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YUAN Yang-Yang, WANG Qing-Feng, CHEN Jin-Ming. Development of SSR Markers in Aquatic Plant Nymphoides peltata (Menyanthaceae) Based on Information from Transcriptome Sequencing[J]. Plant Science Journal, 2013, 31(5): 485-492. DOI: 10.3724/SP.J.1142.2013.50485
Citation: YUAN Yang-Yang, WANG Qing-Feng, CHEN Jin-Ming. Development of SSR Markers in Aquatic Plant Nymphoides peltata (Menyanthaceae) Based on Information from Transcriptome Sequencing[J]. Plant Science Journal, 2013, 31(5): 485-492. DOI: 10.3724/SP.J.1142.2013.50485
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Development of SSR Markers in Aquatic Plant Nymphoides peltata (Menyanthaceae) Based on Information from Transcriptome Sequencing

  • 1.

    Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China

  • 2. University of Chinese Academy of Sciences, Beijing 100049, China

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  • Received Date: April 22, 2013
  • Revised Date: May 07, 2013
  • Published Date: October 29, 2013
    Graphical Abstract
    • Abstract
  • Using the program MISA, a total of 12319 EST-SSRs were sought out from 79536 ESTs of aquatic plant Nymphoides peltata. Dinucleotide and trinucleotide SSRs were the two main motif types, accounting for 57.31% and 30.87%, respectively. The most abundant di-and tri- motifs were AG/CT (29.76%) and AAG/CTT (8.66%), respectively. We randomly selected 130 primer pairs to evaluate their application and polymorphism across two populations of N. peltata. Seventy-eight SSR markers were amplified successfully, yielding clear and discernible bands, among which 37 were found to be polymorphic and the polymorphic rate was 47.44%. Using the polymorphic SSR markers, a total of 114 alleles were detected. The number of alleles per locus ranged from 2 to 6 (mean 3.08). Observed heterozygosity (Ho) and expected value (He) per locus varied from 0.229 to 1.000 and from 0.351 to 0.756, respectively. Polymorphism information content (PIC) ranged from 0.286 to 0.698, with an average of 0.495.The results indicated that the development of SSR molecular markers from the EST dataset generated by next generation sequencing in the aquatic plant N.peltata is valuable and effective. These newly generated SSR makers will provide new tools for studying genetic diversity and population genetic structure of N.peltata.
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    • References (29)
  • [1]
    中国科学院植物研究所.中国植物志: 第 62 卷[M].北京: 科学出版社, 1999.
    [2]
    朱静.睡菜科睡菜与莕菜的发育形态学研究及其分类学意义[D].哈尔滨:哈尔滨师范大学, 2011.
    [3]
    雷泽湘.太湖大型水生植被及其环境效应研究[D].广州: 暨南大学, 2006.
    [4]
    Liao Y Y,Yue X L,Guo Y H,Gituru W R,Wang Q F,Chen J M.Genotypic diversity and genetic structure of populations of the distylous aquatic plant Nymphoides peltata (Menyanthaceae) in China[J].J Syst Evol,2013, DOI: 10.1111/jse.12023.
    [5]
    李美琼,高浦新,朱友林,李绍波.微卫星 (SSR) 分子标记应用于濒危植物保护的研究进展[J].江西林业科技, 2011, 2: 24-28.
    [6]
    Larson D.Reproduction strategies in introduced Nymphoides peltata populations revealed by genetic markers[J].Aquat Bot,2007, 86(4): 402-406.
    [7]
    Nishihiro J,Uesugi R,Takagawa S,Washitani I.Toward the restoration of a sustainable population of a threatened aquatic plant,Nymphoides peltata: Integrated genetic/demographic studies and practices[J].Biol Conservn, 2009, 142(9): 1906-1912.
    [8]
    Uesugi R,Goka K,Nishihiro J,Washitani I.Allozyme polymorphism and conservation of the Lake Kasumigaura population of Nymphoides peltata[J].Aquat Bot, 2004, 79(3): 203-210.
    [9]
    Uesugi R,Nishihiro J,Tsumura Y,Washitani I.Restoration of genetic diversity from soil seed banks in a threatened aquatic plant,Nymphoides peltata[J].Conservn Genet, 2007, 8(1): 111-121.
    [10]
    Uesugi R,Nishihiro J,Washitani I.Population status and genetic diversity of Nymphoides peltata in Japan[J].Japanese J Conserv Ecol, 2009, 14(1): 13-24.
    [11]
    Uesugi R,Tani N,Goka K,Nishihiro J,Tsumura Y,Washitani I.Isolation and characterization of highly polymorphic microsatellites in the aquatic plant,Nymphoides peltata (Menyanthaceae)[J].Mol Ecol Notes, 2005, 5(2): 343-345.
    [12]
    Iorizzo M,Senalik D A,Grzebelus D,Bowman M,Cavagnaro P F,Matvienko M,Ashrafi H,Van Deynze A,Simon P W.De novo assembly and characterization of the carrot transcriptome reveals novel genes,new markers,and genetic diversity[J].BMC Genomics, 2011, 12: 389.
    [13]
    Kaur S,Cogan N O,Pembleton L W,Shinozuka M,Savin K W,Materne M,Forster J W.Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery[J].BMC Genomics, 2011, 12: 265.
    [14]
    Wei W,Qi X,Wang L,Zhang Y,Hua W,Li D,Lv H,Zhang X.Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers[J].BMC Genomics, 2011, 12(1): 451.
    [15]
    李玉恒,赵明慧,赵紫阳,李峥,袁雪,李昌盛,林增,胡婧,李俭,李士泽.利用梯度 PCR 和降落 PCR 扩增 CIRP 基因的比较[J].黑龙江八一农垦大学学报, 2011, 23(5): 46-49.
    [16]
    Yeh F.Population genetic analysis of codominant and dominant markers and quantitative traits[J].Belgian J Bot, 1997, 129: 157.
    [17]
    Peakall R,Smouse P E.GenAlEx 6.5: genetic analysis in Excel.Population genetic software for teaching and research-an update[J].Bioinformatics, 2012, 28(19): 2537-2539.
    [18]
    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[J].Theor Appl Genet, 2007, 114(2): 359-372.
    [19]
    Gupta P K,Rustgi S,Sharma S,Singh R,Kumar N,Balyan H S.Transferable EST-SSR mar-kers for the study of polymorphism and genetic diversity in bread wheat[J].Mol Genet Genomics, 2003, 270(4): 315-323.
    [20]
    杨春霞,温强,叶金山,朱培林.枳壳 EST-SSR 标记的开发[J].分子植物育种, 2011, 9(1): 123-127.
    [21]
    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[J].Plant Mol Biol, 2002, 48(5-6): 501-510.
    [22]
    Pan L,Xia Q Quan Z,Liu H,Ke W,Ding Y.Development of novel EST-SSRs from sacred lotus (Nelumbo nucifera Gaertn) and their utilization for the genetic diversity analysis of N.nucifera[J].J Hered, 2010, 101(1): 71-82.
    [23]
    Wang D,Liao X,Cheng L,Yu X,Tong J.Development of novel EST-SSR markers in common carp by data mining from public EST sequences[J].Aquaculture, 2007, 271(1-4): 558-574.
    [24]
    Durand J,Bodenes C,Chancerel E,Frigerio J M,Vendramin G,Sebastiani F,Buonamici A,Gailing O,Koelewijn H P,Villani F,Mattioni C,Cherubini M,Goicoechea P G,Herran A,Ikaran Z,Cabane C,Ueno S,Alberto F,Dumoulin P Y,Guichoux E,Daruvar A,Kremer A,Plomion C.A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study[J].BMC Genomics, 2010, 11: 570.
    [25]
    Chavarriaga-Aguirre P, Maya M M, Bonierbale M W, Kresovich S, Fregene M A, Tohme J, Kochert G.Microsatellites in cassava (Manihot esculenta Crantz): discovery, inheritance and variability[J].Theoret Appl Genet, 1998, 97(3): 493-501.
    [26]
    王金雷, 朱庆, 刘益平, 杜华锐.鸡 PRKAB2 基因 PCR-SSCP 分析及其与屠宰性状和肉质性状的相关性[J].遗传, 2008, 30(8): 1033-1038.
    [27]
    向华, 毛盛贤.固定指数理论及其在遗传育种中的应用[J].遗传, 1995, 17: 63-70.
    [28]
    严林俊, 陈宏, 房兴堂, 张润锋, 鲍斌, 张海军.中国荷斯坦牛微卫星基因座遗传多态性研究[J].西北农林科技大学学报: 自然科学版, 2007, 35(7): 23-27.
    [29]
    王勇.花柱二型性水生植物莕菜的繁殖生态学研究[D].武汉: 武汉大学, 2004.
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