Sheep (Ovis aries) genomic structure and diversity and the role of selection programs in breed formation could be useful in genomic prediction programs and maximizing realized genetic gain. In South Africa, sheep commercial farmers rely on several industrial breeds but on smallholder farms, extensively raised breeds predominate. Sheep breeds have been developed for different production systems ranging from mutton, wool, pelt and some dual purpose and non-descript breeds kept by smallholder farmers. Most breeds have been developed for adaptive and functional traits leading to a diverse array of phenotypically distinct breeds. This study investigated genetic diversity, population genetic structure and divergence between breeds in order to gain an insight into breed history and genomic architecture of the various sheep breeds of South Africa. The study used the Illumina OvineSNP50k BeadChip array to estimate and compare heterozygosity, FIS and the level population clustering and divergence among 400 individuals belonging to 11 South African sheep populations representing mutton (23 Dorper, 8 Blackhead Persian, 48 Meatmaster, 30 Nguni, 10 South African Mutton Merino and 10 Namaqua Afrikaner animals), pelt (96 Swakara animals) and mutton and wool dual purpose (56 South African Merino, 50 Dohne Merino and 51 Afrino animals) breeds. Across breeds, genetic diversity ranged from HE = 0.621 (Dohne Merino) to HE = 0.742 (Namaquar Afrikaner) with an overall mean of 0.633. Namaqua Afrikaner (F = 0.330) and Nguni and Blackhead Persian (F = 0.274) were the most inbred breeds with Dohne Merino (F = 0.0162), SA Merino (F = 0.0570) and Afrino (F = 0.0667) the least. The first principal component grouped the Merinos, Swakara, and the other breeds into separate clusters. The second principal component explained approximately 80.55% of the total variation and clustered the breeds according to their function and historical origin splitting the different Merino specialised breeds and distinguishing the Nguni, Namaqua Afrikaner, Blackhead Persian, Afrino and Dorper breeds. Signature of selection analysis revealed divergence between the Namaqua Afrikaner and the (i) Merino and the Merino-derivative group of sheep such as Afrino and (i) Dorper (ii) Meatmaster and (iii) Nguni on SNPs on chromosomes 3 and 6. The study overall demonstrated production system driven population sub-structuring and some selection pressures associated with the different breeding goals and objectives. Key words: ovine SNP50K genotypes, population structure, selection signatures, sheep, South Africa.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Electronic Poster Session - Technologies - Genotyping, , 873, 2018
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