SUMMARY

Prior knowledge of the breed structure, genetic diversity and extent of linkage disequilibrium (LD) is necessary to determine the sample size and number of SNPs necessary to ensure sufficient power of detection in genome-wide association studies (GWAS) and genomic prediction. The OvineSNP50 was used to genotype Blackheaded Dorper, Namaqua Afrikaner (NA), South African Mutton Merino (SAMM) and two flocks of South African Merino to determine genetic diversity and structure within and between the breeds. The NA exhibited the least number of polymorphic loci and was also the least genetically diverse breed tested. The South African Merino samples exhibited high levels of diversity comparable to results of international Merinos. The NA samples exhibited the longest stretches of LD in comparison to the 3 other breeds, while the Merino had the shortest extent of LD. The Dorper and SAMM samples exhibited intermediate LD length in comparison to the 2 aforementioned breeds. A PCA indicated 4 distinct clusters in the data representing the 4 breeds. Inclusion of additional samples per breed may aid in increasing the resolution and clearly defining breeds and subtypes, especially in closely-related breeds such as the South African Merino and Merino-based breeds.