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

Abstract

The composite Bonsmara beef cattle breed in South Africa is in the process of assembling a reference population for genomic selection. For genomic selection to be a success within the breed, which already 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 genotypes with 19119 SNPs in linkage disequilibrium (r2 < 0.2). It was found that the reference population is largely nonhomogenous, and while 121 breeders contributed toward the reference population, a strong herd/breeder effect could also be observed. Results indicate that a larger reference population may be required for genomic selection in the Bonsmara to be practiced accurately.