Population genetics of Swakara sheep inferred using genome-wide SNP genotyping.

Abstract

The pelts of Swakara sheep breed of Namibia are famous for their lustrous features and are unmatched in quality across the globe. These pelts occur in four subpopulations of white, grey, black and brown. The white pelt is the most preferred pelt colour. However, there is a challenge in producing white pelts due to the sub-vital factor that affects homozygous white lambs, thought to be a result of the negative impact of years of inbreeding and selection pressures. Sub-vital performance is a genetic disorder that causes digestive complications in lambs resulting in their death within days of birth. The ability to identify carriers or affected individuals of sub-vital performance at an early stage will save the Swakara industry production costs and reduce mortality rates in the white subpopulation. In this study, high-throughput SNP genotyping was used to perform a population genetics study, which investigates the genetic structure of Swakara with the aim of identifying structural differences between sub-vital individuals and the other coat colours, and by using GWAS to determine the variants contributing to sub-vitality in subtle effects and their associated genes in Swakara. This study will also look at selection pressures in Swakara, the genetic differentiation between subpopulations, level of inbreeding and the presence of ROH segments in Swakara and their associated genes that relate to sub-vital performance. Genetic statistical tools such as PLINK, ARLEQUIN and SVS were used to perform the analyses required for this population study. Ninety Swakara sheep were collected from Namibia and South Africa. These were sub-divided into four colour subpopulations of black (n = 16), grey (n = 22), vital white (n = 35) and sub-vital white (n = 17). The DNA from each of these was then genotyped using the OvineSNP50 beadchip. The genotyping success rate was > 93% across all the colour subpopulations. The quality control (QC) post genotyping was done by removing SNPs that departed from HWE > 0.0001, had low allele frequencies MAF < 0.01, SNP markers that had missing/low call rates (GENO) > 0.01 and individuals that had missing genotypes (MIND) > 0.1. This QC was done for every subpopulation described in this study prior to all other succeeding analyses. The inbreeding coefficient F was high in the black subpopulation (0.04798±0.069) and lowest in the grey (0.01074±0.079) Swakara sheep. The genetic diversity for the Swakara subpopulations showed a consensus in the results and showed the most diversity between the black and white subpopulations. The PCA results also showed the genetically similar subpopulations, as identified by pairwise FST values, clustered together. Forty-two unique ROH were observed across 10 chromosomes in 33 (out of 90) individuals and spanned between 5198.93-7126.85 KB in length in the four colour subpopulations. The white sub-vital group had the highest number of ROHs (18). Seven overlapping/consensus regions of homozygosity were observed on chromosome 2, 7, 9, 10, and 20. There was no correlation between the frequency of ROHs in an individual and the level of inbreeding, however the black subpopulation had the highest level of inbreeding and had the highest average of ROH length among the other subpopulations but this was not a consistent trend with the other subpopulations. The GWAS revealed at least five SNPs associated to sub-vitality located on chromosome 3, 5, and 8. Chromosome 3 had three different SNPs associated to sub-vitality. The most prominent SNPs was located on chromosome 3, which is associated to a gene, IGF1, responsible for insulin-like growth factor and contributes to the development of foetal organs. The genes identified by GWAS and cROH pointed to the cause of sub-vitality due to the contributing effects of biological functions related to metabolic activities. A targeted gene sequencing study would be required to assess the differences in the sequences of the identified significant SNPs, the IGF1 genetic region, in order to examine the possible causal mutations of sub-vitality. A study focussed more on the white and sub-vital subpopulation, with an increased sample size and a targeted gene sequencing approach would assess the differences in the targeted sequences of both case and control individuals.