Development of 54 novel single-nucleotide polymorphism (SNP) assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River
Development of 54 novel single-nucleotide polymorphism (SNP) assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River
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DOI：
10.1111/j.1755-0998.2011.02977.x
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发表时间：
2011-03-01
影响因子：
7.7
通讯作者：
Narum, Shawn R.
中科院分区：
文献类型：
--
作者：
Campbell, Nathan R.;Narum, Shawn R.
单核苷酸多态(SNPs)在种群和保护遗传学中具有广泛的应用潜力，但这些标记在许多非模式物种中的可用性有限。本研究利用近缘鲑科鱼类(Chinook鲑鱼和彩虹鲑鱼)的基因组和表达序列标签(EST)序列设计了用于SNP扩增和测序的SNP。设计了106对引物，对每个物种进行了扩增试验。以来自每个物种的32个不同个体组成的确证小组作为模板，进行PCR扩增和Sanger测序。共筛选出红鲑鱼21647个碱基，鳕鱼20784个碱基，分别鉴定出93个和149个SNP位点。选择了64个SNP位点用于检测，其中54个检测通过与基因和序列数据的比较进行了验证(O.Nerka=23；O.kiutch=31)。这些有效的SNP分析与142种其他可用的SNP分析[O.Nerka=103(126个总数)；O.kiutch=30(61个总数)]用于哥伦比亚河不同地点的O.Nerka(N=5)和O.kiutch(N=4)的基因分型，以评估这些标记在该地区的应用。析因对应分析结果表明，这些SNP标记能够区分尼尔卡稻种群，但由于其共同的祖先，这些SNP标记不能很好地区分种群。
Single-nucleotide polymorphisms (SNPs) have potential for broad application in population and conservation genetics, but availability of these markers is limited in many nonmodel species. In this study, genomic and expressed sequence tagged (EST) sequences from closely related salmonids (Chinook salmon and rainbow trout) were used to design primers for amplification and sequencing of sockeye (Oncorhynchus nerka) and coho (Oncorhynchus kisutch) salmon DNA for SNP discovery. One hundred and six primer sets were designed and tested for amplification in each species. An ascertainment panel of 32 diverse individuals from each species was used as template for PCR amplification and Sanger sequencing. In total, 21 647 bases of consensus sequence were screened in sockeye salmon and 20 784 bases in coho salmon with 93 and 149 SNP sites identified, respectively. Sixty-four SNP sites were chosen for assay development, and 54 of the assays were validated by comparison with genotype and sequence data (O. nerka = 23; O. kisutch = 31). These validated SNP assays along with 142 other available SNP assays [O. nerka = 103 (126 total); O. kisutch = 30 (61 total)] were used to genotype collections of O. nerka (N = 5) and O. kisutch (N = 4) from various sites in the Columbia River to evaluate the utility of these markers in this region. Results from factorial correspondence analysis indicate that these SNP markers are capable of distinguishing O. nerka populations, but O. kisutch collections were less distinct because of their common ancestry.