Of the estimated 150 local cattle breeds in Africa, we have received in our biorepository an estimated 1200 samples of 27 indigenous African cattle breeds from 13 African countries. Importantly, all our sample collection is in full compliance with national and international policy regulations, including the Nagoya protocol. Continued efforts are also being undertaken to ensure the resource is compliant re-access and benefit-sharing legislation of provider countries (i.e. the African partner countries), as well as user countries (Kenya and the United Kingdom). Discussions with partners are on-going in relation to establishing a consortium around these samples and data
Approximately, five hundred and fifty whole-genome sequences have been collated so far including 178 newly generated sequences. The sequences have been generated on the Illumina® HiSeq platform, and the coverages range from 10X to above 30x. All generated sequences are mapped to the latest bovine reference genome (ARS-UCD1.2) for variants discovery. Presently, we have identified more than 52 million single nucleotide polymorphisms (SNPs) and 14 million insertions and deletions (InDels). Further downstream analysis majorly envisaged include genome-wide scans for signatures of natural selection to environmental adaptation (e.g. heat stress, high altitude, disease tolerance (e.g. trypanosomiasis, ECF), tick resistance and production traits (e.g. milk)).
|Breed||number of generated sequences||Number of samples genotyped on high density SNP chip marker||Number of blood/DNA samples||Country|