The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study molecular characterization was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69% (UFH) to 72% PED with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8% of the total genetic variation was due to the genetic differentiation between the populations and 92.2% accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on 2 limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.

Highlights• 240 dairy goats from three breeds were genotyped using 25 microsatellite markers.• Moderate to high levels of genetic diversity was observed in all breeds.• Limited inbreeding was indicated by F IS values.• Populations clustered into three breeds and a crossbred population cluster.• Uncontrolled cross breeding should be avoided to maintain breed integrity. AbstractThe dairy goat industry is a small, but important role player in the South African agricultural sector. The limited number of animals representing the three main breeds (Saanen, British Alpine and Toggenburg) has raised concerns over the genetic diversity of these animals and the impact on their genetic management. In this study 240 dairy goats representing three breeds were genotyped with 25 microsatellite markers. Sufficient levels of genetic diversity were observed in all the breeds, with observed heterozygosity values exceeding 60%. A slight population differentiation was indicated by the low F ST values across and within the populations. This was confirmed by the AMOVA analyses with most of the variation shown within populations (91.7%). Negative F IS values in the three breeds indicated limited inbreeding. Population structure analyses revealed six distinct groups, with the Saanen population clustering into three sub-groups. The Toggenburg and British Alpine breeds formed their own separate cluster, with a last cluster formed by animals from all three pure-bred populations, indicating high levels of admixture. These results caution farmers against uncontrolled crossbreeding practices and recommend routine evaluation of genetic diversity.

Highlights• Establishment of a training population for SA Bonsmara beef cattle.• High density SNP genotypes of 583 cattle used in analysis.• Eight putative sub-populations identified via ADMIXTURE, but no concrete clusters.• Results indicate high levels of diversity and a heterogeneous population. AbstractThe 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 (r 2 < 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.

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