Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

By A. Ramos, R. Crooijmans, N. Affara, A. Amaral, A. Archibald, J. Beever, C. Bendixen, C. Churcher, R. Clark, Patrick Dehais and 17 more. PLoS ONE, 2009

775 citations recorded by the source corpus.

Background 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.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/fe4cc7d532df4a741f99879d594722e58777f695

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In Genetics

Citations in the corpus

Applications of next-generation sequencing to the study of biological invasions (2015, background): “Such high-density arrays (Ramos et al., 2009; Kumar et al., 2012), for example, Illumina’s Infinium assay, can accurately genotype any number of SNPs (up to a million in one assay) across many individuals (Adler et al.”
Genetic diversity in the European wild boar Sus scrofa: phylogeography, population structure and wild x domestic hybridization (2011, background): “A microarray of 60000 SNPs (Illumina Porcine 60K iSelect Beadchip, Lincoln, Nebraska, USA) has been developed to detect variation within and among pig breeds (Ramos et al. 2009).”
Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol (2013, background): “The reference could be a high-quality genome sequence [12–16], de novo assembly from deep sequencing [17–20] or transcriptome sequences [21].”
Development and Application of High-density SNP Arrays in Genomic Studies of Domestic Animals (2010, neutral): “Additionally, the physical locations of some mapped SNPs have been corrected with the production of new genome assemblies (Ramos et al., 2009).”
Applications of next-generation sequencing to phylogeography and phylogenetics. (2013, background): “…of agricultural importance (Van Orsouw et al., 2007; Van Tassell et al., 2008; Wiedmann et al., 2008; Amaral et al., 2009; Kerstens et al., 2009; Ramos et al., 2009; Sánchez et al., 2009; Hyten et al., 2010a,b), most involving many fewer individuals that would normally be assayed in a typical…”
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery (2010, background): “…for a variety of genome-wide variant discovery projects (Hillier et al. 2008; Ossowski et al. 2008; Van Tassel et al. 2008; Wang et al. 2008; Ahn et al. 2009; Amaral et al. 2009; Eck et al. 2009; Huang et al. 2009; Ramos et al. 2009), where a high quality reference genome sequence was available.”
The pig: a model for human infectious diseases (2011, background): “A high-quality bacterial artificial chromosome map of the genome has been assembled and more than 375 000 single nucleotide polymorphisms were identified [79] .”
Sequencing technologies and genome sequencing (2011, methodology): “Ramos et al. 2009 Prenatal transcriptomic profiling by HT-NGS: RNA sequencing of trophectoderm (TE) and embryonic disc (ED) of a single day 12 porcine embryo was performed using the Illumina NGS platform.”