Genetic characterisation of the Tankwa Goat (Capra hircus) using genome-wide SNP data and the identification of genes associated with climate adaptation

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.