The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology
Open accessAbstract
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.
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<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
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Huang, X., & Madan, A. (1999) · Genome Research · doi:10.1101/gr.9.9.868 · Cited by 5,261
International Chicken Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03154 · Cited by 2,750
Genome sequence, comparative analysis and haplotype structure of the domestic dog
members, B. S. P., Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., et al. (2005) · Nature · doi:10.1038/nature04338 · Cited by 2,568
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Meurens, F., Summerfield, A., Nauwynck, H., Saif, L., & Gerdts, V. (2012) · Trends in Microbiology · doi:10.1016/j.tim.2011.11.002 · Cited by 999
Sequencing technologies and genome sequencing
Pareek, C. S., Smoczynski, R., & Tretyn, A. (2011) · Journal of Applied Genetics · doi:10.1007/s13353-011-0057-x · Cited by 868
Lu, F., Lipka, A. E., Glaubitz, J., Elshire, R., Cherney, J. H., Casler, M. D., Buckler, E. S., & Costich, D. E. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003215 · Cited by 659
Strong signatures of selection in the domestic pig genome
Rubin, C.-J., Megens, H.-J., Barrio, A. M., Maqbool, K., Sayyab, S., Schwochow, D., Wang, C., Carlborg, Ö., Jern, P., Jørgensen, C. B., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1217149109 · Cited by 652
Self-citationDaetwyler, H. D., Calus, M. P. L., Pong-Wong, R., de los Campos, G., & Hickey, J. M. (2013) · Genetics · doi:10.1534/genetics.112.147983 · Cited by 455
Metadata
- Authors
- Ramos, A. M., Crooijmans, R. P. M. A., Affara, N. A., Amaral, A. J., Archibald, A. L., Beever, J. E., Bendixen, C., Churcher, C., Clark, R., Dehais, P., Hansen, M. S., Hedegaard, J., Hu, Z.-L., Kerstens, H. H., Law, A. S., Megens, H.-J., Milan, D., Nonneman, D. J., Rohrer, G. A., Rothschild, M. F., Smith, T. P. L., Schnabel, R. D., Van Tassell, C. P., Taylor, J. F., Wiedmann, R. T., Schook, L. B., & Groenen, M. A. M.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2009-08-05
- Volume
- 4
- Issue
- 8
- Pages
- e6524
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2160717298
- Cited by
- 777
- References
- 4
- FWCI
- 27.98
- Type
- journal article
- Language
- en
- Open access
- gold
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- The paper
- Ramos, A. M., Crooijmans, R. P. M. A., Affara, N. A., Amaral, A. J., Archibald, A. L., Beever, J. E., Bendixen, C., Churcher, C., Clark, R., Dehais, P., Hansen, M. S., Hedegaard, J., Hu, Z.-L., Kerstens, H. H., Law, A. S., Megens, H.-J., Milan, D., Nonneman, D. J., Rohrer, G. A., . . . Groenen, M. A. M. (2009). Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology. PLoS ONE. https://doi.org/10.1371/journal.pone.0006524
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
