Abstract:
The feral Tankwa goat is a landrace breed of domesticated goat (Capra Hircus) originating
from the Tankwa Karoo National Park. This landrace breed is being managed and
conserved by the Northern Cape Department of Agriculture, Environmental Affairs, Rural
Development and Land Reform (DAERL) on a farm in Carnarvon. This study aimed to
genetically characterise the Tankwa goat, identify signatures of selection for adaptability and
propose recommendations for the successful management of this landrace breed. A total of
360 Tankwa goats was genotyped on the Illumina GoatSNP50 BeadChip at the
Biotechnology Platform of the Agricultural Research Council. In addition, data on 48 Angora
and 40 dairy genotypes were provided by the University of Pretoria. The two commercial
goat breeds (Angora and dairy) was used as reference for comparison with the Tankwa
goats. Sample and marker based quality control were completed using PLINK. The Tankwa
population was genetically characterised by calculating genetic diversity parameters that
included observed (H O ) and expected (H E ) heterozygosity, minor allele frequency (MAF),
runs of homozygosity (ROH) and linkage disequilibrium (LD), inbreeding using PLINK;
effective population size (N e ) using SNeP; population structure using ADMIXURE and
relatedness using GCTA. Signatures of selection were determined using the F ST method in
PLINK. The Tankwa goat had a MAF of 0.249, Expected and Observed Heterozygosity of
0.368 and 0.367 respectively and LD using r 2 of 0.469. Inbreeding was calculated using the
F IS and F ROH statistics, with low levels reported (Average F IS = -0.107 and Average F ROH =
0.006). N e was estimated at 60 individuals 12 generations ago using SNeP. The Tankwa
goat population showed no sub-structure within the population but had a clear separation
from the other breeds confirming their genetic uniqueness. This result was supported by the
principal component analysis (PCA). Signatures of selection identified 50 SNP’s under
selection, the top 0.1% was considered significant, 49 genes were identified as possibly
significant for adaptation. Of these GJB2, GJB6 and GJA3 on Chromosome 12 were
previously associated with adaptation to heat and drought in other breeds. Genes GJB2 and
GJB6 are involved in the sensory perception of sound, while GJA3 and OPA3 is involved in
visual perception. These genes could be important for foraging or escape from predators.
