Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands.
PLoS One. 2009 Aug 5;4(8):e6524. doi: 10.1371/journal.pone.0006524.
The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay.
METHODOLOGY/PRINCIPAL FINDINGS: A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274.
CONCLUSIONS/SIGNIFICANCE: Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs.
解析对养猪业具有重要经济意义的复杂性状需要大量的遗传标记，如单核苷酸多态性（SNP）。本研究旨在利用下一代测序技术发现数十万头猪的 SNP，并利用这些 SNP 以及来自不同公共资源的其他 SNP，设计一种高密度 SNP 基因分型检测。
方法/主要发现：总共从四个猪品种（杜洛克、长白、大白、皮特兰）和一个野猪群体中获得了 19 个简化代表性文库，并使用 Illumina 的基因组分析仪（GA）对其进行测序。该 SNP 发现工作共鉴定出 372000 多个 SNP。超过 549000 个 SNP 用于设计 Illumina 猪 60K+SNP iSelect Beadchip，现在商业上称为 PorcineSNP60。Beadchip 共包含 64232 个 SNP。对用于测序的 158 个个体进行基因分型的结果显示，总体 SNP 调用率很高（97.5%）。在可以可靠评分的 62621 个位点中，58994 个是多态性的，SNP 转换成功率为 94%。所有可评分 SNP 的平均次要等位基因频率（MAF）为 0.274。
结论/意义：总的来说，这项研究的结果表明，利用下一代测序技术可以识别大量可靠的 SNP。此外，PorcineSNP60 Beadchip 的验证表明，该检测是一种极好的工具，可能会在未来猪的各种研究中得到应用。
