Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology.
<h4>Background</h4>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 porci...
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2009
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oai:doaj.org-article:de3e489388a44e97891edd5caa3bd6e02021-12-02T20:12:07ZDesign of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology.1932-620310.1371/journal.pone.0006524https://doaj.org/article/de3e489388a44e97891edd5caa3bd6e02009-08-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19654876/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>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.Antonio M RamosRichard P M A CrooijmansNabeel A AffaraAndreia J AmaralAlan L ArchibaldJonathan E BeeverChristian BendixenCarol ChurcherRichard ClarkPatrick DehaisMark S HansenJakob HedegaardZhi-Liang HuHindrik H KerstensAndy S LawHendrik-Jan MegensDenis MilanDanny J NonnemanGary A RohrerMax F RothschildTim P L SmithRobert D SchnabelCurt P Van TassellJeremy F TaylorRalph T WiedmannLawrence B SchookMartien A M GroenenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 4, Iss 8, p e6524 (2009) |
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| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Antonio M Ramos Richard P M A Crooijmans Nabeel A Affara Andreia J Amaral Alan L Archibald Jonathan E Beever Christian Bendixen Carol Churcher Richard Clark Patrick Dehais Mark S Hansen Jakob Hedegaard Zhi-Liang Hu Hindrik H Kerstens Andy S Law Hendrik-Jan Megens Denis Milan Danny J Nonneman Gary A Rohrer Max F Rothschild Tim P L Smith Robert D Schnabel Curt P Van Tassell Jeremy F Taylor Ralph T Wiedmann Lawrence B Schook Martien A M Groenen Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. |
| description |
<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>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. |
| format |
article |
| author |
Antonio M Ramos Richard P M A Crooijmans Nabeel A Affara Andreia J Amaral Alan L Archibald Jonathan E Beever Christian Bendixen Carol Churcher Richard Clark Patrick Dehais Mark S Hansen Jakob Hedegaard Zhi-Liang Hu Hindrik H Kerstens Andy S Law Hendrik-Jan Megens Denis Milan Danny J Nonneman Gary A Rohrer Max F Rothschild Tim P L Smith Robert D Schnabel Curt P Van Tassell Jeremy F Taylor Ralph T Wiedmann Lawrence B Schook Martien A M Groenen |
| author_facet |
Antonio M Ramos Richard P M A Crooijmans Nabeel A Affara Andreia J Amaral Alan L Archibald Jonathan E Beever Christian Bendixen Carol Churcher Richard Clark Patrick Dehais Mark S Hansen Jakob Hedegaard Zhi-Liang Hu Hindrik H Kerstens Andy S Law Hendrik-Jan Megens Denis Milan Danny J Nonneman Gary A Rohrer Max F Rothschild Tim P L Smith Robert D Schnabel Curt P Van Tassell Jeremy F Taylor Ralph T Wiedmann Lawrence B Schook Martien A M Groenen |
| author_sort |
Antonio M Ramos |
| title |
Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. |
| title_short |
Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. |
| title_full |
Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. |
| title_fullStr |
Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. |
| title_full_unstemmed |
Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. |
| title_sort |
design of a high density snp genotyping assay in the pig using snps identified and characterized by next generation sequencing technology. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2009 |
| url |
https://doaj.org/article/de3e489388a44e97891edd5caa3bd6e0 |
| work_keys_str_mv |
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