Population Structure and Breed Relations of South African Indigenous Goat Ecotypes Using Genome-Wide SNP Data

Commercial meat-type goat breeds in South Africa such as the Boer, Savanna and Kalahari Red were developed through artificial selection from unimproved ecotype populations. The genetic diversity is however not fully understood. In the current study, 192 animals were genotyped using the Illumina Goat 60K SNP BeadChip representing meat-type breeds (Boer (n = 20), Savanna (n = 21), Kalahari Red (n = 17)), the feral breed (Tankwa (n = 25), and unimproved local village ecotypes (n = 99) from four goat-producing provinces (Eastern Cape, KwaZulu-Natal, Limpopo, and North West). The multi-coloured Nguni (iMbuzi) ecotype from KwaZulu-Natal province (n = 10) was included. Overall, 93% of the total SNPs (51,928) were polymorphic. The overall observed and expected mean heterozygosities were 0.38±0.09 and 0.42±0.09, respectively. Mean individual inbreeding coefficients (F_IS) were highest in the Tankwa (0.19) and Boer (0.14), and lowest in the Eastern Cape population (0.01). The higher PC1 (6%) and PC2 (4.2%) supported the clustering of populations according to their breed type, partially explained breed origin and revealing the Tankwa as a distinct breed. This finding was corroborated by ADMIXTURE analysis at K=5. Cluster analysis also illustrated subpopulation diversity within the village ecotype population. Highest F_ST values were observed for all pair-wise combinations in the Tankwa (F_ST = range 0.12 to 0.18) and least among the Limpopo and KwaZulu-Natal ecotypes (F_ST = 0.001). This study presents information on the genomic architecture of the SA indigenous goat populations that could be of use in breed development and conservation.