Genetic diversity and population structure of the South African Hereford population

Abstract

In this study both microsatellite and SNP data was evaluated, with the aim to quantify genetic variation, inbreeding and population structure at a genomic level to provide reference data for the South African (SA) Hereford breed. A total of 1799 microsatellite profiles were obtained from UNISTEL generated with 11 ISAG recommended microsatellite markers. Two data sets were evaluated, a complete data set of 1799 samples and a selected, representative subset of 500 samples. The mean number of microsatellite alleles was 10 and 8.5 for the complete and subset data sets, respectively across the 11 loci analysed. Heterozygosity and FIS estimates across the loci were (0.663± 0.003) and (-0.014) for the complete data set and (0.661± 0.006) and (-0.009) for the subset data set, respectively, indicating relatively high genetic diversity present within the populations and low inbreeding. Population structure analysis assigned the animals to six inferred clusters, with three herds forming distinct herd clusters and the remaining herds assigning evenly across the inferred clusters. The SNP data set contained 184 SA and 316 Irish Herefords, which were analysed separately and then as a merged data set. The two data sets were subjected to quality control, utilising the following parameters, namely a sample call rate of <98%, a SNP call rate of <98%, MAF of <5% and deviation from HWE (p<0.001). The observed HO for the SA and Irish Hereford in this study were similar, while inbreeding differed slightly, but was low in both cases (SA: -0.002± 0.051; Irish: -0.007± 0.034). Principal component analysis for the SA Hereford observed three genetically distinct herds, with the remainder of the herds sharing a close genetic relationship. The ADMIXTURE analysis assigned the SA Hereford to seven inferred clusters, supporting the PCA analysis. The Irish Hereford formed one distinct cluster in the PCA results, supported by the ADMIXTURE analysis, indicating one homogenous population. The merged data set population structure analysis, allocated the SA and Irish Herefords into two diverse clusters, with slight overlap, indicating the two populations are genetically distinct. The microsatellite and SNP data supported each other, indicating the SA Hereford are sufficiently genetically diverse for improvement and development of the breed. The results provide reference data on genomic diversity in the SA Hereford for application in the development of the current training population for genomic selection.