SNP-based genetic diversity and population structure of South African beef cattle breeds

Abstract

Evaluation of genetic diversity in cattle populations is important to understand breed structure and for maintaining diversity. The aim of this study was to assess SNP based genomic diversity and population structure of eight South African beef cattle breeds. In this study 2110 beef cattle genotypes, generated within the BGP, representing eight South African beef cattle breeds (Bonsmara, Beefmaster, Boran, Charolais, Hereford, Drakensberger, Nguni and Tuli) were included for analyses. Genotypic data were generated using the GGP 150k SNP array for all registered, genotyped animals participating in Logix Beef Recording. PLINK was used to estimate genetic diversity parameters within populations and biological types. GCTA and ADMIXTURE were used for population structure analysis. SNeP was used to estimate effective population size for all populations. Results indicated limited loss of heterozygosity for the Beefmaster, Boran, Drakensberg and Hereford breeds (𝐻𝑒>𝐻𝑜) and no loss of heterozygosity for Bonsmara, Charolais and Nguni breeds. Results further indicated no loss in genetic diversity for all eight populations. The eight populations were grouped into specific biological types namely indigenous (Drakensberger, Nguni and Tuli), composite (Beefmaster and Bonsmara) and exotic types (Boran, Charolais and Hereford) and population diversity parameters were estimated. Analysis of the percentage of low-MAF SNP (MAF<0.05) was done and revealed the indigenous breed group had the highest percentage of low-MAF SNP across the genome. Inbreeding estimates based on 𝐹𝐼𝑆 and 𝐹𝑅𝑂𝐻 indicated limited inbreeding across the populations (𝐹𝐼𝑆:-0.009 to 0.016 and 𝐹𝑅𝑂𝐻 : 0.001-0.005). ROH analysis revealed that any inbreeding was due to ancient inbreeding, based upon the high number of ROH segments that had a length of between 0 and 3.9 MB. Effective population size (𝑁𝑒) analysis showed a decline in the 𝑁𝑒 for all eight breeds. A principal component analysis (PCA) and admixture plot identified eight distinctive breeds with some admixture present. The indigenous populations clustered together due to common ancestry and time divergence. The study concluded that they SA beef populations in this study exhibit moderate to high levels of genetic diversity with low inbreeding.