Genome-wide marker discovery in three South African indigenous cattle breeds (Afrikaner, Drakensberger and Nguni) using whole genome sequencing

The aim of this study was to perform genome-wide marker discovery in three South African indigenous cattle breeds through whole genome sequencing of pooled DNA samples, with specific objectives to search for new variants, validate newly identified variants using 1000 Bull Genomes Project data, perform functional annotation and enrichment analysis on identified SNPs, identify selective sweeps and a panel of breed-specific markers to discriminate between breeds