Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology.
Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology.
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DOI：
10.1371/journal.pone.0006524
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发表时间：
2009-08-05
期刊：
影响因子：
3.7
通讯作者：
Groenen MA
中科院分区：
文献类型：
--
作者：
Ramos AM;Crooijmans RP;Affara NA;Amaral AJ;Archibald AL;Beever JE;Bendixen C;Churcher C;Clark R;Dehais P;Hansen MS;Hedegaard J;Hu ZL;Kerstens HH;Law AS;Megens HJ;Milan D;Nonneman DJ;Rohrer GA;Rothschild MF;Smith TP;Schnabel RD;Van Tassell CP;Taylor JF;Wiedmann RT;Schook LB;Groenen MA
对养猪业具有经济重要性的复杂性状的剖析需要大量遗传标记的可用性，例如单核苷酸多态性（SNP）。本研究旨在利用下一代测序技术发现数十万个猪SNP，并利用这些SNP以及来自不同公共来源的其他SNP设计高密度SNP基因分型检测。使用Illumina的基因组分析仪（GA）对来自四个猪品种（杜洛克猪、长白猪、大白色猪、皮特兰猪）和一个野猪群体的总共19个简化代表文库和三种限制性内切酶（BamHI、HaeIII和MspI）进行测序。SNP发现工作导致了超过372K SNP的重新鉴定。使用超过549K SNP来设计Illumina Porcine 60K+SNP iSelect Beadchip，现在可作为PorcineSNP 60商购获得。在Beadchip上总共包括64，232个SNP。用于测序的158个个体的基因分型结果显示出高的总体SNP调用率（97.5%）。在62，621个可以可靠评分的位点中，58，994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。总体而言，本研究的结果表明使用下一代测序技术来鉴定大量可靠的SNP的实用性。此外，PorcineSNP60 Beadchip的验证表明，该检测试剂盒是一种很好的工具，可能会用于未来的各种猪研究。
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. 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. 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.
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影响因子：
7
作者：
Li, Heng;Ruan, Jue;Durbin, Richard
通讯作者：
Durbin, Richard
影响因子：
3.7
作者：
Jungerius, BJ;Gu, JJ;Pas, MFWT
通讯作者：
Pas, MFWT
猪基因组的高实用性集成图。
影响因子：
12.3
作者：
Humphray, Sean J.;Scott, Carol E.;Clark, Richard;Marron, Brandy;Bender, Clare;Camm, Nick;Davis, Jayne;Jenks, Andrew;Noon, Angela;Patel, Manish;Sehra, Harminder;Yang, Fengtang;Rogatcheva, Margarita B.;Milan, Denis;Chardon, Patrick;Rohrer, Gary;Nonneman, Dan;de Jong, Pieter;Meyers, Stacey N.;Archibald, Alan;Beever, Jonathan E.;Schook, Lawrence B.;Rogers, Jane
通讯作者：
Rogers, Jane
影响因子：
30.8
作者：
Karlsson, Elinor K.;Baranowska, Izabella;Lindblad-Toh, Kerstin
通讯作者：
Lindblad-Toh, Kerstin
影响因子：
3.3
作者：
Amaral, Andreia J.;Megens, Hendrik-Jan;Groenen, Martien A. M.
通讯作者：
Groenen, Martien A. M.