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日本落叶松EST-SSR标记挖掘及特征分析

刘超 ,  张力鹏 ,  王春国 ,  宋文芹 ,  陈成彬

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日本落叶松EST-SSR标记挖掘及特征分析

  • 1.

    南开大学生命科学学院, 天津 300071

  • 中图分类号: S791.223

Development and Characterization of EST-SSR Molecular Markers in Larix kaempferi

  • 1.

    College of Life Sciences, Nankai University, Tianjin 300071, China

  • CLC number: S791.223

  • 摘要: 基于日本落叶松转录组测序(RNA-seq)结果,利用SSRIT工具查找SSR位点,检测到1 788个EST-SSR位点,平均长度是17.5 bp。进一步统计分析发现在落叶松中重复类型SSR位点出现次数最多的是六、三核苷酸,其余依次是五、二、四核苷酸重复类型;同时检测到656种重复基元类型,种类丰富。用Primer Premier 5.0设计500对引物,随机合成102对,以红豆杉科、柏科、松科材料为模板进行检测,结果显示在红豆杉科和柏科里的扩增率分别为95%、50%;在松科不同属的通用性为落叶松属99.01%、黄杉属67.4%、雪松属63.8%、冷杉属67.4%、云杉属70.2%和松属75.7%。利用101对SSR引物对7种不同落叶松品种亲缘关系进行了分析,获得79个多态性位点,在遗传相似系数0.69处将其区分为4个类群。
    Abstract: Based on RNA sequences information of Larix kaempferi, 1 788 EST-SSR loci were found by SSRIT, with an average length of 17.5 bp. The most abundant SSRs within Larix were hexanucleotide and trinucleotide, followed by pentanucleotide, dinucleotide, and tetranucleotide. At the meantime, 656 kinds of repeat primitives were detected. In this study, a total of 500 primers were designed by "Primer Premier 5.0" and 102 pairs were synthesized. These SSR primers were used to assess the amplification efficiency of Taxaceae, Cupressaceae, and Pinaceae. The results showed that 95% and 50% of all primers could be amplified successfully in Taxaceae and Cupressaceae. And in Pinaceae, the transferability of Larix SSR in Larix, Pseudotsuga, Abies, Cedrus, Picea and Pinus was 99.01%, 67.4%., 67.4%, 63.8%, 70.2%, and 75.7% respectively. Seven different varieties of Larix genetic relationship were analyzed by using 101 pairs of SSR primers. 79 polymorphism loci were obtained, and Larix was divided into four groups at the genetic similarity coefficient of 0.69.
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日本落叶松EST-SSR标记挖掘及特征分析

  • 1. 南开大学生命科学学院, 天津 300071
  • 收稿日期: 2013-08-23

摘要: 基于日本落叶松转录组测序(RNA-seq)结果,利用SSRIT工具查找SSR位点,检测到1 788个EST-SSR位点,平均长度是17.5 bp。进一步统计分析发现在落叶松中重复类型SSR位点出现次数最多的是六、三核苷酸,其余依次是五、二、四核苷酸重复类型;同时检测到656种重复基元类型,种类丰富。用Primer Premier 5.0设计500对引物,随机合成102对,以红豆杉科、柏科、松科材料为模板进行检测,结果显示在红豆杉科和柏科里的扩增率分别为95%、50%;在松科不同属的通用性为落叶松属99.01%、黄杉属67.4%、雪松属63.8%、冷杉属67.4%、云杉属70.2%和松属75.7%。利用101对SSR引物对7种不同落叶松品种亲缘关系进行了分析,获得79个多态性位点,在遗传相似系数0.69处将其区分为4个类群。

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