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Kumar A, Aggarwal RAK, Tantia MS. Deciphering genetic diversity in conserved cattle bulls to achieve sustainable development goals. Sci Rep 2024; 14:10794. [PMID: 38734757 PMCID: PMC11088680 DOI: 10.1038/s41598-024-61542-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 05/07/2024] [Indexed: 05/13/2024] Open
Abstract
The primary objective of Sustainable Development Goal target 2.5 established by the United Nations is to ensure the preservation of genetic diversity in domesticated animals. The ICAR-National Bureau of Animal Genetic Resources in India has been actively engaged in the conservation of cattle and buffalo bull semen for long-term storage. This present study aimed to assess the genetic diversity present in the conserved cattle bull semen, which would aid in determining the most suitable strategy for future conservation management. A total of 192 bull semen belonging to 19 cattle breeds were selected to evaluate genetic diversity using 17 pairs of FAO recommended microsatellite primers. Total 267 alleles were detected across all the samples which indicates substantial amount of allelic variation is being maintained in conserved bulls. Further, all cattle bulls semen conserved showed higher observed heterozygosity than expected heterozygosity which indicates excess genetic diversity in all the populations. The FST, F IT and FIS value across the loci and population is 0.146 ± 0.009, 0.054 ± 0.038, and - 0.105 ± 0.035, respectively, which suggests lack of inbreeding in conserved cattle bull semen. This study has established genetic diversity in conserved cattle semen samples to achieve sustainable development goals. In addition, it provides compelling evidence that the current approach for conserving cattle bull semen is heading in the correct direction.
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Affiliation(s)
- Amod Kumar
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resource, Karnal, Haryana, 132001, India.
| | - Rajeev Anand Kumar Aggarwal
- Animal Genetic Resources Division, ICAR-National Bureau of Animal Genetic Resource, Karnal, Haryana, 132001, India
| | - M S Tantia
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resource, Karnal, Haryana, 132001, India
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Corredor FA, Figueroa D, Estrada R, Salazar W, Quilcate C, Vásquez HV, Gonzales J, Maicelo JL, Medina P, Arbizu CI. Genetic diversity and population structure of a Peruvian cattle herd using SNP data. Front Genet 2023; 14:1073843. [PMID: 36968592 PMCID: PMC10036791 DOI: 10.3389/fgene.2023.1073843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
New-generation sequencing technologies, among them SNP chips for massive genotyping, are useful for the effective management of genetic resources. To date, molecular studies in Peruvian cattle are still scarce. For the first time, the genetic diversity and population structure of a reproductive nucleus cattle herd of four commercial breeds from a Peruvian institution were determined. This nucleus comprises Brahman (N = 9), Braunvieh (N = 9), Gyr (N = 5), and Simmental (N = 15) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N = 9), were incorporated. Female individuals were genotyped with the GGPBovine100K and males with the BovineHD. Quality control, and the proportion of polymorphic SNPs, minor allele frequency, expected heterozygosity, observed heterozygosity, and inbreeding coefficient were estimated for the five breeds. Admixture, principal component analysis (PCA), and discriminant analysis of principal components (DAPC) were performed. Also, a dendrogram was constructed using the Neighbor-Joining clustering algorithm. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 51.42% in Gyr to 97.58% in AFB. Also, AFB showed the highest expected heterozygosity estimate (0.41 ± 0.01), while Brahman the lowest (0.33 ± 0.01). Besides, Braunvieh possessed the highest observed heterozygosity (0.43 ± 0.01), while Brahman the lowest (0.37 ± 0.02), indicating that Brahman was less diverse. According to the molecular variance analysis, 75.71% of the variance occurs within individuals, whereas 24.29% occurs among populations. The pairwise genetic differentiation estimates (FST) between breeds showed values that ranged from 0.08 (Braunvieh vs. AFB) to 0.37 (Brahman vs. Braunvieh). Similarly, pairwise Reynold's distance ranged from 0.09 (Braunvieh vs. AFB) to 0.46 (Brahman vs. Braunvieh). The dendrogram, similar to the PCA, identified two groups, showing a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh, Simmental, and AFB). Simmental and Braunvieh grouped closely with the AFB cattle. Similar results were obtained for the population structure analysis with K = 2. The results from this study would contribute to the appropriate management, avoiding loss of genetic variability in these breeds and for future improvements in this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.
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Affiliation(s)
- Flor-Anita Corredor
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Deyanira Figueroa
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Richard Estrada
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Wilian Salazar
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Carlos Quilcate
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Héctor V. Vásquez
- Facultad de Ingenierŕa Zootecnista, Agronegocios y Biotecnología, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Amazonas, Peru
| | - Jhony Gonzales
- Laboratorio de Biología Molecular, Universidad Nacional de Frontera, Piura, Peru
| | - Jorge L. Maicelo
- Facultad de Ingenierŕa Zootecnista, Agronegocios y Biotecnología, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Amazonas, Peru
| | - Percy Medina
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
| | - Carlos I. Arbizu
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima, Peru
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Liu B, Tao W, Feng D, Wang Y, Heizatuola N, Ahemetbai T, Wu W. Revealing Genetic Diversity and Population Structure of Endangered Altay White-Headed Cattle Population Using 100 k SNP Markers. Animals (Basel) 2022; 12:3214. [PMID: 36428441 PMCID: PMC9686749 DOI: 10.3390/ani12223214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/17/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Understanding the genetic basis of native cattle populations that have adapted to the local environment is of great significance for formulating appropriate strategies and programs for genetic improvement and protection. Therefore, it is necessary to understand the genetic diversity and population structure of Altay white-headed cattle so as to meet the current production needs under various environments, carry out continuous genetic improvement, and promote rapid adaptation to changing environments and breeding objectives. A total of 46 individual samples of endangered Xinjiang Altay white-headed cattle were collected in this study, including nine bulls and 37 cows. To collect genotype data, 100 k SNP markers were used, and then studies of genetic diversity, genetic structure, inbreeding degree, and family analysis were carried out. A total of 101,220 SNP loci were detected, and the genotype detection rate for individuals was ≥90%. There were 85,993 SNP loci that passed quality control, of which 93.5% were polymorphic. The average effective allele number was 0.036, the Polymorphism Information Content was 0.304 and the minimum allele frequency was 0.309, the average observed heterozygosity was 0.413, and the average expected heterozygosity was 0.403. The average genetic distance of Idengtical By State (IBS) was 0.3090, there were 461 ROH (genome-length homozygous fragments), 76.1% of which were between 1 and 5 MB in length, and the average inbreeding coefficient was 0.016. The 46 Altay white-headed cattle were divided into their families, and the individual numbers of each family were obviously different. To sum up, the Altay white-headed cattle conservation population had low heterozygosity, a high inbreeding degree, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the follow-up seed conservation process, seed selection and matching should be carried out according to the divided families to ensure the long-term protection of Altay white-headed cattle genetic resources.
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Affiliation(s)
- Bo Liu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool Sheep & Cashmere Goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, China
| | - Weikun Tao
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool Sheep & Cashmere Goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, China
| | - Donghe Feng
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool Sheep & Cashmere Goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, China
| | - Yue Wang
- Animal Husbandry Workstation in Altay Region, Altay 836000, China
| | | | - Tenes Ahemetbai
- Animal Husbandry Workstation in Altay Region, Altay 836000, China
| | - Weiwei Wu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool Sheep & Cashmere Goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, China
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Hall SJG. Genetic Differentiation among Livestock Breeds-Values for F st. Animals (Basel) 2022; 12:1115. [PMID: 35565543 PMCID: PMC9103131 DOI: 10.3390/ani12091115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
(1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06-0.12, SNP 0.08-0.15; sheep: microsatellite 0.06-0.10, SNP 0.06-0.17; horses: microsatellite 0.04-0.11, SNP 0.08-0.12; goats: microsatellite 0.04-0.14, SNP 0.08-0.16; pigs: microsatellite 0.06-0.27, SNP 0.15-0.22; chickens: microsatellite 0.05-0.28, SNP 0.08-0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world's livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.
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Affiliation(s)
- Stephen J G Hall
- Department of Environmental Protection and Landscape, Estonian University of Life Sciences, Kreutzwaldi 5, 51014 Tartu, Estonia
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An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds. Animals (Basel) 2021; 11:ani11072016. [PMID: 34359144 PMCID: PMC8300386 DOI: 10.3390/ani11072016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary The number of local farm animal breeds is declining worldwide. However, these breeds have different degrees of genetic diversity. Measuring genetic diversity is important for the development of conservation strategies and, therefore, various genomic analysis techniques are available. The aim of the present work was to shed light on the use of these techniques in diversity studies of local breeds. In summary, a total of 133 worldwide studies that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that over time, almost all available genomic techniques were used and various diversity parameters were calculated. Therefore, the present results provide a comprehensive overview of the application of these techniques in the field of local breeds. This can provide helpful insights into the advancement of the conservation of breeds with high genetic diversity. Abstract Globally, many local farm animal breeds are threatened with extinction. However, these breeds contribute to the high amount of genetic diversity required to combat unforeseen future challenges of livestock production systems. To assess genetic diversity, various genotyping techniques have been developed. Based on the respective genomic information, different parameters, e.g., heterozygosity, allele frequencies and inbreeding coefficient, can be measured in order to reveal genetic diversity between and within breeds. The aim of the present work was to shed light on the use of genotyping techniques in the field of local farm animal breeds. Therefore, a total of 133 studies across the world that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that diversity of cattle was most often investigated with microsatellite use as the main technique. Furthermore, a large variety of diversity parameters that were calculated with different programs were identified. For 15% of the included studies, the used genotypes are publicly available, and, in 6%, phenotypes were recorded. In conclusion, the present results provide a comprehensive overview of the application of genotyping techniques in the field of local breeds. This can provide helpful insights to advance the conservation of breeds.
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Assessment of genetic diversity and population structure of Colombian Creole cattle using microsatellites. Trop Anim Health Prod 2021; 53:122. [PMID: 33443652 DOI: 10.1007/s11250-021-02563-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
To establish the diversity, structure, and phylogenetic relationships among Colombian Creole cattle, six native breeds and one introduced breed were genotyped for 20 microsatellite loci. The average number of alleles per breed ranged from 7050 (Romosinuano) to 10,100 (Casanareño), and the expected heterozygosity ranged from 0.691 (San martinero) to 0.785 (Casanareño). The deviation from the Hardy-Weinberg equilibrium (HWE) was statistically significant (p < 0.05) in 59 out of 120 tests carried out in the six breeds for the 20 microsatellite loci analyzed. Colombian Creole bovine breeds have maintained a high level of genetic differentiation within the same populations (93%), and the rest is explained by differences between breeds (7%). The differentiation pattern and the genetic relationships between the Colombian Creole bovine breeds showed high consistency with the evolutionary history of each. Both the Bayesian grouping analysis and the neighbor-joining tree exhibited a reliable grouping pattern, which revealed two main groups: one comprised by the breeds Blanco Orejinegro, Hartón del Valle, Costeño Con Cuernos, Romosinuano, and San Martinero, and the other one by the Creole breed Casanareño and Zebu. These were probably caused by different historical, reproductive, and geographic isolation precedents, as well as by different levels of inbreeding. This study will help understand the genetic characteristics of Colombian Creole cattle and will benefit future conservation programs.
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Madilindi MA, Banga CB, Bhebhe E, Sanarana YP, Nxumalo KS, Taela MG, Magagula BS, Mapholi NO. Genetic diversity and relationships among three Southern African Nguni cattle populations. Trop Anim Health Prod 2019; 52:753-762. [PMID: 31529304 DOI: 10.1007/s11250-019-02066-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 09/06/2019] [Indexed: 10/26/2022]
Abstract
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.
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Affiliation(s)
- Matome A Madilindi
- Department of Animal Science, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa. .,ARC-Animal Production, Private Bag X2, Irene, 0062, South Africa.
| | - Cuthbert B Banga
- ARC-Animal Production, Private Bag X2, Irene, 0062, South Africa
| | - Evison Bhebhe
- Department of Animal Science, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa
| | | | | | - Maria G Taela
- Directorate of Animal Science, Agrarian Research Institute of Mozambique, Av. Namaacha Km 11.5, P.O. Box 1410, Maputo, Mozambique
| | - Bongani S Magagula
- Department of Veterinary and Livestock Services, Ministry of Agriculture, P.O. Box 162, Mbabane, Swaziland
| | - Ntanganedzeni O Mapholi
- Department of Life and Consumer Sciences, University of South Africa, Private Bag X6, Florida, 1710, South Africa
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Campos BM, do Carmo AS, do Egito AA, da Mariante AS, do Albuquerque MSM, de Gouveia JJS, Malhado CHM, Verardo LL, da Silva MVGB, Carneiro PLS. Genetic diversity, population structure, and correlations between locally adapted zebu and taurine breeds in Brazil using SNP markers. Trop Anim Health Prod 2017; 49:1677-1684. [PMID: 28808902 DOI: 10.1007/s11250-017-1376-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/02/2017] [Indexed: 12/28/2022]
Abstract
Genetic diversity is one of the most important issues in studies on conservation of cattle breeds and endangered species. The objective of this study was to estimate the levels of genetic differentiation between locally adapted taurine (Bos taurus taurus) and zebu (Bos taurus indicus) breeds in Brazil, which were genotyped for more than 777,000 SNPs. The fixation index (F ST), principal component analysis (PCA), and Bayesian clustering were estimated. The F ST highlighted genetic differentiation between taurine and zebu breeds. The taurine lines, Caracu and Caracu Caldeano, had significant genetic differentiation (F ST close to 5%) despite their recent selection for different uses (meat and milk). This genetic variability can be used for conservation of locally adapted animals, as well as for breeding programs on zebu breeds. Introgression of zebu in locally adapted breeds was identified, especially in Curraleiro Pé-Duro breed. The Gyr breed, however, had low breed purity at genomic level due to its very heterogeneous mixing pattern.
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Affiliation(s)
- Bárbara Machado Campos
- Graduate Program of Animal Science, Universidade Estadual do Sudoeste da Bahia, 40 Praça Primavera, Bairro Primavera, Itapetinga, Bahia, 457000-000, Brazil. .,, Crescêncio Silveira Ave., Mercadão, Box 123, Vitória da Conquista, Bahia, 45000-340, Brazil.
| | | | - Andrea Alves do Egito
- Brazilian Agricultural Research Corporation (Embrapa Genetic Resources and Biotechnology), Brasília, Distrito Federal, 70770-901, Brazil
| | - Arthur Silva da Mariante
- Brazilian Agricultural Research Corporation (Embrapa Genetic Resources and Biotechnology), Brasília, Distrito Federal, 70770-901, Brazil
| | | | | | | | - Lucas Lima Verardo
- Brazilian Agricultural Research Corporation (Embrapa Dairy Cattle), Juiz de Fora, Minas Gerais, 36038-330, Brazil
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Menéndez-Buxadera A, Palacios-Espinosa A, Espinosa-Villavicencio JL, Guerra-Iglesias D. Genotype Environment interactions for milk production traits in Holstein and crossbred Holstein-Zebu cattle populations estimated by a character state multibreed model. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Maretto F, Cassandro M. Temporal Variation in Genetic Diversity and Population Structure of Burlina Cattle Breed. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2014.3091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sanarana Y, Visser C, Bosman L, Nephawe K, Maiwashe A, van Marle-Köster E. Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers. Trop Anim Health Prod 2015; 48:379-85. [PMID: 26611262 DOI: 10.1007/s11250-015-0962-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
Abstract
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 characterisation 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 the 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 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.
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Affiliation(s)
- Yandisiwe Sanarana
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.,Agricultural Research Council, Private Bag X2, Irene, 0062, South Africa
| | - Carina Visser
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Lydia Bosman
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Khathutshelo Nephawe
- Department of Animal Science, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | | | - Este van Marle-Köster
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
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Suh S, Kim YS, Cho CY, Byun MJ, Choi SB, Ko YG, Lee CW, Jung KS, Bae KH, Kim JH. Assessment of Genetic Diversity, Relationships and Structure among Korean Native Cattle Breeds Using Microsatellite Markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:1548-53. [PMID: 25358313 PMCID: PMC4213698 DOI: 10.5713/ajas.2014.14435] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/27/2014] [Accepted: 09/23/2014] [Indexed: 11/27/2022]
Abstract
Four Korean native cattle (KNC) breeds-Hanwoo, Chikso, Heugu, and Jeju black-are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO). The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120) and exotic breeds (Holstein and Charolais, n = 56). Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources.
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Affiliation(s)
- Sangwon Suh
- Gangwon Provincial Livestock Research Center, Hoengseong, Gangwon 225-831, Korea
| | - Young-Sin Kim
- Gangwon Provincial Livestock Research Center, Hoengseong, Gangwon 225-831, Korea
| | - Chang-Yeon Cho
- Gangwon Provincial Livestock Research Center, Hoengseong, Gangwon 225-831, Korea
| | - Mi-Jeong Byun
- Gangwon Provincial Livestock Research Center, Hoengseong, Gangwon 225-831, Korea
| | - Seong-Bok Choi
- Gangwon Provincial Livestock Research Center, Hoengseong, Gangwon 225-831, Korea
| | - Yeoung-Gyu Ko
- Gangwon Provincial Livestock Research Center, Hoengseong, Gangwon 225-831, Korea
| | - Chang Woo Lee
- Gangwon Provincial Livestock Research Center, Hoengseong, Gangwon 225-831, Korea
| | - Kyoung-Sub Jung
- Chungbuk Institute of Livestock and Veterinary Research, Cheongwon, Chungbuk 363-931, Korea
| | - Kyoung Hun Bae
- Jeju Special Self-Governing Province Livestock Promotion, Jeju 690-802, Korea
| | - Jae-Hwan Kim
- Gangwon Provincial Livestock Research Center, Hoengseong, Gangwon 225-831, Korea
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