Insight into the genetic composition of South African Sanga cattle using SNP data from cattle breeds worldwide

Abstract

BackgroundUnderstanding the history of cattle breeds is important because it provides the basis for developing appropriate selection and breed improvement programs. In this study, patterns of ancestry and admixture in Afrikaner, Nguni, Drakensberger and Bonsmara cattle of South Africa were investigated. We used 50 K single nucleotide polymorphism genotypes that were previously generated for the Afrikaner (n = 36), Nguni (n = 50), Drakensberger (n = 47) and Bonsmara (n = 44) breeds, and for 394 reference animals representing European taurine, African taurine, African zebu and Bos indicus.Results and discussionOur findings support previous conclusions that Sanga cattle breeds are composites between African taurine and Bos indicus. Among these breeds, the Afrikaner breed has significantly diverged from its ancestral forebears, probably due to genetic drift and selection to meet breeding objectives of the breed society that enable registration. The Nguni, Drakensberger and Bonsmara breeds are admixed, perhaps unintentionally in the case of Nguni and Drakensberger, but certainly by design in the case of Bonsmara, which was developed through crossbreeding between the Afrikaner, Hereford and Shorthorn breeds.ConclusionsWe established patterns of admixture and ancestry for South African Sanga cattle breeds, which provide a basis for developing appropriate strategies for their genetic improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0266-1) contains supplementary material, which is available to authorized users.

Genetic diversity in Zimbabwean Sanga cattle breeds using microsatellite markers

“…However, the Mashona is genetically more distant from the Nkone compared with the Tuli. These breeds have similar evolutionary patterns, having descended from the same Ethiopian ancestral cattle (Ramsay, 2010) and then separated geographically through ethnic or tribal ownership (Rowlands et al, 2003;Makina et al, 2016). Carr et al (1966) used biochemical markers (serum transferrin type and haemoglobin loci) on indigenous cattle genotypes of Zimbabwe and Zambia (Nkone, Mashona, Tuli, Angoni and Afrikaner) and found them to be distinct breeds.…”

“…In southern Africa, microsatellite markers have been used in population genetic studies of some Sanga cattle genotypes such as the Mozambican Landim (Bessa et al, 2009) and the South African Nguni (Sanarana et al, 2016). The genetic diversity of cattle has also recently been studied using SNP markers in Ethiopia (Edea et al, 2013) and South Africa (Makina et al, 2016).…”

Genomics for the advancement of livestock production: A South African perspective

“…The availability of DNA markers such as microsatellites provided the opportunity to perform population studies and contributed to knowledge of genetic diversity of farm animals, especially indigenous genetic resources (Hassen et al, 2009;Qwabe et al, 2012;Greyvenstein et al, 2016;Makina et al, 2016;Mdladla et al, 2016). In 1998 the Food and Agricultural Organisation (FAO) documented guidelines for conservation of farm animal genetic resources and listed the recommended microsatellite marker panels from the International Society for Animal Genetics (ISAG) for the evaluation of genetic diversity in farm animal species (FAO, 1998).…”

Genotype imputation as a cost-saving genomic strategy for South African Sanga cattle: A review

“…Zwane et al (2016) and Lashmar et al (2018) confirmed the tendency towards low MAF in Sanga breeds using GeneSeek®'s GGP 80K and GGP 150K bead chips, respectively. In a series of successive studies, the authors who did the original validation, investigated the genetic diversity (Makina et al, 2014;Makina et al, 2016), linkage disequilibrium (LD) and effective population size (N e ) (Makina et al, 2015a) as well as selection signatures (Makina et al, 2015b) of indigenous breeds. The SNP50 bead chip was also utilized to identify copy number variations (CNVs) in Nguni cattle (Wang et al, 2015).…”