A homozygosity-based investigation of the South African feral Tankwa goat population

Abstract

The Tankwa goat is a known feral goat landrace that originated in the Karoo region of South Africa. These goats are able to thrive with no managerial intervention, and prosper in the harsh, arid conditions that characterizes their natural habitat. This study aimed to use a ROH-approach to describe the Tankwa goat in terms of autozygosity and to identify possible signatures of selection. Genome-wide SNP data for 360 Tankwa goats were used to calculate diversity statistics, detect runs of homozygosity and estimate individual genetic inbreeding coefficients. SNP genotypes of 48 Angora and 40 Dairy individuals were compared using the FST approach to detect signatures of selection. Relatively low minor allele frequency (0.249), and high linkage disequilibrium (r2 = 0.469) levels were estimated for the Tankwa population, with moderate levels of heterozygosity (HE = 0.368; HO = 0.367). The results for both the detected runs of homozygosity and inbreeding estimate, indicates an ancient origin of inbreeding for the Tankwa goats with low levels of autozygosity. Signatures of selection were identified in 50 SNPs, of which 0.1% was considered significant. A total of 49 genes were identified that may possibly be significant in various biological pathways. Three of these genes, namely GJB2, GJB6 and GJA3 on CHI12, were previously associated with adaptation to heat and drought resistance in other breeds. Genes GJB2 and GJB6 are known to be linked to the sensory perception of sound, while GJA3 and OPA3 are linked to visual perception. These genes could play an important role in the survival of an individual existing in a harsh environment in terms of foraging and evading predators. Understanding the genetic background of these genes, as well as the metabolic pathways that they control, could assist in further investigating production efficiency of domesticated species in a climate change environment.