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作物学报 ›› 2015, Vol. 41 ›› Issue (10): 1500-1509.doi: 10.3724/SP.J.1006.2015.01500

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

小麦株高相关性状与SNP标记全基因组关联分析

陈广凤1,2,陈建省1,田纪春1,*   

  1. 1山东农业大学作物生物学国家重点实验室 / 山东省作物生物学重点实验室,山东泰安 271018;2德州学院生态与园林建筑学院,山东德州 253023
  • 收稿日期:2014-10-23 修回日期:2015-04-06 出版日期:2015-10-12 网络出版日期:2015-07-09
  • 通讯作者: 田纪春, Tel: 0538-8242040, E-mail: jctian@sdau.edu.cn
  • 基金资助:

    本研究由国家自然科学基金项目(31171554), 国家转基因生物新品种培育重大专项(2013ZX08002003), 山东省农业良种工程项目(种质资源保护与评价2014)资助。

Genome-Wide Association Analysis between SNP Markers and Plant Height Related Traits in Wheat

CHEN Guang-Feng1,2,CHEN Jian-Sheng1,TIAN Ji-Chun1,*   

  1. 1State Key Laboratory of Crop Biology / Shandong Provincial Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; 2College of Ecology and Garden Architecture, Dezhou University, Dezhou 253023, China
  • Received:2014-10-23 Revised:2015-04-06 Published:2015-10-12 Published online:2015-07-09
  • Contact: 田纪春, Tel: 0538-8242040, E-mail: jctian@sdau.edu.cn

摘要:

株高是影响小麦产量和控制倒伏的重要因素,研究小麦株高相关性状的遗传机制对高产育种具有指导意义。205中国冬麦区小麦品种()为材料,利用分布于小麦全基因组的24 355个单核苷酸多态性(SNP)标记对株高相关性状进行关联分析。共发现38SNP与株高相关性状显著关联(P < 0.0001)的,分布在1B2A2B3A3B3D4A4B5A6D染色体上。其中,11个位点在至少2个环境中稳定表达,可用于开发CAPS标记。同时,发掘了一批株高性状相关基因的优异等位变异,如降低株高的等位变异BobWhite_c48009_52,平均降低株高12.9 cm;降低穗下节间长的等位变异BS00039422_51-CIAAV1698-A,分别降低穗下节间长5.9 cm6.6 cm本研究发掘的控制小麦株高基因位点,为在分子水平上研究小麦株高复杂性状提供了有价值的参考

关键词: 小麦, SNP标记, 株高, 全基因组关联分析

Abstract:

Plant height (PH) has great influence to yield potential and lodging occurrence in wheat (Triticum aestivum L.). In this study, the diverse panel of 205 elite wheat lines was genotyped with the 90k SNP array (24 355 SNPs) based on the Illumina Infinium assay to disclose the PH genetic mechanism. A total of 38 SNPs were found to be associated with PH (P < 0.0001), which were located on chromosomes 1B, 2A, 2B, 3A, 3B, 3D, 4A, 4B, 5A, and 6D, including 11 SNPs detected in two or more environments. These stable SNPs can be used to develop CAPS markers for PH. In addition, a few elite alleles were identified, such as BobWhite_c48009_52 to reduce PH by 12.9 cm, and BS00039422_51-C and IAAV1698-A to decrease length of the first internode below spike by 5.9 cm and 6.6 cm, respectively. These results will facilitate further researches in PH-related traits in wheat.

Key words: Wheat, SNP marker, Plant height, Genome-wide association analysis

[1]李金才, 尹钧, 魏凤珍. 播种密度对冬小麦茎秆形态特征和抗倒指数的影响. 作物学报, 2005, 31: 662–666



Li J C, Yin J, Wei F Z. Effects of planting density on characters of culm and culm lodging resistant index in winter wheat. Acta Agron Sin, 2005, 31: 662–666 (in Chinese with English abstract)



[2]董琦, 王爱萍, 梁素明. 小麦基部茎节形态结构特征与抗倒性的研究. 山西农业大学学报(自然科学版), 2003, 23(3): 188–191



Dong Q, Wang A P, Liang S M. Study on the architectural characteristics of wheat stalks. J Shanxi Agric Univ (Nat Sci Edn), 2003, 23(3): 188–191 (in Chinese with English abstract)



[3]Cadalen T, Sourdille P, Charmet G, Tixier M H, Gay G, Boeuf C, Bernard S, Leroy P, Bernard M. Molecular markers linked to genes affecting plant height in wheat using a double haploid population. Theor Appl Genet, 1998, 96: 933–940



[4]周淼平, 黄益洪, 任丽娟, 王书文, 马鸿翔, 陆维忠. 利用重组自交系检测小麦株高的QTL. 江苏农业学报, 2004, 20: 201–206



Zhou S P, Huang Y H, Ren L J, Wang S W, Ma H X, Lu w Z. Detection of QTLs for plant height in wheat using RILs. Jiangsu J Agric Sci, 2004, 20: 201–206 (in Chinese with English abstract)



[5]刘宾, 赵亮, 张坤普, 朱占玲, 田宾, 田纪春. 小麦株高发育动态QTL定位. 中国农业科学, 2010, 43: 4562–4570



Liu B, Zhao L, Zhang K P, Zhu Z L, Tian B, Tian J C. Genetic dissection of plant height at different growth stages in common wheat. Sci Agric Sin, 2010, 43: 4562–4570 (in Chinese with English abstract)



[6]谭贤杰, 吴子恺, 程伟东, 王天宇, 黎裕.关联分析及其在植物遗传学研究中的应用. 植物学报, 2011, 46: 108-118



Tan X J, Wu Z K, Cheng W D, Wang T Y, Li Y. Association analysis and its application in plant genetic research. Chin Bull Bot, 2011, 46: 108-118 (in Chinese with English abstract)



[7]Zhu C, Gore M, Buckler E S, Yu J. Status and prospects of association mapping in plants. Plant Genome, 2008, 1: 5–20



[8]Ingvarsson P K, Nathaniel R S. Association genetics of complex traits in plants. New Phytol, 2011, 189: 909–922



[9]Altmann T, Roder M S. SNP identification in crop plants. Curr Opin Plant Biol, 2009, 12: 211–217



[10]陈秋玲, 高建明, 罗峰, 魏进招, 裴忠有, 孙守钧. 分子标记技术在禾本科作物基因定位上的研究进展. 中国农学通报, 2010, 26(9): 42–48



Chen Q L, Gao J M, Luo F, Wei J Z, Pei Z Y, Sun S J. Research and development of molecular marker technologies for gene mapping of Gramineous crops. Chin Agric Sci Bull, 2010, 26(9): 42–48 (in Chinese with English abstract)



[11]Palaisa K A, Morgante M, Williams M, Rafalski A. Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell, 2003, 15:1795–1806



[12]Mick E, McGough J J, Middleton F A, Neale B, Faraone S V. Genome-wide association study of blood pressure response to methylphenidate treatment of attention-deficit/hyperactivity disorder. Prog Neuro-Psychopharmacol Biol Psychiatry, 2011, 35: 466–472



[13]Gerrard D T, Fricke C, Edward D A, Edwards D R, Chapman T. Genome-wide responses of female fruit flies subjected to divergent mating regimes. PLoS One, 2013, 8: e68136



[14]Huang X H, Wei X H, Sang T, Zhao Q, Feng Q, Zhao Y, Li C Y, Zhu C R, Lu T T, Zhang Z W, Li M, Fan D L, Guo Y L, Wang A H, Wang L, Deng L M, Lin Z, Edward S Buckler, Qian Q, Zhang Q F, Li J Y, Han B. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet, 2010, 42: 961–967



[15]Wilson L M, Whitt S R, Ibanez A M, Rocheford T R, Goodman M M, Buckler E S. Dissection of maize kernel composition and starch production by candidate gene associations. Plant Cell, 2004, 16: 2719–2733



[16]李永祥, 王阳, 石云素, 宋燕春, 王天宇, 黎裕. 玉米籽粒构型与产量性状的关系及QTL作图. 中国农业科学, 2009, 42: 408–418



Li Y X, Wang Y, Shi Y S, Song Y C, Wang T Y, Li Y. Correlation analysis and QTL mapping for traits of kernel structure and yield components in maize. Sci Agric Sin, 2009, 42: 408–418 (in Chinese with English abstract)



[17]Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M, Bender D, Maller J, Sklar P, Bakker P, Daly M, Sham P. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am Human Genet, 2007, 81: 559–575



[18]Wang S C, Wong D, Forrest K, Allen A, Chao S M, Huang B E, Silvio S, Milner S G, Cattivelli L, Mastrangelo A M, Whan A, Stephen S, Barker G; Wieseke R, Plieske J, International Wheat Genome Sequencing Consortium, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova A, Feuillet C, Salse J, Morgante M, Pozniak C, Luo M C, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards K J, Hayden M, Akhunov E D. Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnol J, 2014, 12: 787–796



[19]Liu K, Muse S V. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics, 2005, 21: 2128–2129



[20]Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol, 2005, 14: 2611–2620



[21]张学勇, 童依平, 游光霞, 郝晨阳, 盖红梅, 王兰芬, 李滨, 董玉琛, 李振声. 选择牵连效应分析: 发掘重要基因的新思路. 中国农业科学, 2006, 39: 1526–1535



Zhang X Y, Tong Y P, You G X, Hao C Y, Ge H M, Wang L F, Li B, Dong Y C, Li Z S. Hitchhiking effect mapping: a new approach for discovering agronomic important genes. Sci Agric Sin, 2006, 39: 1526–1535 (in Chinese with English abstract)



[22]Bakker E G, Toomajian C, Kreitman M, Bergelson J. A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell, 2006, 18: 1803–1818



[23]Zanke C, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, Argillier O, Stiewe G, Hinze M, Beier S, Ganal M W, Röder M S. Genetic architecture of main effect QTL for heading date in European winter wheat. Front Plant Sci, 2014, 5: 1–12



[24]Zhang K P, Wang J J, Zhang L Y, Rong C W, Zhao F W, Peng T, Li M M, Cheng D M, Liu X, Qin H J, Zhang A M, Tong Y P, Wang D W. Association analysis of genomic loci important for grain weight control in elite common wheat varieties cultivated with variable water and fertiliser supply. PLoS One, 2013, 8: e57853



[25]慕美财, 刘勇, 郭小丽, 张曰秋,于凯, 刘冬成, 张爱民. 山东小麦品种中矮秆基因Rht-B1b、Rht-D1b分布的分子鉴定. 分子植物育种, 2005, 3: 473–478



Mu M C, Liu Y, Guo X L, Zhang Y Q, Yu K, Liu D C, Zhang A M. Distribution of Rht-B1b and Rht-D1b in wheat cultivars in Shandong detected by molecular markers. Mol Plant Breed, 2005, 3: 473–478 (in Chinese with English abstract)



[26]嵇怡, 缪旻珉, 陈学好. 植物矮生性状的分子遗传研究进展. 分子植物育种, 2006, 4: 753–771



Ji Y, Miu W M, Chen X H. Progresses on the molecular genetics of dwarf character in plants. Mol Plant Breed, 2006, 4: 753–771 (in Chinese with English abstract)



[27]Börner A, Schumann E, Furste A, Coster H, Leithold B, Röder M S, Weber W E. Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet, 2002, 105: 921–936



[28]Zhang K P, Zhao L, Tian J C, Chen G F, Jiang X L, Liu B. A genetic map conducted using a doubled haploid population derived from two elite Chinese common wheat (Triticum aestivum L.) varieties. J Integr Plant Biol, 2008, 50: 1–10



[29]Huang X Q, Coster H, Ganal M W, Röder M S. Advanced backcross QTL analysis for the identification of quantitative trait loci alleles from wild relatives of wheat (Triticum aestivum L.). Theor Appl Genet, 2003, 106: 1379–1389



[30]王竹林, 王辉, 孙道杰, 何中虎, 夏先春, 刘曙东. 小麦株高的QTL分析. 西北农林科技大学学报(自然科学版), 2008, 36(12): 60–63



Wang Z L, Wang H, Sun D J, He Z H, Xia X C, Liu S D. QTL mapping for plant height of wheat. J Northwest A&F Univ (Nat Sci Edn), 2008, 36(12): 59–63 (in Chinese with English abstract)



[31]魏添梅, 昌小平, 闵东红, 景蕊莲. 小麦抗旱品种的遗传多样性分析及株高优异等位变异挖掘. 作物学报, 2010, 36: 895–904



Wei T M, Chang X P, Min D H, Jing R L. Analysis of genetic diversity and tapping elite alleles for plant height in drought-tolerant wheat varieties. Acta Agron Sin, 2010, 36: 895–904 (in Chinese with English abstract)



[32]张国华, 高明刚, 张桂芝, 孙金杰, 靳雪梅, 王春阳, 赵岩, 李斯深. 黄淮麦区小麦品种(系)产量性状与分子标记的关联分析. 作物学报, 2013, 39: 1187–1199



Zhang G H, Gao M G, Zhang G Z, Sun J J, Jin X M, Wang C Y, Zhao Y, Li S S. Association analysis of yield traits with molecular markers in Huang-Huai River Valley Winter Wheat region, China. Acta Agron Sin, 2013, 39: 1187–1199 (in Chinese with English abstract)



[33]Lu Y L, Yan J B, Guimaraes C T, Taba S, Hao Z F, Gao S B, Chen S J, Li J S, Zhang S H, Vivek B S, Magorokosho C, Parentoni S N, Shah T, Rong T Z, Crouch J H, Xu Y B. Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theor Appl Genet, 2009, 120: 93–115

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