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

2015 ◽  
Vol 44 (5) ◽  
pp. 80-84
Author(s):  
L Pienaar ◽  
JP Grobler ◽  
FWC Neser ◽  
MM Scholtz ◽  
H Swart ◽  
...  
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Genetic Structure ◽  
South African ◽  
Bos Taurus ◽  
Cattle Breed ◽  
Significant Loss ◽  
Indigenous Cattle ◽  
Loss Of Genetic Diversity ◽  
High Degree

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 = 4). Estimates of genetic diversity did not support the hypothesis of significant loss of genetic diversity in any individual Afrikaner herd. Heterozygosity estimates ranged from 0.456 - 0.737 within individual populations, with an overall heterozygosity estimate of 0.568 for the Afrikaner breed. The average number of alleles per locus was regarded as being 2.67 - 7.78, with an average of 5.18 alleles per locus. It could be concluded that a moderate to high degree of variation is still present within the Afrikaner cattle breed, despite the recent decline in numbers of this indigenous breed.Keywords: Bos taurus africanus, heterozygosity, inbreeding, microsatellite markers

scholarly journals Genetic structure of the Southern meat cattle breed based on microsatellite markers

2019 ◽  
Vol 21 (91) ◽  
pp. 21-28
Author(s):  
A. S. Kramarenko
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Microsatellite Markers ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Cattle Breed ◽  
Animal Husbandry ◽  
State Enterprise ◽  
Tissue Samples ◽  
Cattle Breeds

The Southern Meat cattle is a composite breed developed by crossing Cuban zebu (Bos indicus) with different cattle breeds (Bos taurus) – local the Red Steppe, Hereford, Charolais, Santa Gertrudis, Dairy Shorthorn. Genetic structure of the Southern meat cattle breed from the State Enterprise Experimental Farm “Askaniyske” NAAS Ukraine (Kherson region) were investigated based on the microsatellite DNA loci. Analysis included 192 animals. A panel of 12 bovine-specific microsatellite markers (TGLA227, BM2113, TGLA53, ETH10, SPS115, TGLA122, INRA23, TGLA126, BM1818, ETH3, ETH225 and BM1824), recommended of the ISAG for cattle genetic diversity studies, was selected for genetic characterization and revealing the extent of genetic diversity in the Southern Meat cattle breed. Genomic DNA was extracted from tissue samples using Nexttec column (Nexttec Biotechnology GmbH, Germany) following the manufacturer's instructions. All laboratory tests were conducted in the laboratory of Molecular Genetics, Animal Center of Biotechnology and Molecular Diagnostics, All-Russian Research Institute for Animal Husbandry named after academy member L.K. Ernst. We report the distribution and the frequency of a taurine and an indicine specific alleles in the Southern Meat cattle breed using literature data about the Zebu and different cattle breeds genetic structure based on microsatellite loci from our list. It can be assumed that the TGLA22777, BM2113141-143, ETH10209-211, TGLA122149, INRA23194-198, TGLA126123, ETH225156-158-160 alleles among the Southern Meat cattle breed examined individuals were inherited from a B. indicus ancestor. On the other hand, the TGLA53156, ETH10217-219, TGLA122143, INRA23202, TGLA126115, ETH225148-150, BM1824188-190 alleles in the Southern Meat cattle gene pool may be inherited from a B. taurus ancestor (i.e., taurine breeds diagnostic alleles).

Genetic Diversity of Kedah Kelantan Cattle Breed and Its Crossbred types in Malaysia Based on Microsatellite Markers

2019 ◽  
Author(s):  
Haytham Hago Abdelwahid ◽  
Jothi M Panandam ◽  
Reuben S K Sharma ◽  
Halimatun Yaakub
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Cattle Breed ◽  
Meat Production ◽  
Indigenous Cattle ◽  
Maternal Line ◽  
Genetic Characteristics ◽  
Lack Of Information ◽  
Compact Body ◽  
Loss Of Genetic Diversity

Abstract Background The Kedah Kelantan (KK) is the indigenous cattle breed of Malaysia and is mainly kept by small farmers for meat production because of its small and compact body, and low maintenance requirement. This breed faces risk of germplasm dilution due to extensive crossbreeding and breeds replacement practices in the country. The population size of purebred KK is fast decreasing and most of the commercial populations are actually crossbreds. There is a lack of information on the genetic characteristics of KK. The genetic relationships between the KK, the synthetic breeds developed using the KK as the maternal line, as well as the non-descriptive KK crossbred types are also unknown. It is with these in mind that the present study was conducted. The objective of the study was to evaluate the genetic variability within and among the indigenous KK cattle and its crossbred types in Malaysia using 30 microsatellites loci. Results All the 30 microsatellites loci used were polymorphic in all populations. Heterozygosity values observed were moderate and lower than the expected values. The inbreeding was present in all populations and could lead to loss of genetic diversity if not addressed. In general, the genetic differentiation measures were moderate, with a mean FST of 0.054. The structure analysis grouped the populations into three clusters. Analysis of zebu and taurine diagnostic alleles showed that all population had high proportion of Indian zebu alleles and very low proportions of African taurine and European taurine diagnostic alleles. Conclusions It may be concluded that there is still some genetic variation present in the KK. However, this genetic diversity is at risk of being lost if no appropriate breeding practices are implemented.

Distribution and genetic diversity of Coguvirus eburi in South African citrus and the development of a real-time RT-PCR assay for citrus-infecting coguviruses

Plant Disease ◽  
2022 ◽  
Author(s):  
Rochelle de Bruyn ◽  
Rachelle Bester ◽  
Glynnis Cook ◽  
Chanel Steyn ◽  
Johannes Hendrik Jacobus Breytenbach ◽  
...  
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Real Time ◽  
South African ◽  
High Throughput Sequencing ◽  
Rna Virus ◽  
Citrus Paradisi ◽  
Virus Elimination ◽  
Shoot Tip Grafting ◽  
Citrus Production

Citrus virus A (CiVA), a novel negative-sense single-stranded RNA virus assigned to the species Coguvirus eburi in the genus Coguvirus, was detected in South Africa with the use of high-throughput sequencing (HTS) after its initial discovery in Italy. CiVA is closely related to citrus concave gum-associated virus (CCGaV), recently assigned to the species Citrus coguvirus. Disease association with CiVA is however incomplete. CiVA was detected in grapefruit (Citrus paradisi Macf.), sweet orange (C. sinensis (L.) Osb.) and clementine (C. reticulata Blanco) in South Africa and a survey to determine the distribution, symptom association and genetic diversity was conducted in three provinces and seven citrus production regions. The virus was detected in ‘Delta’ Valencia trees in six citrus production regions and a fruit rind symptom was often observed on CiVA-positive trees. Additionally, grapefruit showing symptoms of citrus impietratura disease were positive for CiVA. This virus was primarily detected in older orchards that were established prior to the application of shoot tip grafting for virus elimination in the South African Citrus Improvement Scheme. The three viral encoded genes of CiVA isolates from each cultivar and region were sequenced to investigate sequence diversity. Genetic differences were detected between the ‘Delta’ Valencia, grapefruit and clementine samples, with greater sequence variation observed with the nucleocapsid protein (NP) compared to the RNA-dependent RNA polymerase (RdRp) and the movement protein (MP). A real-time detection assay, targeting the RdRp, was developed to simultaneously detect citrus infecting coguviruses, CiVA and CCGaV, using a dual priming reverse primer to improve PCR specificity.

scholarly journals The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
N. Z. Gebrehiwot ◽  
E. M. Strucken ◽  
H. Aliloo ◽  
K. Marshall ◽  
J. P. Gibson
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Large Population ◽  
Bos Indicus ◽  
Principal Component ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
African Cattle ◽  
Snp Data

Abstract Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

scholarly journals Genetic Variation and Population Differentiation in the Bovine Lymphocyte Antigen DRB3.2 Locus of South African Nguni Crossbred Cattle

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1651
Author(s):  
Lwamkelekile Sitshilelo Mkize ◽  
Oliver Tendayi Zishiri
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
South African ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Heterozygote Advantage ◽  
Crossbred Cattle ◽  
High Genetic Diversity ◽  
Lymphocyte Antigen ◽  
Bovine Lymphocyte

The bovine lymphocyte antigen (BoLA-DRB3) gene is an important region that codes for glycoproteins responsible for the initiation of an immune response. BoLA-DRB3 alleles have been demonstrated to be associated with disease resistance/tolerance. Therefore, great genetic diversity is correlated with better adaptation, fitness, and robustness. The current study was conducted to assess the population genetic structure of the BoLA-DRB3 gene in Nguni crossbred cattle using polymerase chain reaction-sequence based typing (PCR-SBT). High genetic diversity was detected, with 30 alleles, 11 of which are novel to the study. Alleles DRB3*0201, DRB3*0701, DRB*0901, and DRB*1601 were present in all populations and accounted for nearly around 50% of all observed alleles. A mean genetic diversity (HE) of 0.93 was detected. The high overall genetic diversity is possibly associated with pathogen-assisted selection and heterozygote advantage. Such high diversity might explain the hardiness of the Nguni crossbred cattle to the Southern African region. Low population genetic structure was identified (FST = 0.01), suggesting possible gene flow between populations and retention of similar alleles. The study was undertaken to bridge the dearth of such studies in South African breeds and it is imperative for effective sustainability of indigenous breeds and the implementation of effective breeding strategies.

An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas

2015 ◽  
Vol 63 (5) ◽  
pp. 455 ◽  
Author(s):  
Linda M. Broadhurst ◽  
Graham Fifield ◽  
Bindi Vanzella ◽  
Melinda Pickup
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Seed Production ◽  
Significant Loss ◽  
Evolutionary Potential ◽  
Seed Collection ◽  
Seed Sources ◽  
Significant Difference ◽  
Genetic Bottlenecks ◽  
Production Areas

Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs.

scholarly journals Genetic Structure and Pod Morphology of Inga edulis Cultivated vs. Wild Populations from the Peruvian Amazon

Forests ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 655 ◽  
Author(s):  
Alexandr Rollo ◽  
Maria M. Ribeiro ◽  
Rita L. Costa ◽  
Carmen Santos ◽  
Zoyla M. Clavo P. ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Ice Cream ◽  
Peruvian Amazon ◽  
Wild Populations ◽  
Inga Edulis ◽  
Loss Of Genetic Diversity ◽  
Cultivated Populations ◽  
The Impact ◽  
Pod Length

Research Highlights: This study assesses the genetic diversity and structure of the ice-cream-bean (Inga edulis Mart.; Fabaceae) in wild and cultivated populations from the Peruvian Amazon. This research also highlights the importance of protecting the biodiversity of the forest in the Peruvian Amazon, to preserve the genetic resources of species and allow further genetic improvement. Background and Objectives: Ice-cream-bean is one of the most commonly used species in the Amazon region for its fruits and for shading protection of other species (e.g., cocoa and coffee plantations). Comprehensive studies about the impact of domestication on this species’ genetic diversity are needed, to find the best conservation and improvement strategies. Materials and Methods: In the current study, the genetic structure and diversity were assessed by genotyping 259 trees, sampled in five wild and 22 cultivated I. edulis populations in the Peruvian Amazon, with microsatellite markers. Pod length was measured in wild and cultivated trees. Results: The average pod length in cultivated trees was significantly higher than that in wild trees. The expected genetic diversity and the average number of alleles was higher in the wild compared to the cultivated populations; thus, a loss of genetic diversity was confirmed in the cultivated populations. The cultivated trees in the Loreto region had the highest pod length and lowest allelic richness; nevertheless, the wild populations’ genetic structure was not clearly differentiated (significantly different) from that of the cultivated populations. Conclusions: A loss of genetic diversity was confirmed in the cultivated populations. The species could have been simultaneously domesticated in multiple locations, usually from local origin. The original I. edulis Amazonian germplasm should be maintained. Cultivated populations’ new germplasm influx from wild populations should be undertaken to increase genetic diversity.

scholarly journals Race Determination and Vegetative Compatibility Grouping of Fusarium oxysporum f. sp. melonis from South Africa

Plant Disease ◽  
2000 ◽  
Vol 84 (3) ◽  
pp. 231-234 ◽  
Author(s):  
W. Schreuder ◽  
S. C. Lamprecht ◽  
G. Holz
Keyword(s):  
South Africa ◽  
Fusarium Oxysporum ◽  
South African ◽  
Geographic Region ◽  
Vegetative Compatibility ◽  
Vegetative Compatibility Group ◽  
Compatibility Group ◽  
Race 1 ◽  
Race 2 ◽  
High Degree

Isolates of Fusarium oxysporum f. sp. melonis (72 total) obtained from 30 fields in 17 melonproducing regions in South Africa were race typed, using differential cvs. CM 17187, Doublon, Perlita, and Topmark, and grouped on the basis of vegetative compatibility. Fifty-four isolates were identified as race 0, eight as race 1, and ten as race 2. Race 0 occurred in 15 of 17 regions, whereas race 1 was sporadically recovered. Race 2 was obtained from only four fields located in one geographic region. Perlita plants (carrying the gene Fom3) inoculated with local isolates of races 0 and 2 and reference isolates of race 0 became stunted, and their leaves became yellow, thickened, and brittle. Using two inoculation methods, similar symptoms were induced by reference and local isolates of race 0 on Perlita seedlings. The results indicated that Fom3 in Perlita confers a tolerant reaction compared with the resistant reaction of gene Fom1 in Doublon and, therefore, should not be used alone in race determination tests. All isolates belonged to vegetative compatibility group 0134, indicating a high degree of genetic homogeneity among the South African F. oxysporum f. sp. melonis population.

scholarly journals Genetic diversity and effective population sizes of thirteen Indian cattle breeds

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Eva M. Strucken ◽  
Netsanet Z. Gebrehiwot ◽  
Marimuthu Swaminathan ◽  
Sachin Joshi ◽  
Mohammad Al Kalaldeh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Allele Frequencies ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Population Sizes ◽  
Indian Cattle

Abstract Background The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds. Results Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds. Conclusions The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle.

Allocation discourses: South African water rights reform

Water Policy ◽  
2010 ◽  
Vol 13 (2) ◽  
pp. 161-177 ◽  
Author(s):  
Synne Movik
Keyword(s):  
South Africa ◽  
South African ◽  
Water Use ◽  
Reform Process ◽  
Political Issue ◽  
Water Legislation ◽  
Continued Use ◽  
High Degree ◽  
Past Injustices ◽  
South African Water

Perceptions of increasing water scarcity have caused many countries to reform their water legislation. South Africa, in the vanguard of reform efforts, passed the National Water Act in 1998. The Act was lauded as a progressive piece of policy as it posited the redress of past injustices as one of its overarching aims. But there has been little progress in terms of redistribution of water use rights. This paper argues that bringing water under the ambit of the state, in combination with the particular political conjunctures in post-apartheid South Africa, opened up space for the emergence of narratives around water use rights that framed the continued use of existing users as pivotal for sustainability and that redistribution is associated with a high degree of risk. Although water allocation reform is essentially a deeply political issue, the increasing technocratisation and bureaucratisation of the reform process served to mask contested understandings through, for example, the use of innocuous-sounding terms such as “existing lawful use”. This, in combination with a highly under-resourced water management sector tasked with the responsibility of shouldering a heavy and complex system of licensing, resulted in reform efforts ending in a temporary impasse.

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