Genetic diversity in selected stud and commercial herds of the Afrikaner cattle breed (original) (raw)
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Genetic diversity of Afrikaner cattle in southern Africa
Tropical animal health and production, 2017
The Afrikaner is an indigenous South African breed of "Sanga" type beef cattle along with breeds such as the Drakensberger and Nguni. Six composite breeds have been developed from crosses with the Afrikaner. Additionally, Afrikaner has been the base from which exotic breeds were established in South Africa through backcrossing. The study examined genetic diversity of Afrikaner cattle by genotyping 1257 animals from 27 herds in different geographic areas of South Africa and Namibia using 11 microsatellite markers. Multiple-locus assignment, performed using the Bayesian clustering algorithm of STRUCTURE, revealed three underlying genotypic groups. These groups were not geographically localized. Across herds and markers, the proportion of unbiased heterozygosity ranged from 0.49 to 0.72 averaging 0.57; mean number of alleles per locus ranged from 3.18 to 7.09, averaging 4.81; and allelic richness ranged from 2.35 to 3.38, averaging 2.67. It is concluded that a low inbreeding ...
Genetic diversity and relationships among three Southern African Nguni cattle populations
Tropical Animal Health and Production, 2019
The Nguni cattle breed has distinct populations that are adapted to the different ecological zones of Southern Africa. This study was carried out to assess genetic diversity and establish the relationships among South African (SA), Mozambican (Landim), and Swazi Nguni cattle populations, using 25 microsatellite markers. Genotypic data were generated from deoxyribonucleic acid (DNA) samples of 90 unrelated individuals of the three cattle populations, collected from government conservations and stud herds. DNA profiles of five local beef breeds were used as the reference populations. Most of the 25 microsatellite markers were highly polymorphic across the studied populations, with an overall polymorphic information content (PIC) mean of 0.676. Genetic diversity within populations was high with expected heterozygosity varying from 0.705 ± 0.024 (Landim) to 0.748 ± 0.021 (SA Nguni) and mean number of alleles being highest in the SA Nguni (7.52 ± 0.42). Average observed heterozygosity (0.597 ± 0.046) compared to the expected heterozygosity (0.719 ± 0.022) was lowest for the Swazi Nguni, which also had a high number of Hardy-Weinberg Equilibrium (HWE) deviated loci (13), confirming the relatively high level of inbreeding (0.158 ± 0.058) in that population. Analysis of molecular variance revealed only 9.61% of the total variation between the populations and 90.39% within populations. A short genetic distance (0.299) was observed between Landim and Swazi Nguni, with the SA Nguni (> 0.500) being the most genetically distant population. The distant relationship between SA Nguni and the other two Nguni cattle populations was further confirmed by a principal coordinates analysis. The three Nguni populations clustered independently from each other, despite some evidence of admixture. Therefore, it can be concluded that SA Nguni, Landim, and Swazi Nguni populations in Southern Africa exhibit high levels of genetic diversity and are genetically distant; with the two latter populations being less genetically apart. These results present useful information for the development of strategies for regional management of animal genetic resources, through conservation and sustainable utilisation.
Genetic variability and relationships among nine southern African and exotic cattle breeds
2018
An existing 11 microsatellite marker database that resulted from parentage verification in response to requests from industry, was used to assess genetic diversity among nine breeds of cattle. These breeds were drawn from B. indicus (Boran (BOR) and Brahman (BRA)), B. taurus (Angus (ANG) and Simmental (SIM)), and B. taurus africanus (Afrikaner (AFR), Bonsmara (BON), Drakensberger (DRA), Nguni (NGU), and Tuli (TUL)). Due to the cost of genotyping, genetic diversity studies using SNPs rely on relatively low numbers of animals to represent each of the breeds. Large numbers of animals have been genotyped for parentage verification using microsatellite markers, therefore, the microsatellite information on large numbers of animals has the potential to provide more accurate estimates of genomic diversity. A minimum of 300 animals were randomly chosen from each breed and were used to assess withinand between breed genetic diversity. All breeds had high levels of heterozygosity and minimal i...
Genetic characterisation of non-descript cattle populations in communal areas of South Africa
Animal Production Science, 2020
Context Indigenous cattle breeds represent an important genetic resource for livelihood of communal-area inhabitants. Indigenous breeds have the ability to withstand harsh climatic conditions, can adapt genetically to poor-quality forages and are resistant to parasites and diseases. These unique traits possessed by indigenous breeds are under threat because of unrestrained crossing with exotic commercial breeds, and this can lead to total loss of a breed. Aims The study was conducted to assess the genetic diversity and population structure of South African non-descript communal beef cattle populations by using 25 microsatellite markers. Methods Unrelated and non-descript animals (n = 150) were sampled from communal areas from five (5) provinces of South Africa, namely, Eastern Cape, KwaZulu–Natal, Limpopo, Mpumalanga and the North West, with 30 samples per breed taken. Six (6) known cattle breeds (n = 180) were used as a reference population. This included Angus, Afrikaner, Bonsmara...
2021
In southern Africa, the Nguni cattle breed is classified as an indigenous and transboundary animal genetic resource that manifests unique adaptation abilities across distinct agroecological zones. The genetic integrity of various ecotypes is under potential threat due to both indiscriminate crossbreeding and uncontrolled inbreeding. The aim of this study was to assess the genetic diversity and autozygosity that exists both across countries (ES: eSwatini; SA: South Africa) and within-country (SA), between purebred stud animals (SA-S) and research herds (SA-R). Subsets of 96 ES, 96 SA-S and 96 SA-R genotyped for 40 930 common SNPs were used to study inbreeding, runs of homozygosity (ROH) and heterozygosity (ROHet) profiles as well as population structure. The highest proportion (0.513) of the 3 595 ROH was <4Mb in length, while the majority (0.560) of the 4 409 ROHet segments fell within the 0.5-1Mb length category. Inbreeding coefficients indicated low inbreeding (FROH range: 0.02...
Frontiers in Genetics, 2014
In this study, genetic diversity among 177 oat (Avena sativa L.) accessions including both white and red oat landraces and 36 commercial cultivars was studied for simple sequence repeat (SSR) loci. Thirty-one genomic and expressed sequence tags (EST)-derived primer pairs were selected according to high polymorphism from an initial 66 SSR batch. Markers revealed a high level of polymorphism, detecting a total of 454 alleles. The average gene diversity for the whole sample was 0.29. Genetic similarity, calculated using the Dice coefficient, was used for cluster analysis, and principal component analysis was also applied. In addition, population structure using a Bayesian clustering approach identified discrete subpopulation based on allele frequency and showed similar clustering of oat genotypes in four groups. Accessions could be classified into four main clusters that clearly separated the commercial cultivars, the red oat landraces and two clusters of white oat landraces. Cultivars showed less diversity than the landraces indicating a reduction of genetic diversity during breeding, whereas white oat landraces showed higher diversity than red ones. The average polymorphic information content of 0.80 for the SSR loci indicated the usefulness of many of the SSR for genotype identification. In particular, two markers, MAMA5 and AM04, with a total of 50 alleles and a high discrimination power (>0.90), were sufficient to discriminate among all commercial cultivars studied highlighting their potential use for variety identification.
Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers
Tropical Animal Health and Production, 2015
The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study molecular characterization was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69% (UFH) to 72% PED with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8% of the total genetic variation was due to the genetic differentiation between the populations and 92.2% accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on 2 limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.
Genetics, selection, evolution : GSE, 2016
Understanding the history of cattle breeds is important because it provides the basis for developing appropriate selection and breed improvement programs. In this study, patterns of ancestry and admixture in Afrikaner, Nguni, Drakensberger and Bonsmara cattle of South Africa were investigated. We used 50 K single nucleotide polymorphism genotypes that were previously generated for the Afrikaner (n = 36), Nguni (n = 50), Drakensberger (n = 47) and Bonsmara (n = 44) breeds, and for 394 reference animals representing European taurine, African taurine, African zebu and Bos indicus. Our findings support previous conclusions that Sanga cattle breeds are composites between African taurine and Bos indicus. Among these breeds, the Afrikaner breed has significantly diverged from its ancestral forebears, probably due to genetic drift and selection to meet breeding objectives of the breed society that enable registration. The Nguni, Drakensberger and Bonsmara breeds are admixed, perhaps uninten...
Genetic diversity and population structure of three native cattle populations in Mozambique
2021
In the present work, the population diversity and structure of three populations of native Mozambican cattle were studied, to develop knowledge that is required for sound conservation and genetic improvement programs of these genetic resources. A total of 228 animals (Landim, Angone, and Tete) were genotyped using the International Dairy and Beef version three (IDBV3) SNP BeadChip array. Population parameters varied within a limited scope, with the average minor allele frequency (MAF) ranging from 0.228 ± 0.154 in the Angone to 0.245 ± 0.145 in the Tete population, while estimates of expected heterozygosities varied from 0.304 ± 0.166 in the Angone to 0.329 ± 0.148 in the Tete population. Low positive (0.065 ± 0.109) inbreeding rates were detected in the three cattle groups. Population structure and admixture analyses indicated low genetic differentiation and various degrees of admixture among the populations. The effective population size has decreased over time and at 12 generatio...
Animals
The Nguni cattle of South Africa are a Sanga breed, characterized by many eco-types and research populations that have been established in an effort to conserve the diversity within the breed. The aim of this study was to investigate the overall genetic diversity as well as similarities and differences within and between two conservation herds of the South African Nguni Cattle. Mean LD (r2) estimates were 0.413 ± 0.219 for Bartlow Combine and 0.402 ± 0.209 for Kokstad. Genome-wide average LD (r2) decreased with increasing genetic marker distance for both populations from an average of 0.76 ± 0.28 and 0.77 ± 0.27 at 0–1 kb bin to 0.31 ± 0.13 and 0.32 ± 0.13 at 900–1000 kb bin in Bartlow Combine and Kokstad populations, respectively. Variation in LD levels across autosomes was observed in both populations. The results showed higher levels of LD than previously reported in Nguni field populations and other South African breeds, especially at shorter marker distances of less than 20 kb....