Novel SNP discovery in African buffalo, Syncerus caffer, using high-throughput sequencing

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dc.contributor.authorLe Roex, Nikkien_ZA
dc.contributor.authorNoyes, Harryen_ZA
dc.contributor.authorBrass, Andrewen_ZA
dc.contributor.authorBradley, Daniel G.en_ZA
dc.contributor.authorKemp, Steven J.en_ZA
dc.contributor.authorKay, Suzanneen_ZA
dc.contributor.authorVan Helden, Paul D.en_ZA
dc.contributor.authorHoal, Eileen G.en_ZA
dc.date.accessioned2013-03-01T08:05:37Z
dc.date.available2013-03-01T08:05:37Z
dc.date.issued2012-11-07
dc.descriptionThe original publication is available at http://journals.plos.org/plosoneen_ZA
dc.descriptionPlease cite as follows: Le Roex, N. et al. 2012. Novel SNP discovery in African buffalo, Syncerus caffer, using high-throughput sequencing. PLoS ONE, 7(11):e48792, doi:10.1371/journal.pone.0048792.en_ZA
dc.description.abstractThe African buffalo, Syncerus caffer, is one of the most abundant and ecologically important species of megafauna in the savannah ecosystem. It is an important prey species, as well as a host for a vast array of nematodes, pathogens and infectious diseases, such as bovine tuberculosis and corridor disease. Large-scale SNP discovery in this species would greatly facilitate further research into the area of host genetics and disease susceptibility, as well as provide a wealth of sequence information for other conservation and genomics studies. We sequenced pools of Cape buffalo DNA from a total of 9 animals, on an ABI SOLiD4 sequencer. The resulting short reads were mapped to the UMD3.1 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.76coverage over the mapped regions was obtained. Btau4 gene annotation was added to all SNPs identified within gene regions. Bowtie and BWA identified a maximum of 2,222,665 and 276,847 SNPs within the buffalo respectively, depending on analysis method. A panel of 173 SNPs was validated by fluorescent genotyping in 87 individuals. 27 SNPs failed to amplify, and of the remaining 146 SNPs, 43–54% of the Bowtie SNPs and 57–58% of the BWA SNPs were confirmed as polymorphic. dN/dS ratios found no evidence of positive selection, and although there were genes that appeared to be under negative selection, these were more likely to be slowly evolving house-keeping genes.en_ZA
dc.description.sponsorshipFunding for sequencing was provided by the Wellcome Trust (GR066764MA to SJK). Financial support was provided by WOTRO (W01.65.321.00; http:// www.nwo.nl/wotro/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en_ZA
dc.description.urihttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048792
dc.description.versionPublisher's versionen_ZA
dc.format.extent6 pagesen_ZA
dc.identifier.citationLe Roex, N. et al. 2012. Novel SNP discovery in African buffalo, Syncerus caffer, using high-throughput sequencing. PLoS ONE, 7(11):e48792, doi:10.1371/journal.pone.0048792.en_ZA
dc.identifier.issn1932-6203 (online)
dc.identifier.otherdoi:10.1371/journal.pone.0048792
dc.identifier.urihttp://hdl.handle.net/10019.1/79626
dc.language.isoen_ZAen_ZA
dc.publisherPLoSen_ZA
dc.rights.holderAuthors retain copyrighten_ZA
dc.subjectAfrican buffalo -- Geneticsen_ZA
dc.subjectGenetic polymorphismsen_ZA
dc.subjectHigh-throughput sequencingen_ZA
dc.subjectSingle nucleotide polymorphisms (SNP)en_ZA
dc.titleNovel SNP discovery in African buffalo, Syncerus caffer, using high-throughput sequencingen_ZA
dc.typeArticleen_ZA
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