Cattle may have been domesticated in North Africa 8,000 years ago and have been adapting to vast range of environments and diseases in Africa ever since. Olivier Hanotte has published a paper in Science describing how this genetic diversity is at risk of being lost by the rapid introduction of European breeds of high yielding cattle that are often poorly adapted to African conditions
In order to describe this diversity and discover Single Nucleotide Poplymorphisms (SNP) for our genetic research we have sequenced the genomes of Boran, N'Dama and Sahiwal cattle breeds to identify Single Nucleotide Polymorphisms (SNP) in the genomes of these breeds. The objective is to discover SNP that can be used as markers in subsequent genetic studies. We are also examining the polymorphisms in the regions of the genome that we know are associated with response to trypanosome infection in order to identify any differences that might have an effect on function of genes and hence contribute to differences in phenotype after infection.
In order to maximize the number of SNP that we will discover we used pools of DNA samples from 10 animals for the Boran and the Sahiwal and 20 animals for the N'dama. Each pool was sequenced to a depth of 10-17x coverage on an ABI SOLiD3 sequencer at the Liverpool Centre for Genomic Research or An Illumina Genome Analyser IIe at the Roslin Institute. This is unlikely to have detected all the polymorphisms in these sequences but nevertheless has given us 10-20million SNP in each breed.
We have developed a SNP selection and primer design webpage where you can select SNP by annotation and or by genome region. The selected SNP loci can then be piped directly into the Primer3 primer design programme. It is also possible to select SNP that are cut by a given restriction enzyme and then design primers for them to develop PCR-RFLP assays to test them in a population.
We are currently analyzing the data to identify non-synonymous SNP in genes that would cause changes in amino acid sequence. We are also looking for regions where the alternate allele of all SNP is exceptionally rare. In these regions one allele of a gene(s) might have been selected during breeding because it might be associated with a particularly desirable trait.
Cape Buffalo (Syncerus caffer) are infected with trypanosomes but show no signs of disease due to their ability to increase levels of hydrogen peroxide which is toxic to parasites (Black et al 2002). Our paper Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing. PLoS ONE 2012 7(11) describes a large set of SNP in African buffalo. The data can be queried to obtain sets of SNP suitable for PCR-RFLP assays or for SNP in genes or regions of interest from our Cape Buffalo SNP web page.
Cape buffalo are one of the closest relatives to domestic cattle and our main objective is to use the Cape Buffalo data to annotate the cow genome data. Where there are differences between individuals in the cattle the Cape Buffalo data will tell us which version was ancestral and which one evolved in cattle. This will help us identify the genes that contribute to the distinctive qualities of cattle.
Prof Paul Van Helden of Stellenbosch University in South Africa has been studying an epidemic of tuberculosis (TB) that has been sweeping through South African wildlife and we will include DNA from Cape Buffalo that show symptoms of TB and others that have been infected but have no symptoms. The data will be used to develop markers for the identification of tuberculosis resistance genes in Cape Buffalo.