ArticleFrontiers in genetics2019
Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa.
Article in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 42 citations in OpenAlex.
- Exploring Genomic Variability in the Mediterranean Buffalo Breed: A Step Towards Custom SNP Array.Animals : an open access journal from MDPI · 2026Article
- Detection of genomic regions affecting thermotolerance traits in growing pigs during acute and chronic heat stress.Genetics, selection, evolution : GSE · 2025Article
- Four Target Resequencing for the Bovine Major Histocompatibility Complex Region. Proof of Concept.HLA · 2025Article
- Tailoring Genomic Selection forGenes · 2024Review
- Study on Single Nucleotide Polymorphism ofFoods (Basel, Switzerland) · 2024Article
- Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data.Animal bioscience · 2024Article
- Candidate genes associated with heat stress and breeding strategies to relieve its effects in dairy cattle: a deeper insight into the genetic architecture and immune response to heat stress.Frontiers in veterinary science · 2023Review
- Detection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattle.BMC genomics · 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
- Assessing Bos taurus introgression in the UOA Bos indicus assembly.Genetics, selection, evolution : GSE · 2021Article
- 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
- Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin.Frontiers in genetics · 2021Article
- Genetic diversity and relationships among three Southern African Nguni cattle populations.Tropical animal health and production · 2020Article
- SNP Diversity inGenes · 2020Article
- Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Frontiers in genetics · 2020Article
- Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform.PeerJ · 2020Article
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single nucleotide polymorphism arrays have created new possibilities for performing genome-wide studies to detect genomic regions harboring sequence variants that affect complex traits. However, the majority of validated SNPs for which allele frequencies have been estimated are limited primarily to European breeds. The objective of this study was to perform SNP discovery in three South African indigenous breeds (Afrikaner, Drakensberger, and Nguni) using whole genome sequencing. DNA was extracted from blood and hair samples, quantified and prepared at 50 ng/μl concentration for sequencing at the Agricultural Research Council Biotechnology Platform using an Illumina HiSeq 2500. The fastq files were used to call the variants using the Genome Analysis Tool Kit. A total of 1,678,360 were identified as novel using Run 6 of 1000 Bull Genomes Project. Annotation of the identified variants classified them into functional categories. Within the coding regions, about 30% of the SNPs were non-synonymous substitutions that encode for alternate amino acids. The study of distribution of SNP across the genome identified regions showing notable differences in the densities of SNPs among the breeds and highlighted many regions of functional significance. Gene ontology terms identified genes such as
Indexed as
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.