title: Novel SNP Discovery in African Buffalo, Syncerus caffer, using high-throughput Sequencing.
abstract: 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 2.7× coverage 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.
authors.affiliation: DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa.
authors.forename: Nikki
authors.initials: N
authors.lastname: le Roex
authors.forename: Harry
authors.initials: H
authors.lastname: Noyes
authors.forename: Andrew
authors.initials: A
authors.lastname: Brass
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Bradley
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Kemp
authors.forename: Suzanne
authors.initials: S
authors.lastname: Kay
authors.forename: Paul D
authors.initials: PD
authors.lastname: van Helden
authors.forename: Eileen G
authors.initials: EG
authors.lastname: Hoal
mesh_terms: D000818:Animals; D002020:Buffaloes / Q000235:genetics*; D002874:Chromosome Mapping; D059014:High-Throughput Nucleotide Sequencing; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA