title: Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel.
abstract: Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. This study investigated genetic diversity and the population structure among six cattle breeds in South African (SA) including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31), and Holstein (n = 29). Genetic diversity within cattle breeds was analyzed using three measures of genetic diversity namely allelic richness (AR), expected heterozygosity (He) and inbreeding coefficient (f). Genetic distances between breed pairs were evaluated using Nei's genetic distance. Population structure was assessed using model-based clustering (ADMIXTURE). Results of this study revealed that the allelic richness ranged from 1.88 (Afrikaner) to 1.73 (Nguni). Afrikaner cattle had the lowest level of genetic diversity (He = 0.24) and the Drakensberger cattle (He = 0.30) had the highest level of genetic variation among indigenous and locally-developed cattle breeds. The level of inbreeding was lower across the studied cattle breeds. As expected the average genetic distance was the greatest between indigenous cattle breeds and Bos taurus cattle breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The results of this study provided useful insight regarding genetic structure of SA cattle breeds.
authors.affiliation: Agricultural Research Council-Animal Production Institute Irene, South Africa ; Department of Animal and Wildlife Sciences, University of Pretoria Hatfield, South Africa.
authors.forename: Sithembile O
authors.initials: SO
authors.lastname: Makina
authors.affiliation: Agricultural Research Council-Biotechnology Platform Onderstepoort, South Africa.
authors.forename: Farai C
authors.initials: FC
authors.lastname: Muchadeyi
authors.affiliation: Department of Animal and Wildlife Sciences, University of Pretoria Hatfield, South Africa.
authors.forename: Este
authors.initials: E
authors.lastname: van Marle-Köster
authors.affiliation: Agricultural Research Council-Animal Production Institute Irene, South Africa ; Department of Animal, Wildlife and Grassland Sciences, University of Free State Bloemfontein, South Africa ; Delta G, Miles City MT, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: MacNeil
authors.affiliation: Agricultural Research Council-Animal Production Institute Irene, South Africa ; Department of Animal, Wildlife and Grassland Sciences, University of Free State Bloemfontein, South Africa.
authors.forename: Azwihangwisi
authors.initials: A
authors.lastname: Maiwashe
keywords: South Africa; cattle breeds; genetic diversity; genetic resources; population structure