Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua).
Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua).
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DOI：
10.1186/1471-2164-11-191
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发表时间：
2010-03-22
期刊：
影响因子：
4.4
通讯作者：
Bowman S
中科院分区：
文献类型：
--
作者：
Hubert S;Higgins B;Borza T;Bowman S
大西洋鳕鱼（Gadus morhua）是一种对水产养殖业具有日益重要的经济意义的物种。鳕鱼的遗传改良将在成功实现大规模水产养殖中发挥关键作用。虽然在鳕鱼中开发了许多微卫星标记，但目前单核苷酸多态性（SNPs）的数量有限。在这里，我们报告了大规模表达序列标签（EST）程序生成的序列数据中snp的鉴定，重点是来自加拿大水域的鱼类。共组装了97976条est，生成13448条contigs。我们检测到4753个snp符合我们的选择标准（覆盖深度≥4 reads；次要等位基因频率> 25%）。选取3072个snp进行检测。检测成功率为75%，正确扩增2291个snp。其中607个（26%）snp在所有被测人群中都是单态的。总的来说，64个（4%）snp可能代表重复基因或基因家族中高度相似的成员，而不是同一基因的替代等位基因，因为它们表现出高频率的杂合性。剩余的多态性snp（1620个）被归类为验证的snp。检测到的小等位基因平均频率为0.258（±0.141）。在1514个经过验证的snp序列中，31%具有显著的爆炸效应。对于预测发生在编码区域的snp(141)，我们确定36%（51）是非同义的。许多位点（1033个snp，占64%）在所有测试人群中都是多态的。然而，在西大西洋中多态的少数snp（184个）在来自三个欧洲种群的鱼类中是单态的。初步构建了23个主要连锁组和924个snp图谱。这些snp是加速鳕鱼养殖遗传改良的有力工具。它们已被用于构建可用于数量性状位点（QTL）发现的遗传连锁图谱。由于这些snp是由ESTs产生的，它们与特定的基因有关。在QTL区间内定位的基因可以优先进行测试，以确定它们是否有助于观察到的表型。
Atlantic cod (Gadus morhua) is a species with increasing economic significance for the aquaculture industry. The genetic improvement of cod will play a critical role in achieving successful large-scale aquaculture. While many microsatellite markers have been developed in cod, the number of single nucleotide polymorphisms (SNPs) is currently limited. Here we report the identification of SNPs from sequence data generated by a large-scale expressed sequence tag (EST) program, focusing on fish originating from Canadian waters. A total of 97976 ESTs were assembled to generate 13448 contigs. We detected 4753 SNPs that met our selection criteria (depth of coverage ≥ 4 reads; minor allele frequency > 25%). 3072 SNPs were selected for testing. The percentage of successful assays was 75%, with 2291 SNPs amplifying correctly. Of these, 607 (26%) SNPs were monomorphic for all populations tested. In total, 64 (4%) of SNPs are likely to represent duplicated genes or highly similar members of gene families, rather than alternative alleles of the same gene, since they showed a high frequency of heterozygosity. The remaining polymorphic SNPs (1620) were categorised as validated SNPs. The mean minor allele frequency of the validated loci was 0.258 (± 0.141). Of the 1514 contigs from which validated SNPs were selected, 31% have a significant blast hit. For the SNPs predicted to occur in coding regions (141), we determined that 36% (51) are non-synonymous. Many loci (1033 SNPs; 64%) are polymorphic in all populations tested. However a small number of SNPs (184) that are polymorphic in the Western Atlantic were monomorphic in fish tested from three European populations. A preliminary linkage map has been constructed with 23 major linkage groups and 924 mapped SNPs. These SNPs represent powerful tools to accelerate the genetic improvement of cod aquaculture. They have been used to build a genetic linkage map that can be applied to quantitative trait locus (QTL) discovery. Since these SNPs were generated from ESTs, they are linked to specific genes. Genes that map within QTL intervals can be prioritized for testing to determine whether they contribute to observed phenotypes.
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