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作物学报 ›› 2010, Vol. 36 ›› Issue (3): 410-421.doi: 10.3724/SP.J.1006.2010.00410

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

源于大豆EST的花生属（Arachis）同源SSR标记的开发及利用

洪彦彬,陈小平,刘海燕,周桂元,李少雄,温世杰,梁炫强*   

  1. 广东省农业科学院作物研究所，广东广州 510640
  • 收稿日期:2009-10-12 修回日期:2009-12-08 出版日期:2010-03-12 网络出版日期:2009-12-21
  • 通讯作者: 梁炫强, E-mail: liang804@yahoo.com; Tel: 020-87597315
  • 基金资助:

    本研究由国家高技术研究发展计划（863计划）项目（2006AA10Z156），现代农业生产技术体系建设专项，国家自然科学基金项目（30900907）和广东省自然科学基金项目（07117967）资助。

Development and Utiligaiton of Orthologous SSR Markers in Arachis through Soybean (Glycine max) EST

HONG Yan-Bin,CHEN Xiao-Ping,LIU Hai-Yan,ZHOU Gui-Yuan,LI Shao-Xiong,WEN Shi-Jie,LIANG Xuan-Qiang*
  

  1. Crops Research Institute, Guangdong Academy of Agricultural Sciences, Wushan 510640, China
  • Received:2009-10-12 Revised:2009-12-08 Published:2010-03-12 Published online:2009-12-21
  • Contact: LIANG Xuan-Qiang, E-mail: liang804@yahoo.com; Tel: 020-87597315

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被引次数

22

摘要：

通过拼接394 370条大豆EST共获得82 614条Uni-EST，其中2 082条包含2 191个SSR位点，平均每22.96 kb EST出现1个SSR。二核苷酸重复在大豆EST-SSR中占比例最大(63.5%)，其次是三核苷酸重复(30.9%)；AG/CT在SSR基序(motif)中出现频率最高(35.8%)，AT/AT (25.4%)次之。2082条SSR-EST共设计引物685对，其中582对在4个大豆品种中得到有效扩增，98对检测出多态性。582对可扩增引物在花生属中的可转移性分析表明，大豆EST-SSR在花生属9大区组间的可转移性有所差异(12.4%~15.7%)，匍匐区组最高，大根区组最低，平均为14.2%。79对可转移性同源标记在花生区组中的多态性分析表明，供试SSR有69个在10野生种间检测出多态性，仅5个在22个栽培品种中具多态性。对引物ES-105在大豆和花生区组中的扩增产物测序结果显示，两个大豆品种间仅SSR位点存在3个AT重复差异，其余序列均一致，而大豆与花生区组间的扩增产物在序列上存在较大差异，花生区组除缺失SSR位点外，侧翼序列也存在频密的插入/缺失和置换。研究结果表明，通过大豆EST开发花生属同源SSR标记具可行性。作为有功能的分子标记，大豆EST-SSR在花生区组内多态性丰富，可直接用于大豆-花生比较基因组研究。

关键词: 大豆, 花生属（Arachis）, EST, SSR

Abstract:

Lack of sufficient molecular markers hindered current genetic research in peanuts (Arachis hypogaea L.). It is necessary to enrich molecular markers for potential use in peanut breeding programs. Recently, EST-SSRs have received much attention with the higher level of transferability to closely related species and it can be rapidly developed from EST database by data mining at low cost. In this study, we mined SSRs from the soybean EST and analyzed their transferability in peanuts (Arachis hypogaea L.) and its wild species. A total of 394 370 soybean ESTs were clustered to generate 82 614 Uni-ESTs, 2 082 ESTs of which contained 2 191 SSRs with 1 SSR in 22.96 kb EST. Di-nucleotide motif (63.5%), followed by tri-nucleotide (30.9%), were the most abundant in soybean EST-SSR. The top two motif sequence types with high frequency were AG/CT (35.8%) and AT/AT (25.4%). Based on the 2082 SSR-ESTs, a total of 685 primer pairs were successfully designed and synthesized to test the amplification in four soybean cultivars. There were 582 primer pairs amplified effectively in soybean cultivars, 98 of which exhibited polymorphism. The cross-transferability of soybean EST-SSR was different among nine sections in Arachis, ranging from 12.4% to 15.7% with an average of 14.2%. Polymorphism analysis in Arachis section showed that 69 of the 79 orthologous SSR markers displayed polymorphsim in ten wild species, while only five markers had polymorphism in 22 cultivars. The PCR bands amplified in soybean and Arachis section by primer ES-105 were cloned and sequenced. The results revealed that the polymorphism among two soybean cultivarswas caused by little variation in SSR motif (AT)n, while the polymorphsim between soybean and Arachis section was contributed not only by the indel in SSR loci, but also by the frequence of the indel and substitution in franking region.The work indicated that the development of orthologous SSR markers for Arachis from soybean EST is feasible. There was a high level of polymorphism in Arachis sections for soybean-derived EST-SSR, therefore, the research of comparative genomics of Glycine and Arachis can be performed due to the high transferability of functional molecular markers.

Key words: Soybean, Arachis, EST, SSR

[1] Kochert G, Halward R, Branch W D, Simpson C E. RFLP variability in peanut (Arachis hypogaea L.) cultivars and wild species. Theor Appl Genet, 1991, 81: 565-570

[2] Stalker H T, Dhesi J S, Kochert G. Genetic diversity within the species Arachis duranensis Krapov. & W.C. Gregory, a possible progenitor of cultivated peanut. Genome, 1995, 38: 1201-1212

[3] Raina S N, Rani V, Kojima T, Ogihara Y, Singh K P, Devarumath R M. RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification, and phylogenetic relationships in peanut (Arachis hypogaea) cultivars and wild species. Genome, 2001, 44: 763-772

[4] Subramanian V, Gurtu S, Rao R C N, Nigam S N. Identification of DNA polymorphism in cultivated groundnut using random amplified polymorphic DNA (RAPD) assay. Genome, 2000, 43: 656-660

[5] Milla S R, Isleib T G, Stalker H T, Taxonomic relationships among Arachis sect: Arachis species as revealed by AFLP markers. Genome, 2005, 8: 1-11

[6] Tang R H, Gao G Q, He L Q, Hang Z Q, Shan S H, Zhong R C, Zhou C Q, Jiang Q, Li Y R, Zhuang W J. Genetic diversity in cultivated groundnut based on SSR markers. J Genet Genom, 2007, 34: 449-459

[7] Hong Y-B(洪彦彬), Liang X-Q(梁炫强), Chen X-P(陈小平), Lin K-Y(林坤耀), Zhou G-Y(周桂元), Li S-X(李少雄), Liu H-Y(刘海燕). Genetic diversity analysis in botanical varieties of the cultivated peanut (Arachis hypogaea L.) based on SSR polymorphism. Mol Plant Breed(分子植物育种), 2008, 6(1): 71-78 (in Chinese with English abstract)

[8] Hong Y B, Liang X Q, Chen X P, Liu H Y, Zhou G Y, Li S X, Wen S, Construction of genetic linkage map based on SSR markers in peanut (Arachis hypogaea L.). Agric Sci China, 2008, 7: 915-921

[9] Hong Y-B(洪彦彬), Liang X-Q(梁炫强), Chen X-P(陈小平), Liu H-Y(刘海燕), Zhou G-Y(周桂元), Li S-X(李少雄), Wen S-J(温世杰). Construction of genetic linkage map in peanut (Arachis hypogaea L.) cultivars. Acta Agron Sin (作物学报), 2009, 35: 395-402 (in Chinese with English abstract)

[10] Liang X Q, Chen X P, Hong Y B, Liu H Y, Guo B Z. Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species. BMC Plant Biol, 2009, 9: 35

[11] Benson G, Tandem repeats finder: A program to analyze DNA sequences. Nucl Acids Res, 1999, 27: 573-580

[12] Castelo A T, Martins W, Gao G R. TROLL - Tandem repeat occurrence locator. Bioinformatics, 2002, 18: 634-636

[13] Varshney R K, Graner A, Sorrells M E. Genic microsatellite markers in plants: Features and applications. Trends Biotechnol, 2005, 23: 48-55

[14] Choudhary S, Sethy N K, Shokeen B, Bhatia S. Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet, 2009, 118: 591-608

[15] Kantety R V, La Rota M, Matthews D E, Sorrells M E. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol, 2002, 48: 501-510

[16] Yu J K, Dake T M, Singh S, Benscher D, Li W, Gill B, Sorrells M E. Development and mapping of EST-derived simple sequence repeat (SSR) markers for hexaploid wheat. Genome, 2004, 47, 805-818

[17] Rossi M, Araujo P G, Paulet F, Garsmeur O, Dias V M, Chen H, Van Sluys M A, D'Hont A. Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane. Mol Genet Genom, 2003, 269: 406-419

[18] Castillo A, Budak H, Varshney R K, Dorado G, Graner A, Hernandez P. Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense. BMC Plant Biol, 2008, 8: 97

[19] Luro F L, Costantino G, Terol J, Argout X, Allario T, Wincker P, Talon M, Ollitrault P, Morillon R. Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other citrus species and their effectiveness for genetic mapping. BMC Genomics, 2008, 9: 287

[20] Aggarwal R K, Hendre P S, Varshney R K, Bhat P R, Krishnakumar V, Singh L. Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species Theor Appl Genet, 2006, 114: 359-372

[21] Varshney R K, Sigmund R, Borner A, Korzun V, Stein N, Sorrells M E Langridge P, Graner A. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci, 2005, 168: 195-202

[22] Gutierrez M V, Patto M C V, Huguet T, Cubero J I, Moreno M T, Torres A M, Cross-species amplification of Medicago truncatula microsatellites across three major pulse crops. Theor Appl Genet, 2005, 110: 1210-1217

[23] He G H, Woullard F E, Marong I, Guo B Z. Transferability of soybean markers in peanut (Arachis hypogaea L.). Peanut Sci, 2006, 33: 22-28

[24] Lu S-D(卢圣栋). Current Protocols for Molecular Biology (现代分子生物学实验技术). Beijing: Chinese Academy of Medical Sciences & Peking Union Medical College Press, 1999. pp 101-136

[25] Varshney R K, Thiel T, Stein N, Langridge P, Graner A. In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett, 2002, 7: 537-546

[26] Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with non-repetitive DNA in plant genomes. Nat Genet, 2002, 30: 194-200

[27] Gao L F, Tang J F, Li H W, Jia J Z. Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed, 2003, 12: 245-261

[28] Jayashree B, Punna R, Prasad P, Bantte K, Hash C T, Chandra S, Hoisington D A, Varshney R K. A database of simple sequence repeats from cereal and legume expressed sequence tags mined in silico: Survey and evaluation. In silico Biol, 2007, 6: 607-620

[29] Saha M C, Mian M A, Eujayl I, Zwonitzer J C, Wang L, May G D. Tall fescue EST-SSR markers with transferability across several grass species. Theor App1 Genet, 2004, 109: 783-791

[30] Thiel T, Michalek W, Varshney R K, Graner A. Exploiting EST databases for the development of cDNA derived microsatellite markers in barley (Hordeum vulgare L.). Theor App1 Genet, 2003, 106: 411-422

[31] Cordeiro G M, Casu R, McIntyre C L, Manners J M, Henry R J. Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci, 2001, 160: 1115-112

[32] Gupta P K, Rustgi S, Sharma S, Singh R, Kumar N, Balyan H S. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genom, 2003, 270, 315-323

[33] Sreenivasulu N, Kavikishor P B, Varshney R K, Altschmied L. Mining functional information from cereal genomes—the utility of expressed sequence tags. Curr Sci, 2002, 83: 965-973

[34] Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A. Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: Implications for the transferability of SSRs in plants. Mol Biol Evol, 1998, 15: 1275-1287

[35] Treuren V R, Kuittinen H, Karkkainen K, Baenagonzalez E, Savolainen O. Evolution of microsatellites in Arabis petraea and Arabis lyrata, outcrossing relatives of Arabidopsis thaliana. Mol Biol Evol, 1997, 14: 220-229

[36] Provan J, Powell W, Waugh R. Microsatellite analysis of relationships within cultivated potato (Solanum tuberosum). Theor App1 Genet, 1996, 92: 1078-1084

[37] Röder M S, Plaschke J, König S U, Börner A, Sorrells M E, Tanksley S D, Ganal M W, Abundance, variability and chromosomal location of microsatellites in wheat. Mol General Genet, 1995, 246: 327-333

[38] Ellegren H, Primmer C R, Sheldon B C. Microsatellite ‘evolution’: Directionality or bias. Nat Genet, 1995, 11: 360-362

[39] Ellegren H, Moore S, N. Robinson, Byrne K, Ward W, Sheldon B C. Microsatellite evolution: A reciprocal study of repeat lengths at homologous loci in cattle and sheep. Mol Biol Evol, 1997, 14: 854-860

[40] Ellgren H. Microsatellites: Simple sequences with complex evolution. Nat Genet, 2004, 5: 435-445
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