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Acta Agron Sin ›› 2008, Vol. 34 ›› Issue (12): 2077-2084.doi: 10.3724/SP.J.1006.2008.02077

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Development and Utilization of EST-derived Microsatellites in Sesame (Sesamum indicum L.)

WEI Li-Bin1,ZHANG Hai-Yang2*,ZHENG Yong-Zhan2,GUO Wang-Zhen1*,ZHANG Tian-Zhen1   

  1. 1 National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, Jiangsu; 2 Henan Key Laboratory of Crop Improvement, Zhengzhou 450002, Henan, China
  • Received:2008-05-04 Revised:2008-07-15 Online:2008-12-12 Published:2008-10-10
  • Contact: GUO Wang-Zhen

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Abstract:

The deficiencies of markers in Sesamum indicum L. that can be used at home and aboard seriously restrict its studies in molecular field. To accelerate the application of molecular markers in sesame, EST-SSR markers development and utilization using publicly available sesame EST data were performed. A total of 1 785 non-redundant EST sets were assembled among the 3 328 identified sesame EST. 148 microsatellites sequences containing 155 EST-SSR were detected from these EST. The total length of the non-redundant EST sequences was 774.266 kb, on average one EST-SSR each 4.99 kb. The distribution characteristics of the EST-SSR markers was analyzed. Among the SSR, dinucleotide AG/TC was the most abundant (occurring 58 times), with frequency of 37.42%. According to these EST sequences containing SSR, 50 primer pairs were designed and tested on 36 sesame accessions, 2 cotton accessions, 2 soybean accessions and 2 oil sunflower accessions to detect polymorphisms and transferability. With 44 EST-SSR, 108 loci were successfully amplified in sesame, with an average of 2.45 loci per primer pair. Of the 44 amplified primer pairs, 27(61.4%) primer pairs revealed polymorphisms in the 36 sesame accessions. The PIC (polymorphism information content) ranged from 0.105 to 0.844, with an average of 0.390. Based on genetic similarity coefficient, the UPGMA dendrogram grouped 26 of 36 accessions in to two sub-clusters (III and IV), but it revealed no association between genotypes and geographical sources. In addition, 2, 3 and 4 SSR markers could be transferred to the PCR of cotton, soybean and oil sunflower respectively. This study effectively proved that EST-SSR from sesame is valuable for genetic analysis, linkage mapping and transferability study among oil plants.

Key words: Sesame (Sesamum indicum L.), EST, SSR, PIC, Genetic diversity

[1]Bhat K V, Babrekar P P, Lakhanpaul S. Study of genetic di-versity in Indian and exotic sesame (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers. Euphytica, 1999, 110: 21-33
[2]Ercan A G, Taskin M, Turgut K. Analysis of genetic diversity in Turkish sesame (Sesamum indicum L.) populations using RAPD markers. Genet Res Crop Evol, 2004, 51: 599-607
[3]Kim D H, Zur G, Danin-Poleg Y, Lee S, Shim K, Kang C, Kashi Y. Genetic relationships of sesame germplasm collec-tion as revealed by inter-simple sequence repeats. Plant Breed, 2002, 121: 259-262
[4]Hernan E L, Petr K. Genetic relationship and diversity in a sesame (Sesamum indicum L.) germplasm collection using amplified fragment length polymorphism (AFLP). BMC Genet, 2006, 7: 10
[5]Dixit A A, Jin M H, Chung J W, Yu J W, Chung H K, Ma K H, Park Y J, Cho E G. Development of polymorphic microsatel-lite markers in sesame (Sesamum indicum L.). Mol Ecol Notes, 2005, 5: 736-738
[6]Yu J K, LaRota M, Kantety R V, Sorrells M E. EST derived SSR markers for comparative mapping in wheat and rice. Mol Gen Genet, 2004, 271: 742-751
[7]Varshney R K, Sigmund R, Borner A, Korzun V, Stein N, Sorrells M E, Langridge P, Graner A. Interspecific transfer-ability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci, 2005, 168: 195-202
[8]Wang C-B(王长彪), Guo W-Z(郭旺珍), Cai C-P(蔡彩平), Zhang T-Z(张天真). Characterization, development and ex-ploitation of EST-derived microsatellites in Gossypium rai-mondii Ulbrich. Chin Sci Bull (科学通报), 2006, 51(3): 316-320(in Chinese)
[9]Jia X P, Shi Y S, Song Y C. Development of EST-SSR in foxtail millet (Setaria italica). Genet Resour Crop Evol, 2007, 54: 233-236
[10]Paterson A H, Brubaker C, Wendel J F. A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Mol Biol, 1999, 11: 122-127
[11]Zhang J (张军), Wu Y-T(武耀廷), Guo W-Z(郭旺珍), Zhang T-Z(张天真). Fast screening of microsatellite markers in cot-ton with PAGE/silver staining. Acta Gossypii Sin (棉花学报), 2000, 12(5): 267-269 (in Chinese with English abstract)
[12]Park Y H, Alabady M S, Ulloa M. Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an in-terspecific recombinant inbred (RIL) cotton population. Mol Genet Genom, 2005, 274: 428-441
[13]Rohlf F J. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.1, User Guide. New York: Exeter Software, 2000
[14]Sokal R R, Michener C D. A statistical method for evaluating systematic relationships. Univ Kansas Sci Bull, 1958, 28: 1409-1438
[15]Sneath P H, Sokal R R. Numerical Taxonomy: The Principal and Practice of Numerical Classification. San Francisco: W. H. Freeman and Company, 1973
[16]Weber J L. Informativeness of human (dC-dA)n·(dG-dT)n polymorphisms. Genomics, 1990, 7: 524-530
[17]Cardle L, Ramsay L, Milbourne D. Computational and ex-perimental characterization of physically clustered simple sequence repeats in plants. Genetics, 2000, 156: 847-854
[18]Morgante M, Hanafey M, Powell W. Microsatellites are pref-erentially associated with nonrepetitive DNA in plant ge-nomes. Nat Genet, 2002, 30: 194-200
[19]Gao L F, Tang J F, Li H W. Analysis of microsatellites in major crops assessed by computational and experimental ap-proaches. Mol Breed, 2003, 12: 245-261
[20]Xin Y(忻雅), Cui H-R(崔海瑞), Zhang M-L(张明龙), Lim Y-P(林容杓), Choi S-R(崔水莲). Development of EST (ex-pressed sequence tags) marker in Chinese cabbage and its transferability to rapeseed. Hereditas (遗传), 2005, 27(3): 410-416 (in Chinese with English abstract)
[21]Kantety R V, Rota M L, Matthews D 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
[22]Sook J, Abbott A, Jesudurai C. Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae EST. Funct Integr Genom, 2005, 5: 136-143
[23]Li H-S(李华盛), Fan S-L(范术丽), Shen F-F(沈法富). Screening of microsatellite markers from cotton EST. Acta Gossypii Sin (棉花学报), 2005, 17(4): 211-216(in Chinese with English abstract)
[24]Lewin B, Genes V. New York: Oxford University Press, 1994
[25]Chabane K, Ablett G A, Cordeiro G M. EST versus genomic derived microsatellite markers for genotyping wild and culti-vated barley. Genet Resour Crop Evol, 2005, 52: 903-909
[26]Cho Y G, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch S R, Park W D, Ayres N, Cartinhour S. Diversity of microsa-tellites derived from genomic libraries and GenBank se-quences in rice (Oryza sativa L.). Theor Appl Genet, 2000, 100: 713-722
[27]Scott K D, Eggler P, Seaton G, Rossetto M, Ablett E M, Lee L S, Henry R J. Analysis of SSR derived from grape EST. Theor Appl Genet, 2000, 100: 723-726
[28]Cordeiro G M, Casu R, McIntyre C L, Manners J M, Henry R J. Microsatellite markers from sugarcane (Saccharum spp.) EST cross transferable to erianthus and sorghum. Plant Sci, 2001, 160: 1115-1123
[29]Saha M C, Rouf Mian M A, Eujayl I, John C Z, Wang L J, May G D. Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet, 2004, 109: 783-791
[30]Gupta P K, Rustgi S, Sharma S, Singh R, Kumar N, Balyan H S. Transferable EST-SSR markers for the study of polymor-phism and genetic diversity in bread wheat. Mol Gen Genet, 2003, 270: 315-323
[31]Ellegren H. Microsatellites: Simple sequences with complex evolution. Nat Rev Genet, 2004, 5: 435-445
[32]Sharopova N, McMullen M D, Schultz L, Schroeder S, San-chez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Melia-Hancock S, Musket T, Duru N, Polacoo M. Develop-ment and mapping of SSR markers for maize. Plant Mol Biol, 2002, 48: 463-481
[33]Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartin-hour S, McCouch S. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker poten-tial. Genome Res, 2001, 11: 1441-1452
[34]Yi G, Lee J M, Lee S, Choi D, Kim B D. Exploitation of pepper EST-SSR and an SSR-based linkage map. Theor Appl Genet, 2006, 114: 113-130
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