NDama Whole Genome Sequencing and SNP discovery
SNP discovery in African taurine and Zebu cattle by whole genome sequencing of pooled DNA
African taurine and Zebu cattle breeds differ in their susceptibility to many diseases, most notably trypanosomiasis and rinderpest. African taurine breeds have been evolving in Africa for over 6000 years and are have high levels of resistance or tolerance to many endemic diseases. However introduced Bos indicus (zebu) animals are rapidly replacing the taurine breeds. Bos indicus and Bos taurus cattle are believed to have diverged over 200000 years ago making it likely that there will be large numbers of differences between taurine and indicine breeds. In order to monitor the introgression of the indicine genomes into Africa we have obtained whole genome shotgun sequence of the African taurine N'Dama breed and the zebu Sahiwal. Pools of DNA from 11 Sahiwal and 20 N'dama were sequenced to at least ten times coverage. The primary analysis of the genome will identify informative SNP between the two breeds that can be used to develop African SNP chips. The genomes were sequenced from paired-end and mate pair libraries. We will use this information to identify structural variation and genome rearrangements between these very divergent breeds and the European taurine cattle represented by the Hereford reference genome.