SNP discovery in South African indigenous cattle breeds. Bos indicus breed:Afrikaner, Drakensberger, Nguni

The objective of this study was to search for new SNPs in three indigenous SA breeds (Afrikaner, Drakensberger and Nguni) using next generation sequencing. Approximately 1.8 billion sequence reads were aligned to the UMD3.1 reference genome generating an average depth of 21-fold sequence coverage for each breed. A total of 15.7 million SNPs were identified across the breeds with the highest number of SNPs identified in Nguni. Verification of SNPs against Run 5 data from the 1000 Bull Genomes project suggested that 15% of the SNPs were novel variants.