A genome-wide single nucleotide polymorphism-based investigation of coat colour variation in indigenous South African goats

Abstract

Studying the foundation of coat colour diversity and its origins is essential for classifying goats into distinct ecotypes. This study offers insights into coat colour patterns of indigenous South African goats using single nucleotide polymorphism (SNP) data. A group of 192 goats from three recognised and five non-descript ecotypes alongside 96 South African Angora goats underwent genotyping using the Illumina® Goat SNP50 genotyping panel. Quality control (QC) procedures were carried out using PLINK version 1.9 software, while GCTA software was utilised for principal component analysis (PCA) to study population substructure. Distinct populations substructure was observed, with the highly selected Angora goats forming a separate, tight cluster. Indigenous goat types were clustered into two main groupings, one containing the Jozini, Mboza and Osca types, and the other consisting of a mixture of the ecotypes and remaining non-descript goats. Selection signature investigations employing the FST method and the Manhattan plots for the pairwise FST comparison between the Angora and indigenous goats indicated FST values for specific SNP ranging from 0.8 (least differentiated) to 1 (most differentiated). Twenty-six protein-coding genes were identified close to the ten most differentiated SNP. Genome-wide association studies (GWAS) were conducted with PLINK as well as EMMAX. Fourteen SNP markers linked to coat colour were identified in the GWAS study using PLINK, while the EMMAX analysis identified 16 markers associated with coat colour and its variation. Several genes with a well-recognized role in coat colour expression, including the KIT, MC1R, ASIP, and TYRP1 genes, were harboured in the genomic regions surrounding differentiated and/or phenotype-associated SNPs. These genes were in concordance with those previously reported for commercial goat breeds, which supports the idea of conserved coat colour genetics as a result of shared ancestry. This study highlights how the dispersal of goats into different environments with different ecological pressures led to varied coat colour patterns across populations. It enables classification and conservation and lays the groundwork for further studies on both the genetic and ecological adaptation of these animals.