用生物信息学技术构建cSSR分子标记开发体系

Mining cSSRs from EST Data Using Bioinformatics Approaches

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,并用此算法编写了程序SSRFinder。利用该程序不但可以从大量的EST序列中发掘cSSR标记,还能比较准确地进行统计和分析。JgeneMap完善了GeneMap的图形显示功能,增加了图片保存及调整图片大小和字体类型、大小的功能,具有友好的用户图形界面。用此体系已从小麦的37 270条EST中挖掘了1228个精确cSSR(perfect cSSR) 和875个复合型cSSR(compound cSSR);根据1228个精确cSSR标记序列成功设计了597对引物,其中478对为有效扩增引物,在小麦遗传图谱上已经定位了66个标记。

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.