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.
Highlights
Investigating genetic variation between individuals, populations or species provides the basis for understanding the heritability of traits and phenotypes, and provides researchers with the opportunity to study complex issues in conservation, disease susceptibility, molecular ecology and many other disciplines [1]
The African buffalo has become a species of interest in recent years due to its role as a wildlife maintenance host for a variety of infectious and zoonotic diseases, such as corridor disease, foot-andmouth disease and bovine tuberculosis [13]
There is no African buffalo reference genome available for use in disease association studies, and much benefit would be gained by the generation of sequence data and large-scale SNP discovery in this species
Summary
Investigating genetic variation between individuals, populations or species provides the basis for understanding the heritability of traits and phenotypes, and provides researchers with the opportunity to study complex issues in conservation, disease susceptibility, molecular ecology and many other disciplines [1]. If the genome of a closely related species is available, this can be used as a reference, the proportion of data that can be mapped to the genome may be significantly reduced, and the data obtained will indicate variation seen between species as well as between individuals of the same species [9,10,11]. Other considerations such as depth of coverage and quality must be taken into account, when using this approach
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