| 用生物信息学技术构建cSSR分子标记开发体系 |
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| 引用本文： | 汤继凤,曹永生,高丽锋,贾继增.用生物信息学技术构建cSSR分子标记开发体系[J].中国农业科学,2004,37(3):328-328. |
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| 作者姓名： | 汤继凤 曹永生 高丽锋 贾继增 |
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| 作者单位： | 中国农业科学院作物品种资源研究所重点实验室,北京,100081 |
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| 基金项目： | 国家“973”资助项目(19980102)，国家“863”资助项目(2001AA211031) |
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| 摘 要： | 存在于基因编码区的简单重复序列(又称cSSR或者EST-SSR),既可用作分子标记又可用于基因功能研究。Internet上大量的EST数据为cSSR标记的开发提供了丰富的资源。生物信息学是cSSR分子标记开发的有力工具。笔者构建的cSSR分子标记开发体系包括自行编制的SSR标记发掘程序SSRFinder,生物学家常用的引物设计程序Primer3和DNAstar, 以及遗传定位程序MapMaker和图形显示程序JgeneMap。根据SSR分子标记发掘中存在的问题,提出了SSR分子标记发掘算法,并用此算法编写了
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| 关 键 词： | cSSR EST-SSR 精确cSSR 复合型cSSR 遗传图谱 小麦 |
Mining cSSRs from EST Data Using Bioinformatics Approaches |
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| TANG Ji-feng,CAO Yong-sheng,GAO Li-feng,JIA Ji-zeng.Mining cSSRs from EST Data Using Bioinformatics Approaches[J].Scientia Agricultura Sinica,2004,37(3):328-328. |
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| Authors: | TANG Ji-feng CAO Yong-sheng GAO Li-feng JIA Ji-zeng |
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| Abstract: | The SSRs in protein-coding region were called cSSRs or EST-SSRs, which could be used as genetic markers andfor studying gene function. Public EST data bases have become available, such as GenBank, DDBJ and EMBL. Bioinformaticswould be an effective method for mining cSSRs from EST data. A system was developed for mining cSSRs from EST data,including SSRFinder for mining cSSRs, primer designing programs Primer3 and DNAstar generated by others and geneticmapping programs MapMaker and JgeneMap. According to the problems in mining SSRs from a large number of sequences, theprogram SSRFinder was generated, which could be used to find cSSRs, but also give exactly statistic files about all kinds ofcSSRs. JgeneMap had improved the function of GeneMap, and enhanced the capability of saving picture and adjusting the sizeof picture and the size and type of word with friendly user interface. Using the system have mined 1228 perfect cSSRs and 875compound ones from 37 270 EST sequences of wheat and 597 EST-derived SSRs primer pairs were developed, of which 478had functional amplification, and 66 perfect cSSRs makers have been located onto wheat genetic linkage maps. |
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| Keywords: | cSSRs EST-SSRs Perfect cSSRs Compound cSSRs Genetic map Wheat |
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