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South Africa has a diverse array of phenotypically distinct and locally adapted sheep breeds that have been developed for different production systems ranging from mutton to wool and pelt, and some dual-purpose and nondescript breeds kept by smallholder farmers. This study investigated genetic diversity, population genetic structure and divergence between South African sheep breeds in order to gain an insight into breed history and genomic architecture aligned to breeding goals and production systems. The Illumina OvineSNP50 BeadChip was
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