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

Le Roex, Nikki ; Noyes, Harry ; Brass, Andrew ; Bradley, Daniel G. ; Kemp, Steven J. ; Kay, Suzanne ; Van Helden, Paul D. ; Hoal, Eileen G. (2012-11-07)

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Please 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.


The 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.

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