ArticleFrontiers in genetics2015
Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds.
Article in Frontiers in genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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32 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genomic Advancements in Assessing Growth Performance, Meat Quality, and Carcass Characteristics of Goats in Sub-Saharan Africa: A Systematic Review.International journal of molecular sciences · 2025Pooled it
- Integrated transcriptomic analysis unveils molecular mechanisms regulating meat quality in newly improved black goat breeds.NPJ science of food · 2025Article
- Genetic diversity and population structure of non-descript cattle in South African smallholder systems.Frontiers in genetics · 2025Article
- Accuracy of genomic prediction using multiple Atlantic salmon populations.Genetics, selection, evolution : GSE · 2024Article
- Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat.Frontiers in genetics · 2024Article
- Unraveling genetic admixture in the Indian crossbred cattle by different approaches using Bovine 50K BeadChip.Tropical animal health and production · 2022Article
- Sustained Effects of Muscle Calpain System Genotypes on Tenderness Phenotypes of South African Beef Bulls during Ageing up to 20 Days.Animals : an open access journal from MDPI · 2022Article
- Assessing accuracy of genotype imputation in the Afrikaner and Brahman cattle breeds of South Africa.Tropical animal health and production · 2022Article
- Genetics of Base Coat Colour Variations and Coat Colour-Patterns of the South African Nguni Cattle Investigated Using High-Density SNP Genotypes.Frontiers in genetics · 2022Article
- Assessing single-nucleotide polymorphism selection methods for the development of a low-density panel optimized for imputation in South African Drakensberger beef cattle.Journal of animal science · 2021Article
- Genetic diversity and population structure of three native cattle populations in Mozambique.Tropical animal health and production · 2021Article
- Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations.Frontiers in genetics · 2021Article
- Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data.PloS one · 2021Article
- SNP-Based Genotyping Provides Insight Into the West Asian Origin of Russian Local Goats.Frontiers in genetics · 2021Article
- Multiple Country and Breed Genomic Prediction of Tick Resistance in Beef Cattle.Frontiers in immunology · 2021Article
- Article
- Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds.Animals : an open access journal from MDPI · 2020Article
- Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle.Scientific reports · 2020Article
- Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data.Frontiers in genetics · 2020Article
- Comparisons of improved genomic predictions generated by different imputation methods for genotyping by sequencing data in livestock populations.Journal of animal science and biotechnology · 2020Article
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Abstract
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 r (2)≥ 0.20 would require about 30,000-50,000 SNPs. However, r (2)≥ 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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