Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA.
Anim Genet. 2010 Jun;41(3):286-94. doi: 10.1111/j.1365-2052.2009.02002.x. Epub 2009 Nov 26.
Pacific white shrimp (Litopenaeus vannamei) are of particular economic importance to the global shrimp aquaculture industry. However, limited genomics information is available for the penaeid species. We utilized the limited public information available, mainly single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex-averaged linkage groups, with approximate coverage of 2071 and 2130 cm for the female and male maps, respectively. The average-squared correlation coefficient (r(2)), a measure of linkage disequilibrium, for markers located more than 50 cm apart on the same linkage group, was 0.15. Levels of r(2) increased with decreasing inter-marker distance from approximately 80 cm, and increased more rapidly from approximately 30 cm. A QTL for shrimp gender was mapped on linkage group 13. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits.
太平洋白对虾（Litopenaeus vannamei）对全球虾类养殖业具有特别重要的经济意义。然而，对虾类物种的基因组学信息有限。我们利用有限的公共信息，主要是单核苷酸多态性（SNPs）和表达序列标签，来发现标记物，以构建第一个太平洋白对虾的 SNP 遗传图谱。总共发现了 1344 个假定的 SNPs，在 825 个 SNP 中，有 418 个 SNP 标记从 347 个连续体映射到 45 个性别平均连锁群，雌性图谱的大致覆盖度为 2071cm，雄性图谱的覆盖度为 2130cm。位于同一连锁群上相隔 50cm 以上的标记物的平均平方相关系数（r²），是衡量连锁不平衡的一个指标，为 0.15。当标记物之间的距离从大约 80cm 减少到大约 30cm 时，r²水平会增加。在连锁群 13 上定位了一个虾类性别 QTL。与模式生物——溞和果蝇的比较作图显示，L. vannamei 的基因组结构发生了广泛的重排，而且 L. vannamei 与溞的关系更为密切。这个 SNP 遗传图谱为未来的虾类基因组学研究奠定了基础，特别是对经济重要性状的遗传标记或区域的鉴定。
