Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha
Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha
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DOI：
10.1111/j.1755-0998.2010.02972.x
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发表时间：
2011-03-01
影响因子：
7.7
通讯作者：
Garza, J. C.
中科院分区：
文献类型：
--
作者：
Clemento, A. J.;Abadia-Cardoso, A.;Garza, J. C.
在过去的二十年里，非模式生物的分子群体遗传学一直以微卫星位点的使用为主导。对许多物种的广泛基因组资源的可用性有助于向使用单核苷酸多态性（SNPs）来研究许多自然种群的过渡。在这里，我们描述了通过对表达序列标签（EST）区域的大规模Sanger测序，在奇努克鲑鱼（Chinook salmon）中发现了大量snp。奇努克鲑鱼是世界上最重要的渔业物种之一。在24条鲑鱼的不同确定小组中，从225个独立的est中收集了近132 kb的独特基因区域的变异调查，收集了超过3 Mb的序列。这项调查产生了117个TaqMan（5’核酸酶）测定，几乎全部来自单独的est，这些测定在美国太平洋沿岸三个最大的盆地（萨克拉门托河、克拉莫斯河和哥伦比亚河）的五个主要鲑鱼种群样本中得到了验证。这些等位基因在各种群中的变异比例为86.3% ~ 90.6%，平均小等位基因频率为0.194 ~ 0.236。这些标记在种群间存在显著差异，平均F-ST估计值为0.107，单个位点的值在0到0.592之间。这种大量的多态性和群体特异性分化表明这些标记将广泛有用，包括谱系重建和遗传种群鉴定应用。
Molecular population genetics of non-model organisms has been dominated by the use of microsatellite loci over the last two decades. The availability of extensive genomic resources for many species is contributing to a transition to the use of single nucleotide polymorphisms (SNPs) for the study of many natural populations. Here we describe the discovery of a large number of SNPs in Chinook salmon, one of the world's most important fishery species, through large-scale Sanger sequencing of expressed sequence tag (EST) regions. More than 3 Mb of sequence was collected in a survey of variation in almost 132 kb of unique genic regions, from 225 separate ESTs, in a diverse ascertainment panel of 24 salmon. This survey yielded 117 TaqMan (5' nuclease) assays, almost all from separate ESTs, which were validated in population samples from five major stocks of salmon from the three largest basins on the Pacific coast of the contiguous United States: the Sacramento, Klamath and Columbia Rivers. The proportion of these loci that was variable in each of these stocks ranged from 86.3% to 90.6% and the mean minor allele frequency ranged from 0.194 to 0.236. There was substantial differentiation between populations with these markers, with a mean F-ST estimate of 0.107, and values for individual loci ranging from 0 to 0.592. This substantial polymorphism and population-specific differentiation indicates that these markers will be broadly useful, including for both pedigree reconstruction and genetic stock identification applications.