Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout
Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout
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DOI：
10.1111/j.1755-0998.2010.02967.x
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发表时间：
2011-03-01
影响因子：
7.7
通讯作者：
Luikart, Gordon
中科院分区：
文献类型：
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作者：
Hohenlohe, Paul A.;Amish, Stephen J.;Luikart, Gordon
基因组技术产生的遗传标记数量的增加有可能识别杂交个体和定位响应选择和促进基因渗入的染色体区域。我们使用限制性位点相关DNA测序技术鉴定了引进虹鳟鱼（Oncorhynchus mykiss）和本地西坡切喉鳟鱼（Oncorhynchus clarkii lewisi）之间存在固定等位基因差异的密集候选SNP位点。我们通过检测观察到的过高杂合性和偏离Hardy-Weinberg比例，将候选snp从同源物（由全基因组重复产生的类似物）中区分出来。我们从一个包含24个条形码标记个体的Illumina测序通道中鉴定出2923个候选物种特异性snp。已公布的序列数据和正在进行的虹鳟鱼基因组测序将允许对SNP位点进行全基因组扫描的物理定位，并将为设计基于qpcr的TaqMan (R)检测提供侧翼序列，用于使用50-100个位点的高通量、低成本杂交鉴定。这项研究表明，即使没有先前的基因组信息，现在也可以以合理的成本快速识别非模式物种中的数千个信息snp。
The increased numbers of genetic markers produced by genomic techniques have the potential to both identify hybrid individuals and localize chromosomal regions responding to selection and contributing to introgression. We used restriction-site-associated DNA sequencing to identify a dense set of candidate SNP loci with fixed allelic differences between introduced rainbow trout (Oncorhynchus mykiss) and native westslope cutthroat trout (Oncorhynchus clarkii lewisi). We distinguished candidate SNPs from homeologs (paralogs resulting from whole-genome duplication) by detecting excessively high observed heterozygosity and deviations from Hardy-Weinberg proportions. We identified 2923 candidate species-specific SNPs from a single Illumina sequencing lane containing 24 barcode-labelled individuals. Published sequence data and ongoing genome sequencing of rainbow trout will allow physical mapping of SNP loci for genome-wide scans and will also provide flanking sequence for design of qPCR-based TaqMan (R) assays for high-throughput, low-cost hybrid identification using a subset of 50-100 loci. This study demonstrates that it is now feasible to identify thousands of informative SNPs in nonmodel species quickly and at reasonable cost, even if no prior genomic information is available.