, 分枝, 基因, QTL

Abstract: Branch number of soybean is one of agronomic traits that closely related with yield in both individual and population levels; therefore, discovering genes related to branching is important for molecular breeding in soybean. In this study, 183 genes related to plant branch development had been collected through GO classification and literatures. Based on the principle of similar sequences and conserved domains, 406 genes possibly related to branching had been identified at the whole genome level in soybean. On the other hand, integration of published QTLs related to branching was carried out using BioMercator2.1, and a total of 35 QTLs was located on 12 chromosomes. Co-localization analysis of QTLs and genes related to branching suggested that 57 genes were located in 20 intergrated QTL regions. These results provided useful in-formation for fine mapping of QTLs related to branching and molecular biology study of branch development in soybean.

Key words: soybean, branches, genes, QTL, co-localization

谭冰郭勇邱丽娟. 大豆全基因组分枝相关基因发掘及与QTL共定位[J]. 遗传, 2013, 35(6): 793-804.

TAN Bing GUO Yong QIU Li-Juan. Whole genome discovery of genes related to branching and co-localization with QTLs in soybean[J]. HEREDITAS, 2013, 35(6): 793-804.

参考文献

[1] 朱洪德, 朱桂英. 大豆超高产及品质改良理论与实践研究进展. 中国农学通报, 2005, 21(12): 154- 158.
[2] 胡珀, 韩天富. 植物茎秆性状形成与发育的分子基础. 植物学通报, 2008, 25(1): 1-13.
[3] 苗以农. 大豆高产潜力限制因素分析及高产类型设想. 大豆通报, 1994, (1): 23-24.
[4] 梁振富, 赵爱莉, 王大秋, 孟庆福, 孙淑贤. 大豆特异高产株型的构思. 大豆通报, 1993, (2): 33- 34.
[5] 张学英, 侯雪琪, 周淑琴, 赵九州, 陈洁敏, 宋力平. 浅谈大豆理想株型育种. 大豆通报, 1994, (4): 15-l6.
[6] 董钻, 张仁双. 大豆特异高产株型材料创新的思路和实践. 大豆通报, 1993, (1): 11-12.
[7] 段国占, 薛培明, 任建军, 马向利, 陈伟伟. 黄淮中南部夏大豆新品种选育技术指标量化分析. 大豆通报, 2007, (5): 35-37.
[8] 冷建田, 陈应志, 王英, 吴存祥. 中国不同地区大豆育成品系的特点分析及品种选育方向的探讨. 大豆科学, 2007, 26(3): 293-299, 304.
[9] 何冉, 关荣霞, 刘章雄, 朱晓丽, 常汝镇, 邱丽娟. 用分离群体中的残余杂合系定位大豆C1连锁群的分枝数qBN-c1-1位点. 中国农业科学, 2009, 42(4): 1152-1157.
[10] 关荣霞. 大豆重要农艺性状的QTL定位及中国大豆与日本大豆的遗传多样性分析[学位论文]. 北京: 中国农业科学院, 2004.
[11] 宋显君. 基于SSR标记的大豆遗传图谱构建与重要农艺性状QTL定位[学位论文]. 沈阳: 沈阳农业大学, 2007.
[12] 周蓉, 王贤智, 陈海峰, 张晓娟, 单志慧, 吴学军, 蔡淑平, 邱德珍, 周新安, 吴江生. 大豆倒伏性及其相关性状的QTL分析. 作物学报, 2009, 35(1): 57-65.
[13] Schmutz J, Cannon SB, Schlueter J, Ma JX, Mitros T, Nelson W, Hyten DL, Song QJ, Thelen JJ, Cheng JL, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhat-tacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu SQ, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du JC, Tian ZX, Zhu LC, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA. Ge-nome sequence of the palaeopolyploid soybean. Nature, 2010, 463(7278): 178-183.
[14] Schumacher K, Schmitt T, Rossberg M, Schmitz G, Theres K. The Lateral suppressor (Ls) gene of tomato encodes a new member of the VHIID protein family. Proc Natl Acad Sci USA, 1999, 96(1): 290-295.
[15] Li XY, Qian Q, Fu ZM, Wang YH, Xiong GS, Zeng DL, Wang XQ, Liu XF, Teng S, Hiroshi F, Yuan M, Luo D, Han B, Li JY. Control of tillering in rice. Nature, 2003, 422(6932): 618-621.
[16] Greb T, Clarenz O, Schäfer E, Müller D, Herrero R, Schmitz G, Theres K. Molecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation. Genes Dev, 2003, 17(9): 1175-1187.
[17] 贺超英, 张志永, 陈受宜. 大豆中NBS类抗病基因同源序列的分离与鉴定. 科学通报, 2001, 46(12): 1017-1021.
[18] 李春来, 张怀渝. 植物抗病基因同源序列(RGA)研究进展. 分子植物育种, 2004, 2(6): 853-860.
[19] 李亚栋, 张芊, 孙学辉, 路铁刚. 植物分枝发育的调控机制. 中国农业科技导报, 2009, 11(4): 1- 9.
[20] Komatsu K, Maekawa M, Ujiie S, Satake Y, Furutani I, Okamoto H, Shimamoto K, Kyozuka J. LAX and SPA: Major regulators of shoot branching in rice. Proc Natl Acad Sci USA, 2003, 100(20): 11765- 11770.
[21] Doebley J, Stec A, Hubbard L. The evolution of apical dominance in maize. Nature, 1997, 386 (6624): 485-488.
[22] Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight S S, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R, Gene Ontology Consortiun. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res, 2004, 32(S1): D258-261.
[23] Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB. A new integrated genetic linkage map of the soybean. Theor Appl Genet, 2004, 109(1): 122-128.
[24] Weir I, Lu JP, Cook H, Causier B, Schwarz-Sommer Z, Davies B. CUPULIFORMIS establishes lateral organ boundaries in Antirrhinum. Development, 2004, 131(4): 915-922.
[25] Müller D, Schmitz G, Theres K. Blind homologous R2R3 Myb Genes control the pattern of lateral meristem initiation in Arabidopsis. Plant Cell, 2006, 18(3): 586-597.
[26] Schmitz G, Tillmann E, Carriero F, Fiore C, Cellini F, Theres K. The tomato Blind gene encodes a MYB transcription factor that controls the formation of lateral meristems. Proc Natl Acad Sci USA, 2002, 99(2): 1064-1069.
[27] Gallavotti A, Zhao Q, Kyozuka J, Meeley RB, Ritter MK, Doebley JF, PèME, Schmidt RJ. The role of barren stalk l in the architecture of maize. Nature, 2004, 432(7017): 630-635.
[28] Emery JF, Floyd Sk, Alvanz J, Eshed Y, Hawker NP, Iz-haki A, Baum SF, Bowman JL. Radial patterning of Ar-abidopsis shoots by class Ⅲ HD-ZIP and KANADI genes. Curr Biol, 2003, 13(20): 1768-1774.
[29] Long JA, Moan EI, Medford JI, Barton MK. A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis. Nature, 1996, 379(6560): 66-69.
[30] Sentoku N, Sato Y, Matsuoka M. Overexpression of rice OSH genes induces ectopic shoots on leaf sheaths of transgenic rice plants. Dev Biol, 2000, 220(2): 358-364.
[31] Smith LG, Greene B, Veit B, Hake S. A dominant mutation in the maize homeobox gene, Knotted -1, causes its ectopic expression in leaf cells with altered fates. Development, 1992, 116(1): 21- 30.
[32] Mayer KF, Schoof H, Haecker A, Lenhard M, Jürgens G, Laux T. Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem. Cell, 1998, 95(6): 805-815.
[33] Trotochaud AE, Jeong S, Clark SE. CLAVATA3, a mul-timeric ligand for the CLAVATA1 receptor- kinase. Science, 2000, 289(5479): 613-617.
[34] Stirnberg P, van De Sande K, Leyser HM. MAX1 and MAX2 control shoot lateral branching in Arabidopsis. Development, 2002, 129(5): 1131-1141.
[35] Beveridge CA, Murfet IC, Kerhoas L, Sotta B, Miginiac E, Rameau C. The shoot controls zeatin riboside export from pea roots. Evidence from the branching mutant rms4. Plant J, 1997, 11(2): 339- 345.
[36] Booker J, Auldridge M, Wills S, McCarty D, Klee H, Leyser O. MAX3/CCD7 is a carotenoid cleavage dioxygenase required for the synthesis of a novel plant signaling mol-ecule. Curr Biol, 2004, 14(14): 1232-1238.
[37] Morris SE, Turnbull CG, Murfet IC, Beveridge CA. Muta-tional analysis of branching in pea. Evidence that Rms1 and Rms5 regulate the same novel signal. Plant Physiol, 2001, 126(3): 1205- 1213.
[38] Zou JH, Zhang SY, Zhang WP, Li G, Chen ZX, Zhai WX, Zhao XF, Pan XB, Xie Q, Zhu LH. The rice HIGH- TILLERING DWARF1 encoding an ortholog of Arabidopsis MAX3 is required for negative regulation of the out-growth of axillary buds. Plant J, 2006, 48(5): 687-698.
[39] Sorefan K, Booker J, Haurogné K, Goussot M, Bainbridge K, Foo E, Chatfield S, Ward S, Beveridge C, Rameau C, Leyser O. MAX4 and RMS1 are orthologous dioxygenase- like genes that regulate shoot branching in Arabidopsis and pea. Genes Dev, 2003, 17(12): 1469-1474.
[40] Foo E, Turnbull CG, Beveridge CA. Long-distance sig-naling and the control of branching in the rms1 mutant of pea. Plant Physiol, 2001, 126(1): 203-209.
[41] Arite T, Iwata H, Ohshima K, Maekawa M, Nakajima M, Kojima M, Sakakibara H, Kyozuka J. DWARF10, an RMS1/MAX4/DAD1 ortholog, controls lateral bud out-growth in rice. Plant J, 2007, 51(6): 1019-1029.
[42] Booker J, Sieberer T, Wright W, Williamson L, Willett B, Stirnberg P, Turnbull C, Srinivasan M, Goddard P, Leyser O. MAX1 encodes a cytochrome P450 family member that acts downstream of MAX3/4 to produce a carotenoid- de-rived branch-inhibiting hormone. Dev Cell, 2005, 8(3): 443-449.
[43] Finlayson SA. Arabidopsis Teosinte Branched1-like 1 regulates axillary bud outgrowth and is homologous to monocot Teosinte Branched1. Plant Cell Physiol, 2007, 48(5): 667-677.
[44] Takeda T, Suwa Y, Suzuki M, Kitano H, Ueguchi-Tanaka M, Ashikari M, Matsuoka M, Ueguchi C. The OsTB1 gene negatively regulates lateral branching in rice. Plant J, 2003, 33(3): 513-520.
[45] Jin J, Huang W, Gao JP, Jun Y, Shi M, Zhu MZ, Luo D, Lin HX. Genetic control of rice plant architecture under domestication. Nat Genet, 2008, 40(11): 1365-1369.
[46] 王珍. 大豆SSR遗传图谱构建及重要农艺性状QTL分析[学位论文]. 南宁: 广西大学, 2004.
[47] 朱晓丽. 大豆遗传图谱构建及在两个群体重要农艺性状的QTL定位[学位论文]. 哈尔滨: 东北农业大学, 2006.
[48] 杨竹丽, 李贵全. 晋大52×晋大57 RIL群体重要农艺性状的QTL定位. 华北农学报, 2010, 25(2): 88-92.
[49] 陈庆山, 张忠臣, 刘春燕, 辛大伟, 单大鹏, 邱红梅, 单彩云. 大豆主要农艺性状的QTL分析. 中国农业科学, 2007, 40(1): 41-47.
[50] 程立国. 大豆遗传图谱构建和重要性状的QTL定位[学位论文]. 南京: 南京农业大学, 2008.
[51] 王志贤. 大豆产量相关性状的遗传与稳定性分析及QTL定位研究[学位论文]. 北京: 中国农业科学院, 2008.
[52] 黄中文, 赵团结, 喻德跃, 陈受宜, 盖钧镒. 大豆产量有关性状QTL的检测. 中国农业科学, 2009, 42 (12): 4155-4165.
[53] 丁卉. 利用SSR标记研究大豆对胞囊线虫抗性和主要农艺性状的自然选择效应[学位论文]. 南京: 南京农业大学, 2009.
[54] Sayama T, Hwang TY, Yamazaki H, Yamaguchi N, Komatsu K, Takahashi M, Suzuki C, Miyoshi T, Tanaka Y, Xia ZJ, Tsubokura Y, Watanabe S, Harada K, Funatsuki H, Ishimoto M. Mapping and comparison of quantitative trait loci for soybean branching phenotype in two locations. Breed Sci, 2010, 60(4): 380-389.
[55] 袁道华. 大豆抗胞囊线虫基因遗传机制及育种价值分析[学位论文]. 郑州: 河南农业大学, 2010.
[56] 蒋春志, 裴翠娟, 荆慧贤, 张孟臣, 王涛, 邸锐, 刘兵强, 闫龙. 大豆品质及农艺性状的QTL分析. 华北农学报, 2011, 26(5): 127-130.
[57] 位艳丽. 大豆农艺和品质性状遗传模型分析与QTL定位[学位论文]. 郑州: 河南农业大学, 2011.
[58] 江树业, 陈启锋, 方宣钧, 李维明, 吴为人. 植物基因分离方法及其评述. 福建农业大学学报 (自然科学版), 2000, 29(3): 261-268.
[59] Arumuganathan K, Earle ED. Estimation of nuclear DNA content of plants by flow cytometry. Plant Mol Biol, 1991, 9(3): 229-241.
[60] 夏启中, 张明菊. 分子标记辅助育种. 黄冈职业技术学院学报, 2002, 4(2): 36-41.
[61] 宋伟, 王凤格, 易红梅, 李翔, 赵久然. 功能标记及在品种鉴定和辅助育种中的应用前景. 分子育种, 2009, 7(3): 612-618.
[62] Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES IV. Dwarf8 polymorphisms asso-ciate with variation in flowering time. Nat Genet, 2001, 28(3): 286-289.
[63] Andersen JR, Lübberstedt T. Functional markers in plants. Trends Plant Sci, 2003, 8(11): 554-560.

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号
总访问:,今日访问:,当前在线:

大豆全基因组分枝相关基因发掘及与QTL共定位

Whole genome discovery of genes related to branching and co-localization with QTLs in soybean

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	杨新萍,于媛,许操. 重新设计与快速驯化创造新型作物[J]. 遗传, 2019, 41(9): 827-835.
[2]	梁承志. 从作物基因组分析到整合组学知识库建设[J]. 遗传, 2019, 41(9): 875-882.
[3]	姜义圣,许执恒. 脑发育疾病及发病机制[J]. 遗传, 2019, 41(9): 801-815.
[4]	刘永鑫,秦媛,郭晓璇,白洋. 微生物组数据分析方法与应用[J]. 遗传, 2019, 41(9): 845-862.
[5]	史晓黎,何伊琳,凌宏清. 小麦A基因组测序与进化研究进展[J]. 遗传, 2019, 41(9): 836-844.
[6]	张秀泉,王建,熊符,吕伟标,周远青,杨少民,张玉婷,田小燕,连蔚,徐湘民. 染色体10q24.31片段重复导致先天性缺指/缺趾畸形的一个家系致病机理分析[J]. 遗传, 2019, 41(8): 716-724.
[7]	张桂权. 基于SSSL文库的水稻设计育种平台[J]. 遗传, 2019, 41(8): 754-760.
[8]	莫健新,王豪强,黄广燕,蔡更元,吴珍芳,张献伟. 微生物源果胶酶在猪PK15细胞中异源表达及其酶学性质分析[J]. 遗传, 2019, 41(8): 736-745.
[9]	王博,刘芳,张二春,沃晨亮,陈振家,钱璞毅,卢浩荣,曾文君,陈泰,危金普,万仟,王韧,徐讯. 国家基因库：共有、共为、共享[J]. 遗传, 2019, 41(8): 761-772.
[10]	张倩倩,商璇,林宛颖,徐湘民. 影响β-地中海贫血表型的遗传修饰作用[J]. 遗传, 2019, 41(8): 669-676.
[11]	梁文权,侯豫,赵存友. 精神分裂症相关单核苷酸多态性调控microRNA功能研究进展[J]. 遗传, 2019, 41(8): 677-685.
[12]	禹奇超,宋彬,邹轩轩,王岭,刘德权,李波,马昆. 乳腺癌癌旁组织特异性表达基因分析[J]. 遗传, 2019, 41(7): 625-633.
[13]	李智,何俊,蒋隽,Richard G. Tait Jr.,Stewart Bauck,过伟,吴晓林. 牛SNP芯片分型检出率和分型错误率对基因型填充准确率的影响[J]. 遗传, 2019, 41(7): 644-652.
[14]	牛煦然,尹树明,陈曦,邵婷婷,李大力. 基因编辑技术及其在疾病治疗中的研究进展[J]. 遗传, 2019, 41(7): 582-598.
[15]	何俊,Fernando B. Lopes,吴晓林. 动物基因组选配方法与应用[J]. 遗传, 2019, 41(6): 486-493.