Short communication: Population structure of the South African Bonsmara beef breed using high density single nucleotide polymorphism genotypes

The composite Bonsmara beef cattle breed in South Africa is in the process of establishing a reference population for genomic evaluations. For successful implementation of genomic selection within the breed, which has large numbers of genotypes and phenotypes available, the marker effects must be accurately determined by estimating the genetic variance in the breed. To this end, the population structure of the Bonsmara reference population was studied using 583 registered individuals. The population studied was largely heterogeneous, and although 121 breeders contributed to the reference population, a strong herd/breeder effect was detected. ADMIXTURE analysis identified eight putative sub-populations within the reference population, but no defined clusters were formed. Results indicate the current reference population is heterogenous and captured high levels of diversity in the breed.