Characterization and comparison of microsatellites derived from repeat-enriched libraries and expressed sequence tags
Characterization and comparison of microsatellites derived from repeat-enriched libraries and expressed sequence tags
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DOI：
10.1111/j.1365-2052.2005.01305.x
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发表时间：
2005-08-01
期刊：
影响因子：
2.4
通讯作者：
Rexroad, CE
中科院分区：
文献类型：
--
作者：
Coulibaly, I;Gharbi, K;Rexroad, CE
构建用于鉴定重要性状基因座的高密度连锁图需要开发大量的以规则间隔跨越整个基因组的多态性遗传标记。作为我们努力开发标记虹鳟鱼（虹鳟鱼mykiss）的一部分，我们进行了微卫星标记之间的等位基因变异的比较表达序列标签（EST）的数据和匿名标记从重复富集库构建的基因组DNA。一个子集的70个标记（37个EST数据库和33个重复富集库）的特点是相对于多态性信息含量（PIC），等位基因数，重复数，基因组内的位点重复和能力，在其他鲑科鱼类的扩增。来自ESTs的二核苷酸微卫星的PIC值高于匿名标记（72.7%比54.0%）。相比之下，匿名微卫星的二核苷酸重复数高于EST衍生的微卫星（27.4 vs. 18.1）。EST微卫星的跨种扩增率较高。每种标记类型的大约一半在基因组内重复。与单拷贝标记不同，在其他鲑科鱼类中重复微卫星的扩增与系统发育距离不相关。基因组微卫星比EST衍生的微卫星在区分鲑科鱼类方面更有用。本研究共开发了428个微卫星标记，用于虹鳟鱼的定位和群体遗传研究。
The construction of high-density linkage maps for use in identifying loci underlying important traits requires the development of large numbers of polymorphic genetic markers spanning the entire genome at regularly spaced intervals. As part of our efforts to develop markers for rainbow trout (Oncorhynchus mykiss), we performed a comparison of allelic variation between microsatellite markers developed from expressed sequence tag (EST) data and anonymous markers identified from repeat-enriched libraries constructed from genomic DNA. A subset of 70 markers (37 from EST databases and 33 from repeat enriched libraries) was characterized with respect to polymorphism information content (PIC), number of alleles, repeat number, locus duplication within the genome and ability to amplify in other salmonid species. Higher PIC was detected in dinucleotide microsatellites derived from ESTs than anonymous markers (72.7% vs. 54.0%). In contrast, dinucleotide repeat numbers were higher for anonymous microsatellites than for EST derived microsatellites (27.4 vs. 18.1). A higher rate of cross-species amplification was observed for EST microsatellites. Approximately half of each marker type was duplicated within the genome. Unlike single-copy markers, amplification of duplicated microsatellites in other salmonids was not correlated to phylogenetic distance. Genomic microsatellites proved more useful than EST derived microsatellites in discriminating among the salmonids. In total, 428 microsatellite markers were developed in this study for mapping and population genetic studies in rainbow trout.