Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data

The sustainability of goat farming in marginal areas of southern Africa depends on local breeds that are adapted to specific agro-ecological conditions. Unimproved non-descript goats are the main genetic resources used for the development of commercial meat-type breeds of South Africa. Little is known about genetic diversity and the genetics of adaptation of these indigenous goat populations. This study investigated the genetic diversity, population structure and breed relations, linkage disequilibrium, effective population size and persistence of gametic phase in goat populations of South Africa. Three locally developed meat-type breeds of the Boer (n=33), Savanna (n=31), Kalahari Red (n=40), a feral breed of Tankwa (n=25) and unimproved non-descript village ecotypes (n=110) from four goat-producing provinces of the Eastern Cape, KwaZulu-Natal, Limpopo and North West were assessed using the Illumina Goat 50K SNP Bead Chip assay. The proportion of SNPs with minor allele frequencies >0.05 ranged from 84.22% in the Tankwa to 97.58% in the Xhosa ecotype, with a mean of 0.32 +/- 0.13 across populations. Principal components analysis, admixture and pairwise F-ST identified Tankwa as a genetically distinct population and supported clustering of the populations according to their historical origins. Genome-wide F-ST identified 101 markers potentially under positive selection in the Tankwa. Average linkage disequilibrium was highest in the Tankwa (r(2)=0.25 +/- 0.26) and lowest in the village ecotypes (r(2) range=0.09 +/- 0.12 to 0.11 +/- 0.14). We observed an effective population size of <150 for all populations 13 generations ago. The estimated correlations for all breed pairs were lower than 0.80 at marker distances >100kb with the exception of those in Savanna and Tswana populations. This study highlights the high level of genetic diversity in South African indigenous goats as well as the utility of the genome-wide SNP marker panels in genetic studies of these populations.