Genetic diversity in selected stud and commercial herds of the Afrikaner cattle breed

Pienaar, L.; Grobler, J. Paul; Neser, F.W.C.; Scholtz, M. M.; Swart, H.; Ehlers, Karen; Marx, Munro

doi:10.4314/sajas.v44i5.16

SA J. An. Sci.

2015

DOI: 10.4314/sajas.v44i5.16

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Genetic diversity in selected stud and commercial herds of the Afrikaner cattle breed

L. Pienaar¹,

J. Paul Grobler²,

F.W.C. Neser³

et al.

Abstract: The Afrikaner is one of three indigenous cattle breeds found in South Africa. Afrikaner cattle were originally extensively used for crossbreeding purposes and breed development. The objective of this study was to determine the genetic diversity of selected stud and commercial herds from the whole South African Afrikaner population, as well as to determine the genetic structure among these herds. Assignment methods (based on STRUCTURE software) revealed a real structure consisting of four genetic populations (K… Show more

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Cited by 3 publications

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Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

et al. 2015

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Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40–60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2≥ 0.20 would require about 30,000–50,000 SNPs. However, r2≥ 0.20 extended only up to 10–20 kb in the Nguni and Drakensberger and 20–40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

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Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

et al. 2015

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Strategies for Sustainable Use of Indigenous Cattle Genetic Resources in Southern Africa

et al. 2019

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Indigenous cattle breeds are the most important livestock species in the Southern African Development Community (SADC) region owing to their role in human food, nutrition, income, and social security. Despite the role of these breeds in the household and national economies, they are currently underutilised, their productivity remains low, and populations are faced with extinction. In addition, there are insufficient measures taken to secure their present and future value. The current review highlights strategies for sustainable use of indigenous cattle genetic resources in the region, including the use of novel production and marketing practices, women and youth empowerment, and development of the appropriate capacity building, legislative, and policy structures. At present, the lack of coordination among the different stakeholders still poses a challenge to the implementation of these strategies. To this end, partnerships, collaboration, and stakeholders’ participation are recommended to effectively implement strategies for sustainable use of indigenous cattle breeds.

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Genotype imputation as a cost-saving genomic strategy for South African Sanga cattle: A review

Lashmar¹,

Muchadeyi²,

Visser³

2019

SA J. An. Sci.

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The South African beef cattle population is heterogeneous and consists of a variety of breeds, production systems and breeding goals. Indigenous cattle breeds are uniquely adapted to their native surroundings, necessitating conservation of these breeds as usable genetic resources to sustain efficient production of beef. Current projections indicate positive growth in human population size, with parallel growth in nutritional demand, in the midst of intensifying environmental conditions. Sanga cattle, therefore, are invaluable assets to the South African beef industry. Modern genomic methodologies allow for an extensive insight into the genome architecture of local breeds. The evolution of these methodologies has also provided opportunities to incorporate deoxyribonucleic acid (DNA) information into breed improvement programs in the form of genomic selection (GS). Certain challenges, such as the high cost of generating adequate numbers of dense genotypic profiles and the introduction of ascertainment bias when non-commercial breeds are genotyped with commercial single nucleotide polymorphism (SNP) panels, have caused a lag in progress on the genomics front in South Africa. Genotype imputation is a statistical method that infers unavailable or missing genotypic data based on shared haplotypes within a population using a population or breed representative reference sample. Genotypes are generated in silico, providing an animal with genotypic information for SNP markers that were not genotyped, based on predictive model-based algorithms. The validation of this method for indigenous breeds will enable the development of cost-effective low-density bead chips, allowing more animals to be genotyped, and imputation to high-density information. The improvement in SNP densities, at lower cost, will allow enhanced power in genome-wide association studies (GWAS) and genomic estimated breeding value (GEBV)-based selection for these breeds. To fully reap the benefits of this methodology, however, will require the setting up of accurate and reliable frameworks that are optimized for its application in Sanga breeds. This review paper aims, first, to identify the challenges that have been impeding genomic applications for Sanga cattle and second, to outline the advantages that a method such as genotype imputation might provide.

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Genetic diversity in selected stud and commercial herds of the Afrikaner cattle breed

Cited by 3 publications

References 11 publications

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

Strategies for Sustainable Use of Indigenous Cattle Genetic Resources in Southern Africa

Genotype imputation as a cost-saving genomic strategy for South African Sanga cattle: A review

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