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Márton J, Szabó F, Zsolnai A, Anton I. Genetic diversity and phylogenetic relationship of Angus herds in Hungary and analyses of their production traits. Anim Biosci 2024; 37:184-192. [PMID: 37641825 PMCID: PMC10766482 DOI: 10.5713/ab.23.0157] [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: 04/25/2023] [Revised: 07/17/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
OBJECTIVE This study aims to investigate the genetic structure and characteristics of the Angus cattle population in Hungary. The survey was performed with the assistance of the Hungarian Hereford, Angus, Galloway Association (HHAGA). METHODS Genetic parameters of 1,369 animals from 16 Angus herds were analyzed using the genotyping results of 12 microsatellite markers with the aid of PowerMarker, Genalex, GDA-NT2021, and STRUCTURE software. Genotyping of DNA was performed using an automated genetic analyzer. Based on pairwise identity by state values of animals, the Python networkx 2.3 library was used for network analysis of the breed and to identify the central animals. RESULTS The observed numbers of alleles on the 12 loci under investigation ranged from 11 to 18. The average effective number of alleles was 3.201. The overall expected heterozygosity was 0.659 and the observed heterozygosity was 0.710. Four groups were detected among the 16 Angus herds. The breeders' information validated the grouping results and facilitated the comparison of birth weight, age at first calving, number of calves born and productive lifespan data between the four groups, revealing significant differences. We identified the central animals/herd of the Angus population in Hungary. The match of our group descriptions with the phenotypic data provided by the breeders further underscores the value of cooperation between breeders and researchers. CONCLUSION The observation that significant differences in the measured traits occurred among the identified groups paves the way to further enhancement of breeding efficiency. Our findings have the potential to aid the development of new breeding strategies and help breeders keep the Angus populations in Hungary under genetic supervision. Based on our results the efficient use of an upcoming genomic selection can, in some cases, significantly improve birth weight, age at first calving, number of calves born and the productive lifespan of animals.
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Affiliation(s)
- Judit Márton
- Hungarian Hereford, Angus, Galloway Association, Dénesmajor 2, H-7400 Kaposvár,
Hungary
| | - Ferenc Szabó
- Széchenyi István University, Albert Kázmér Faculty of Mosonmagyaróvár, Vár tér 2., H-9200 Mosonmagyaróvár,
Hungary
| | - Attila Zsolnai
- Hungarian University of Agriculture and Life Sciences, Institute of Animal Husbandry Sciences, Guba Sándor utca 40., H-7400 Kaposvár,
Hungary
| | - István Anton
- Hungarian University of Agriculture and Life Sciences, Institute of Animal Husbandry Sciences, Guba Sándor utca 40., H-7400 Kaposvár,
Hungary
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Bhati M, Mapel XM, Lloret-Villas A, Pausch H. Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue. Genetics 2023; 225:iyad161. [PMID: 37655920 PMCID: PMC10627265 DOI: 10.1093/genetics/iyad161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/05/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023] Open
Abstract
Structural variants (SVs) and short tandem repeats (STRs) are significant sources of genetic variation. However, the impacts of these variants on gene regulation have not been investigated in cattle. Here, we genotyped and characterized 19,408 SVs and 374,821 STRs in 183 bovine genomes and investigated their impact on molecular phenotypes derived from testis transcriptomes. We found that 71% STRs were multiallelic. The vast majority (95%) of STRs and SVs were in intergenic and intronic regions. Only 37% SVs and 40% STRs were in high linkage disequilibrium (LD) (R2 > 0.8) with surrounding SNPs/insertions and deletions (Indels), indicating that SNP-based association testing and genomic prediction are blind to a nonnegligible portion of genetic variation. We showed that both SVs and STRs were more than 2-fold enriched among expression and splicing QTL (e/sQTL) relative to SNPs/Indels and were often associated with differential expression and splicing of multiple genes. Deletions and duplications had larger impacts on splicing and expression than any other type of SV. Exonic duplications predominantly increased gene expression either through alternative splicing or other mechanisms, whereas expression- and splicing-associated STRs primarily resided in intronic regions and exhibited bimodal effects on the molecular phenotypes investigated. Most e/sQTL resided within 100 kb of the affected genes or splicing junctions. We pinpoint candidate causal STRs and SVs associated with the expression of SLC13A4 and TTC7B and alternative splicing of a lncRNA and CAPP1. We provide a catalog of STRs and SVs for taurine cattle and show that these variants contribute substantially to gene expression and splicing variation.
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Affiliation(s)
- Meenu Bhati
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Xena Marie Mapel
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | | | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
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Weigend S, Romanov M. Current strategies for the assessment and evaluation of genetic diversity in chicken resources. WORLD POULTRY SCI J 2019. [DOI: 10.1079/wps20010020] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- S. Weigend
- Institute for Animal Science and Animal Behaviour, Mariensee, Federal Agricultural Research Centre (FAL), 31535 Neustadt, Germany
| | - M.N. Romanov
- Poultry Research Institute (UAAS), Borky, Zmiiv District, Kharkiv Region 63421, Ukraine
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Sawicka-Zugaj W, Chabuz W, Litwińczuk Z, Kasprzak-Filipek K. Evaluation of reproductive performance and genetic variation in bulls of the Polish White-Backed breed. Reprod Domest Anim 2017; 53:157-162. [PMID: 29076550 DOI: 10.1111/rda.13085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 08/22/2017] [Indexed: 11/30/2022]
Abstract
The aim of the study was to evaluate genetic variation, reproductive performance and the degree of relationship of White-Backed bulls entered in the breed registry and approved for breeding. The study included 32 bulls of the White-Backed (WB) breed with an entry in the breed registry and used for breeding in the years 2003-2015. Eleven microsatellite DNA sequences (TGLA222, BM2113, TGLA53, ETH10, SPS115, TGLA126, TGLA122, INRA23, ETH3, ETH225 and BM1824) were used to analyse variation in the WB bulls. The bulls most often used for breeding were Chilon (1,073 doses), Mak (939 doses) and Jaguar (858 doses). The bulls Mak, Chilon and Jak had the greatest influence on the active population of White-Backed cattle, with the most daughters. In the analysed population of White-Backed bulls, a total of 79 different alleles were identified, with a mean 7.27 per locus. The analysed pool of microsatellite loci was characterized by high values for PIC, HO and HE (>0.6), and the entire population was in genetic equilibrium. The estimated level of inbreeding within the population ranged from -0.2277 (ETH225) to 0.0775 (SPS115), with a mean value of -0.0587.
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Affiliation(s)
- W Sawicka-Zugaj
- Department of Breeding and Protection of Genetic Resources of Cattle, University of Life Sciences in Lublin, Lublin, Poland
| | - W Chabuz
- Department of Breeding and Protection of Genetic Resources of Cattle, University of Life Sciences in Lublin, Lublin, Poland
| | - Z Litwińczuk
- Department of Breeding and Protection of Genetic Resources of Cattle, University of Life Sciences in Lublin, Lublin, Poland
| | - K Kasprzak-Filipek
- Department of Commodity Science and Processing of Raw Animal Materials, University of Life Sciences in Lublin, Lublin, Poland
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Kasarapu P, Porto-Neto LR, Fortes MRS, Lehnert SA, Mudadu MA, Coutinho L, Regitano L, George A, Reverter A. The Bos taurus-Bos indicus balance in fertility and milk related genes. PLoS One 2017; 12:e0181930. [PMID: 28763475 PMCID: PMC5538644 DOI: 10.1371/journal.pone.0181930] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/10/2017] [Indexed: 12/16/2022] Open
Abstract
Numerical approaches to high-density single nucleotide polymorphism (SNP) data are often employed independently to address individual questions. We linked independent approaches in a bioinformatics pipeline for further insight. The pipeline driven by heterozygosity and Hardy-Weinberg equilibrium (HWE) analyses was applied to characterize Bos taurus and Bos indicus ancestry. We infer a gene co-heterozygosity network that regulates bovine fertility, from data on 18,363 cattle with genotypes for 729,068 SNP. Hierarchical clustering separated populations according to Bos taurus and Bos indicus ancestry. The weights of the first principal component were subjected to Normal mixture modelling allowing the estimation of a gene’s contribution to the Bos taurus-Bos indicus axis. We used deviation from HWE, contribution to Bos indicus content and association to fertility traits to select 1,284 genes. With this set, we developed a co-heterozygosity network where the group of genes annotated as fertility-related had significantly higher Bos indicus content compared to other functional classes of genes, while the group of genes associated with milk production had significantly higher Bos taurus content. The network analysis resulted in capturing novel gene associations of relevance to bovine domestication events. We report transcription factors that are likely to regulate genes associated with cattle domestication and tropical adaptation. Our pipeline can be generalized to any scenarios where population structure requires scrutiny at the molecular level, particularly in the presence of a priori set of genes known to impact a phenotype of evolutionary interest such as fertility.
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Affiliation(s)
- Parthan Kasarapu
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia
| | - Laercio R. Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia
| | - Marina R. S. Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sigrid A. Lehnert
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia
| | | | - Luiz Coutinho
- Centro de Genomica Funcional ESALQ, University of São Paulo, Piracicaba, Sao Paulo, Brazil
| | - Luciana Regitano
- Embrapa Southeast Livestock, Rodovia Washington Luiz, São Carlos, Sao Paulo, Brazil
| | - Andrew George
- CSIRO, DATA61, Ecosciences Precinct Brisbane, Brisbane, Queensland, Australia
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia
- * E-mail:
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D’Andrea M, Pariset L, Matassino D, Valentini A, Lenstra JA, Maiorano G, Pilla F. Genetic characterization and structure of the Italian Podolian cattle breed and its relationship with some major European breeds. ITALIAN JOURNAL OF ANIMAL SCIENCE 2017. [DOI: 10.4081/ijas.2011.e54] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Mariasilvia D’Andrea
- Dipartimento Scienze Animali Vegetali e dell’Ambiente, Università del Molise , Campobasso, Italy
| | - Lorraine Pariset
- Dipartimento di Produzioni Animali, Università della Tuscia , Viterbo, Italy
| | - Donato Matassino
- Consorzio per la Sperimentazione, Divulgazione e Applicazione di Biotecniche Innovative , Benevento, Italy
| | - Alessio Valentini
- Dipartimento di Produzioni Animali, Università della Tuscia , Viterbo, Italy
| | | | - Giuseppe Maiorano
- Dipartimento Scienze Animali Vegetali e dell’Ambiente, Università del Molise , Campobasso, Italy
| | - Fabio Pilla
- Dipartimento Scienze Animali Vegetali e dell’Ambiente, Università del Molise , Campobasso, Italy
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Inference of population structure of purebred dairy and beef cattle using high-density genotype data. Animal 2016; 11:15-23. [PMID: 27330040 DOI: 10.1017/s1751731116001099] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Information on the genetic diversity and population structure of cattle breeds is useful when deciding the most optimal, for example, crossbreeding strategies to improve phenotypic performance by exploiting heterosis. The present study investigated the genetic diversity and population structure of the most prominent dairy and beef breeds used in Ireland. Illumina high-density genotypes (777 962 single nucleotide polymorphisms; SNPs) were available on 4623 purebred bulls from nine breeds; Angus (n=430), Belgian Blue (n=298), Charolais (n=893), Hereford (n=327), Holstein-Friesian (n=1261), Jersey (n=75), Limousin (n=943), Montbéliarde (n=33) and Simmental (n=363). Principal component analysis revealed that Angus, Hereford, and Jersey formed non-overlapping clusters, representing distinct populations. In contrast, overlapping clusters suggested geographical proximity of origin and genetic similarity between Limousin, Simmental and Montbéliarde and to a lesser extent between Holstein, Friesian and Belgian Blue. The observed SNP heterozygosity averaged across all loci was 0.379. The Belgian Blue had the greatest mean observed heterozygosity (HO=0.389) among individuals within breed while the Holstein-Friesian and Jersey populations had the lowest mean heterozygosity (HO=0.370 and 0.376, respectively). The correlation between the genomic-based and pedigree-based inbreeding coefficients was weak (r=0.171; P<0.001). Mean genomic inbreeding estimates were greatest for Jersey (0.173) and least for Hereford (0.051). The pair-wise breed fixation index (F st) ranged from 0.049 (Limousin and Charolais) to 0.165 (Hereford and Jersey). In conclusion, substantial genetic variation exists among breeds commercially used in Ireland. Thus custom-mating strategies would be successful in maximising the exploitation of heterosis in crossbreeding strategies.
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Neubauer V, Vogl C, Seregi J, Sáfár L, Brem G. Genetic diversity and population structure of Zackel sheep and other Hungarian sheep breeds. Arch Anim Breed 2015. [DOI: 10.5194/aab-58-343-2015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. More than 6000 samples of 18 different Hungarian sheep breeds were genotyped for 10 unlinked microsatellite loci. After data cleaning, 5434 sheep remained in the analysis. Some locus–breed combinations show deviation from Hardy–Weinberg equilibrium, possibly due to null alleles or the Wahlund effect. All breeds show high genetic variability; the lowest expected heterozygosity is that of the British Milksheep (He = 0.588). The Transylvanian Zackel has the highest expected heterozygosity (He = 0.790). It is also the least differentiated breed (Fst = 0.020). Pairwise genetic distances among breeds range from 0.021 between Hungarian Merino and both Mutton Merino and Transylvanian Zackel to greater than 0.105 between British Milksheep and all other breeds. The three Zackel populations – white, black, and Transylvanian Zackel – show small genetic distances among each other, with pairwise Fst values from 0.030 to 0.058. The Transylvanian Zackel tended to have close relationships to some other breeds too, probably due to its low differentiation. Given the individual genotypic information, a Bayesian analysis assigned individuals to breeds generally correctly.
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Singh G, Thakur Y, Kour A, Sankhyan V, Katoch S. Genetic characterization of Gaddi goat breed of Western Himalayas using microsatellite markers. Vet World 2015; 8:527-31. [PMID: 27047128 PMCID: PMC4774805 DOI: 10.14202/vetworld.2015.527-531] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 03/19/2015] [Accepted: 03/26/2015] [Indexed: 12/03/2022] Open
Abstract
Aim: In the present study, genetic characterization of Gaddi goat breed, a native to north temperate western Himalayan region of India, was carried out for the purpose of breed characterization and assessing existing intra-population genetic diversity. Materials and Methods: Totally, 75 blood samples procured at random from genetically unrelated animals of two sexes and different age groups and true to breed type were collected from different locations in the breeding tract of these goats in Himachal Pradesh, of which only 51 samples with desired quantity and quality were subjected to further processing for DNA isolation. The multi-locus genotype data were generated on 51 Gaddi goats sampled across different regions of the breeding tract in Himachal Pradesh using 15 FAO recommended goat specific microsatellite markers, which gave amplification and observed and effective number of alleles, gene frequency, observed and expected heterozygosity were estimated through PopGene software (1.3.1). Results: A total of 135 distinct alleles were observed with mean observed and effective number of alleles as 9.0000±0.82 and 6.5874±0.56 respectively across all 15 studied loci. The maximum (15) alleles were contributed by loci DRBP1 and P19/DYA and the least (5) by SRCRSP5. The mean heterozygosity was observed to be 0.8347±0.01 ranging from 0.7584 (SRCRSP5) to 0.9156 (P19-DYA) across all loci. The mean observed (HO) and expected (HE) heterozygosities across all loci were 0.7484±0.02 and 0.8431±0.01 respectively. The polymorphism information content (PIC) value ranged from 0.7148 (SRCPS5) to 0.909 (P19-DYA) with mean PIC of 0.8105±0.01 in the present study. The average heterozygosity was observed to be 0.8347±0.01 ranging from 0.7584 (SRCRSP5) to 0.9156 P19 (DYA) across all loci. Conclusion: Microsatellite analysis revealed high level of polymorphism across studied microsatellite markers and informativeness of the markers for genetic diversity analysis studies in Gaddi goats. This high level of polymorphism can be utilized to plan future association studies to exploit the uniqueness and adaptability of indigenous Gaddi goat breed of Western Himalayas. Most studied microsatellite markers had desired neutrality, thus proving to be good candidates for genetic characterization and diversity analysis in Gaddi breed of goats also.
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Affiliation(s)
- Gurdeep Singh
- Department of Animal Genetics and Breeding, CSK Himachal Pradesh Krishi Vishvavidyalaya, College of Veterinary and Animal Sciences, Holta, Palampur - 176 062, Himachal Pradesh, India
| | - Yashpal Thakur
- Department of Animal Genetics and Breeding, CSK Himachal Pradesh Krishi Vishvavidyalaya, College of Veterinary and Animal Sciences, Holta, Palampur - 176 062, Himachal Pradesh, India
| | - Amitoz Kour
- Department of Veterinary Microbiology, CSK Himachal Pradesh Krishi Vishvavidyalaya, College of Veterinary and Animal Sciences, Holta, Palampur - 176 062, Himachal Pradesh, India
| | - Varun Sankhyan
- Department of Animal Genetics and Breeding, CSK Himachal Pradesh Krishi Vishvavidyalaya, College of Veterinary and Animal Sciences, Holta, Palampur - 176 062, Himachal Pradesh, India
| | - Sanjeet Katoch
- Department of Animal Genetics and Breeding, CSK Himachal Pradesh Krishi Vishvavidyalaya, College of Veterinary and Animal Sciences, Holta, Palampur - 176 062, Himachal Pradesh, India
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Wang GD, Xie HB, Peng MS, Irwin D, Zhang YP. Domestication Genomics: Evidence from Animals. Annu Rev Anim Biosci 2014; 2:65-84. [DOI: 10.1146/annurev-animal-022513-114129] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - David Irwin
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
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Abstract
SUMMARYMankind uses some 40 species of animals as domestic livestock to meet our needs for food, clothing, power, etc. Within these species, there are in total some 4,500 breeds that are referred to as the global animal genetic resources. Each breed comprises a unique set of genes. More than 30% of breeds are estimated to be at risk of extinction, and many more, particularly in developing countries, are threatened by inefficient utilization. The Food and Agriculture Organization of the United Nations has been mandated by its member nations to manage the global animal genetic resources, and major progress has been made in the last few years. However, resources are limited, and priorities will have to be set for breed conservation, for breed development programmes and for evaluation studies. Breeds that are taxonomically distinct should be favoured for conservation, the objective being to maintain maximum genetic diversity of each livestock species. Genetic distances and phylogenetic diversity provide the best available objective criterion, and microsatellites are the current markers of choice for obtaining the genetic data. Microsatellite-based genetic distances will describe breed similarities due to common ancestry, but cannot account for consequences of artificial or natural selection. Phylogenetic trees for 11 water buffalo populations in southeast Asia, constructed using 25 polymorphic protein coding loci or 21 microsatellite loci, show differences in both topology and branch lengths, but the microsatellite tree is a better representation of the similarities due to common ancestry. Thus phylogenetic diversity, based on microsatellite loci, should be used as an initial guide in making conservation decisions for livestock breeds.
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Lewis J, Abas Z, Dadousis C, Lykidis D, Paschou P, Drineas P. Tracing cattle breeds with principal components analysis ancestry informative SNPs. PLoS One 2011; 6:e18007. [PMID: 21490966 PMCID: PMC3072384 DOI: 10.1371/journal.pone.0018007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Accepted: 02/18/2011] [Indexed: 01/09/2023] Open
Abstract
The recent release of the Bovine HapMap dataset represents the most detailed survey of bovine genetic diversity to date, providing an important resource for the design and development of livestock production. We studied this dataset, comprising more than 30,000 Single Nucleotide Polymorphisms (SNPs) for 19 breeds (13 taurine, three zebu, and three hybrid breeds), seeking to identify small panels of genetic markers that can be used to trace the breed of unknown cattle samples. Taking advantage of the power of Principal Components Analysis and algorithms that we have recently described for the selection of Ancestry Informative Markers from genomewide datasets, we present a decision-tree which can be used to accurately infer the origin of individual cattle. In doing so, we present a thorough examination of population genetic structure in modern bovine breeds. Performing extensive cross-validation experiments, we demonstrate that 250-500 carefully selected SNPs suffice in order to achieve close to 100% prediction accuracy of individual ancestry, when this particular set of 19 breeds is considered. Our methods, coupled with the dense genotypic data that is becoming increasingly available, have the potential to become a valuable tool and have considerable impact in worldwide livestock production. They can be used to inform the design of studies of the genetic basis of economically important traits in cattle, as well as breeding programs and efforts to conserve biodiversity. Furthermore, the SNPs that we have identified can provide a reliable solution for the traceability of breed-specific branded products.
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Affiliation(s)
- Jamey Lewis
- Department of Computer Science, Rensselaer Polytechnic Institute, Troy, New York, United States of America
| | - Zafiris Abas
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| | - Christos Dadousis
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| | - Dimitrios Lykidis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece
| | - Peristera Paschou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece
- * E-mail: (PP); (PD)
| | - Petros Drineas
- Department of Computer Science, Rensselaer Polytechnic Institute, Troy, New York, United States of America
- * E-mail: (PP); (PD)
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Ripoli M, Rogberg-Muñoz A, Lirón J, Francisco E, Villegas-Castagnasso E, Peral-Garcia P, Giovambattista G. History and selection imprinting on genetic relationships among bovine breeds analyzed trough five genes related with marbling. Res Vet Sci 2011; 90:245-52. [DOI: 10.1016/j.rvsc.2010.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 06/09/2010] [Accepted: 06/14/2010] [Indexed: 11/29/2022]
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Shahbazi S, Mirhosseini SZ, Romanov MN. Genetic diversity in five Iranian native chicken populations estimated by microsatellite markers. Biochem Genet 2007; 45:63-75. [PMID: 17203406 DOI: 10.1007/s10528-006-9058-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Iranian chicken genetic resources are characterized by a long history and a vast diversity. This study represents the first results from the selection and evaluation of five polymorphic microsatellite markers for the genetic assessment of five native chicken populations located in the northwestern (West Azerbaijan), northern (Mazandaran), central (Isfahan, Yazd), and southern (Fars) provinces of Iran. The number of alleles ranged from three to six per microsatellite locus. All populations were characterized by a high degree of genetic diversity, with the lowest heterozygosity found in the Isfahan population (62%) and the greatest in the populations from West Azerbaijan and Mazandaran (79%). The largest Nei's unbiased genetic distance was found between the Isfahan and Fars populations (0.696) and the smallest between the Mazandaran and Yazd populations (0.097). The Isfahan population was found to be the most genetically distant among all populations studied. These results serve as an initial step in the plan for genetic characterization and conservation of Iranian native chickens.
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Affiliation(s)
- Saleh Shahbazi
- Education Division, Iranian Academic Centre for Education, Culture and Research, PO Box 56135-696, Ardabil, Iran
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MacNeil MD, Cronin MA, Blackburn HD, Richards CM, Lockwood DR, Alexander LJ. Genetic relationships between feral cattle from Chirikof Island, Alaska and other breeds. Anim Genet 2007; 38:193-7. [PMID: 17459019 DOI: 10.1111/j.1365-2052.2007.01559.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The origin of cattle on Chirikof Island, off the coast of Alaska, is not well documented. We assessed genetic differentiation of cattle isolated on Chirikof Island from several breeds commonly used for commercial production in North America including breeds popularly believed to have contributed to the Chirikof Island population. A set of 34 microsatellite loci was used to genotype Angus, Charolais, Hereford, Highland, Limousin, Red Angus, Salers, Shorthorn, Simmental, Tarentaise and Texas Longhorn cattle sampled from North America and the Chirikof Island population. Resulting F(ST) statistics for these loci ranged from 0.06 to 0.22 and on average, 14% of total genetic variation was between breeds. Whether population structure was modelled as a bifurcating tree or genetic network, Chirikof Island cattle appeared to be unique and strongly differentiated relative to the other breeds that were sampled. Bayesian clustering for multiple-locus assignment to genetic groups indicated low levels of admixture in the Chirikof Island population. Thus, the Chirikof Island population may be a novel genetic resource of some importance for conservation and industry.
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Affiliation(s)
- M D MacNeil
- USDA, Agricultural Research Service, 243 Fort Keogh Road, Miles City, MT 59301, USA.
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Qu L, Li X, Xu G, Chen K, Yang H, Zhang L, Wu G, Hou Z, Xu G, Yang N. Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers. ACTA ACUST UNITED AC 2006; 49:332-41. [PMID: 16989278 DOI: 10.1007/s11427-006-2001-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F(ST)) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such a Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei's genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.
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Affiliation(s)
- Lujiang Qu
- College of Animal Science and Technology, China Agricultural University, Beijing 100094, China
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17
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18
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Freeman AR, Bradley DG, Nagda S, Gibson JP, Hanotte O. Combination of multiple microsatellite data sets to investigate genetic diversity and admixture of domestic cattle. Anim Genet 2006; 37:1-9. [PMID: 16441289 DOI: 10.1111/j.1365-2052.2005.01363.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microsatellite markers are commonly used for population genetic analyses of livestock. However, up to now, combinations of microsatellite data sets or comparison of population genetic parameters from different studies and breeds has proven difficult. Often different genotyping methods have been employed, preventing standardization of microsatellite allele calling. In other cases different sets of markers have been genotyped, providing differing estimates of population genetic parameters. Here, we address these issues and illustrate a general two-step regression approach in cattle using three different sets of microsatellite data, to combine population genetics estimates of diversity and admixture. This regression-based method is independent of the loci genotyped but requires common breeds in the data sets. We show that combining microsatellite data sets can provide new insights on the origin and geographical distribution of genetic diversity and admixture in cattle, which will facilitate global management of this livestock species.
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Affiliation(s)
- A R Freeman
- Department of Genetics, Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
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19
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Armstrong E, Postiglioni A, Martínez A, Rincón G, Vega-Pla JL. Microsatellite analysis of a sample of Uruguayan Creole bulls (Bos taurus). Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000200012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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20
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Genetic Variability and Relationships of Native Japanese Chickens Based on Microsatellite DNA Polymorphisms-Focusing on the Natural Monuments of Japan. J Poult Sci 2006. [DOI: 10.2141/jpsa.43.12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Cervini M, Henrique-Silva F, Mortari N, Matheucci Jr E. Genetic variability of 10 microsatellite markers in the characterization of Brazilian Nellore cattle (Bos indicus). Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000300015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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22
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Maté ML, Bustamante A, Giovambattista G, de Lamo D, von Thüngen J, Zambelli A, Vidal-Rioja L. Genetic diversity and differentiation of guanaco populations from Argentina inferred from microsatellite data. Anim Genet 2005; 36:316-21. [PMID: 16026342 DOI: 10.1111/j.1365-2052.2005.01307.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genotype data from 14 microsatellite markers were used to assess the genetic diversity and differentiation of four guanaco populations from Argentine Patagonia. These animals were recently captured in the wild and maintained in semi-captivity for fibre production. Considerable genetic diversity in these populations was suggested by the finding of a total of 162 alleles, an average mean number of alleles per locus ranging from 6.50 to 8.19, and H(e) values ranging from 0.66 to 0.74. Assessment of population differentiation showed moderate but significant values of F(ST)=0.071 (P=0.000) and R(ST)=0.083 (P=0.000). An amova test showed that the genetic variation among populations was 5.6% while within populations it was 94.4%. A number of 6.6 migrants per generation may support these results. Unambiguous individual assignment to original populations was obtained for the Pilcaniyeu, Las Heras and La Esperanza populations. The erroneous assignment of 18.75% Rio Mayo individuals to the Las Heras population can be explained by the low genetic differentiation found between these two populations. Thirty-nine of 56 loci per population combinations were in Hardy--Weinberg disequilibrium because of guanaco heterozygote deficiency, which may be explained by population subdivision. The high level of genetic diversity of the guanacos analysed here indicates that the Patagonian guanaco constitutes an important genetic resource for conservation or economic utilization programmes.
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Affiliation(s)
- M L Maté
- Instituto Multidisciplinario de Biología Celular (IMBICE), CC 403, 1900 La Plata, Argentina
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23
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Assessment of Genetic Diversity and Relationships Between Korean Cattle and Other Cattle Breeds by Microsatellite loci. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2005. [DOI: 10.5187/jast.2005.47.3.341] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Grobler J, Hartl G, Grobler N, Kotze A, Botha K, Tiedemann R. The genetic status of an isolated black wildebeest (Connochaetes gnou) population from the Abe Bailey Nature Reserve, South Africa: Microsatellite data on a putative past hybridization with blue wildebeest (C. taurinus). Mamm Biol 2005. [DOI: 10.1078/1616-5047-00174] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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Ibeagha-Awemu E, Erhardt G. Genetic variations between African and German sheep breeds, and description of a new variant of vitamin D-binding protein. Small Rumin Res 2004. [DOI: 10.1016/j.smallrumres.2004.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Wiener P, Burton D, Williams JL. Breed relationships and definition in British cattle: a genetic analysis. Heredity (Edinb) 2004; 93:597-602. [PMID: 15329667 DOI: 10.1038/sj.hdy.6800566] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The genetic diversity of eight British cattle breeds was quantified in this study. In all, 30 microsatellites from the FAO panel of markers were used to characterise the DNA samples from nearly 400 individuals. A variety of methods were applied to analyse the data in order to look at diversity within and between breeds. The relationships between breeds were not highly resolved and breed clusters were not associated with geographical distribution. Analyses also defined the cohesiveness or definition of the various breeds, with Highland, Guernsey and Jersey as the best defined and most distinctive of the breeds.
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Affiliation(s)
- P Wiener
- Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, UK.
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27
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Wyttenbach A, Hausser J. Microsatellites in Sorex Araneus (Insectivora): Highly Polymorphic Markers for Population Genetic Studies Within and Between Chromosomal Races. Hereditas 2004. [DOI: 10.1111/j.1601-5223.1996.00177.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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28
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Chikhi L, Goossens B, Treanor A, Bruford MW. Population genetic structure of and inbreeding in an insular cattle breed, the Jersey, and its implications for genetic resource management. Heredity (Edinb) 2004; 92:396-401. [PMID: 15014423 DOI: 10.1038/sj.hdy.6800433] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The Jersey is a ubiquitous and successful breed of cattle that originates from the UK Channel Island of Jersey. While the breed has been exported extensively, no imports have taken place to the island since 1789, leading to a concern regarding possible losses of genetic diversity and increased inbreeding. We have conducted the first large-scale genetic analysis of the Jersey cattle using only samples from the island. A total of 223 cattle from all parishes except one were genotyped for 12 microsatellite loci. The average number of alleles per locus and expected heterozygosity were found to be comparatively high (n(A)=4, H(e)=0.64) with respect to that observed in a number of continental breeds. Only breeds that have been upgraded and are therefore the result of admixture are clearly more variable than the Jersey. We also found a significant but limited amount of genetic differentiation between parishes (F(st)=0.013), or even between farms (F(st)=0.035) despite an apparent lack of movement. This is confirmed by the application of two recent statistical methods. A Bayesian partition analysis shows that the most probable value of K, the number of possible hidden partitions, is 1 (P approximately 0.98). K=2 has a much lower probability (P approximately 0.02) while other values are essentially zero. Similarly, we were able to show that there was no support for departure from panmixia other than due to population structure, and thus that there is sufficient background gene flow across the island to overcome local drift. Overall, it appears that the current level of genetic diversity and its distribution within the island means it is unnecessary to import unrelated genetic material to the island for management purposes.
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Affiliation(s)
- L Chikhi
- Institute of Zoology, Regent's Park, London NW1 4RY,UK.
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29
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Genetic Variability and Relationships of Japanese Native Chickens Assessed by Means of Microsatellite Profiling Approach-Focusing on the Oh-Shamo (Japanese Large Game) and Its Related Breeds. J Poult Sci 2004. [DOI: 10.2141/jpsa.41.94] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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30
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Bruford MW, Bradley DG, Luikart G. DNA markers reveal the complexity of livestock domestication. Nat Rev Genet 2003; 4:900-10. [PMID: 14634637 DOI: 10.1038/nrg1203] [Citation(s) in RCA: 290] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A series of recent genetic studies has revealed the remarkably complex picture of domestication in both New World and Old World livestock. By comparing mitochondrial and nuclear DNA sequences of modern breeds with their potential wild and domestic ancestors, we have gained new insights into the timing and location of domestication events that produced the farm animals of today. The real surprise has been the high number of domestication events and the diverse locations in which they took place - factors which could radically change our approach to conserving livestock biodiversity resources in the future.
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Affiliation(s)
- Michael W Bruford
- Cardiff School of Biosciences, Main Building, Cathay Park, PO Box 915, Cardiff CF10 3TL, UK.
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31
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Vasconcellos LPDMK, Tambasco-Talhari D, Pereira AP, Coutinho LL, Regitano LCDA. Genetic characterization of Aberdeen Angus cattle using molecular markers. Genet Mol Biol 2003. [DOI: 10.1590/s1415-47572003000200005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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32
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Hansen C, Shrestha JNB, Parker RJ, Crow GH, McAlpine PJ, Derr JN. Genetic diversity among Canadienne, Brown Swiss, Holstein, and Jersey cattle of Canada based on 15 bovine microsatellite markers. Genome 2002; 45:897-904. [PMID: 12416622 DOI: 10.1139/g02-063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genetic diversity among Canadienne, Brown Swiss, Holstein, and Jersey cattle was estimated from relationships determined by genotyping 20 distantly related animals in each breed for 15 microsatellites located on separate chromosomes. The Canadienne, Holstein, and Jersey cattle had an average of six alleles per loci compared with five alleles for Brown Swiss. Furthermore, a number of potentially breed-specific alleles were identified. The allele size variance among breeds was similar, but varied considerably among loci. All of the loci studied were equally heterozygous, as were Brown Swiss, Canadienne, and Holstein cattle (0.68-0.69) whereas Jersey cattle showed lower heterozygosity (0.59). The within-breed estimates of genetic distance were greater than zero and significant. The genetic distance between Canadienne and Holstein (0.156), Brown Swiss (0.243), and Jersey (0.235) was negligible, suggesting close relationship. Concurrently, Brown Swiss and Holstein (0.211) cattle also demonstrated close relationship. In contrast, the Jersey breed was genetically distant from the Brown Swiss and Holstein cattle (0.427 and 0.320, respectively). The characterization of Canadienne cattle, as part of the genetic resource conservation effort currently underway in Canada, underscores the difficulty in scientifically establishing unique breeds. Therefore, the need to consider all relevant morphological characteristics and production performance in combination with available cultural, historical, pedigree, and molecular information becomes relevant when identifying breeds for conservation.
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Affiliation(s)
- C Hansen
- Centre for Food and Animal Research, Agriculture and Agri-Food Canada, Ottawa, ON.
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33
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Lirón J, Ripoli M, De Luca J, Peral-García P, Giovambattista G. Analysis of genetic diversity and population structure in Argentine and Bolivian Creole cattle using five loci related to milk production. Genet Mol Biol 2002. [DOI: 10.1590/s1415-47572002000400010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- J.P. Lirón
- Universidad Nacional de La Plata, Argentina
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34
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Ganai NA, Yadav BR. Genetic variation within and among three Indian breeds of goat using heterologous microsatellite markers. Anim Biotechnol 2001; 12:121-36. [PMID: 11808627 DOI: 10.1081/abio-100108338] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The parameters of genetic variation, genetic distances and time of divergence in three Indian goat breeds were studied using 16 cattle microsatellite markers. The mean number of alleles and mean allele size (bp) per microsatellite marker in goats were 5.37 +/- 0.78 and 143.9 +/- 33.75 bp respectively. The average values of heterozygosity and polymorphism information content were 0.54 +/- 0.2 and 0.48 +/- 0.20, respectively. Five of the eight genetic distance methods were highly correlated, revealing a closer relationship between Jamnapari and Barbari goats. A phylogenetic tree constructed from inter-individual distances revealed that the individuals clustered according to the breed to which they belonged, and the Jamnapari and Barbari goats formed a cluster. The divergence times between Sirohi and Jamnapari, and Sirohi and Barbari were approximately 2000 years, while its value between Barbari and Jamnapari goats was approximately 1370 years.
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Affiliation(s)
- N A Ganai
- Livestock Genome Analysis Laboratory, National Dairy Research Institute, Karnal, India
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35
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Giovambattista G, Ripoli MV, Peral-Garcia P, Bouzat JL. Indigenous domestic breeds as reservoirs of genetic diversity: the Argentinean Creole cattle. Anim Genet 2001; 32:240-7. [PMID: 11683709 DOI: 10.1046/j.1365-2052.2001.00774.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Contrary to highly selected commercial breeds, indigenous domestic breeds are composed of semi-wild or feral populations subjected to reduced levels of artificial selection. As a consequence, many of these breeds have become locally adapted to a wide range of environments, showing high levels of phenotypic variability and increased fitness under natural conditions. Genetic analyses of three loci associated with milk production (alpha(S1)-casein, kappa-casein and prolactin) and the locus BoLA-DRB3 of the major histocompatibility complex indicated that the Argentinean Creole cattle (ACC), an indigenous breed from South America, maintains high levels of genetic diversity and population structure. In contrast to the commercial Holstein breed, the ACC showed considerable variation in heterozygosity (H(e)) and allelic diversity (A) across populations. As expected, bi-allelic markers showed extensive variation in He whereas the highly polymorphic BoLA-DRB3 showed substantial variation in A, with individual populations having 39-74% of the total number of alleles characterized for the breed. An analysis of molecular variance (AMOVA) of nine populations throughout the distribution range of the ACC revealed that 91.9-94.7% of the total observed variance was explained by differences within populations whereas 5.3-8.1% was the result of differences among populations. In addition, the ACC breed consistently showed higher levels of genetic differentiation among populations than Holstein. Results from this study emphasize the importance of population genetic structure within domestic breeds as an essential component of genetic diversity and suggest that indigenous breeds may be considered important reservoirs of genetic diversity for commercial domestic species.
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Affiliation(s)
- G Giovambattista
- Centro de Investigaciones en Genética Básica y Aplicada, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
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36
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Visscher PM, Smith D, Hall SJ, Williams JL, Williams JA. A viable herd of genetically uniform cattle. Nature 2001; 409:303. [PMID: 11201728 DOI: 10.1038/35053160] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- P M Visscher
- Institute of Cell, Animal and Population Biology, University of Edinburgh, UK.
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37
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38
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Edwards CJ, Dolf G, Looft C, Loftus RT, Bradley DG. Relationships between the endangered Pustertaler-Sprinzen and three related European cattle breeds as analysed with 20 microsatellite loci. Anim Genet 2000; 31:329-32. [PMID: 11105215 DOI: 10.1046/j.1365-2052.2000.00651.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We estimated the genetic relationships between the endangered German Pustertaler-Sprinzen cattle breed and the Pinzgauer, Vosges and Simmental breeds--decided upon after consultation of the available historical literature. Within-breed diversity of the four breeds was also assessed. Twenty microsatellite markers were amplified in 27-50 unrelated individuals from populations of each breed. Within-breed variation was estimated from average heterozygosity values and mean number of alleles. Breed relationships were evaluated by genetic distance and a neighbour-joining tree was calculated from these estimates. Bootstrap resampling of loci tested the robustness of the tree topology obtained. A tree was also constructed from distance matrices using individual animals as operational taxonomic units. From both the average heterozygosity values and mean number of alleles calculated, the Pustertaler breed appears to be no more genetically impoverished than the other breeds analysed. The breed tree showed an 85% support for the Pustertaler-Pinzgauer grouping, and this result is echoed in the genetic distance values and allele-sharing individual tree.
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Affiliation(s)
- C J Edwards
- Department of Genetics, Trinity College, Dublin, Ireland
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39
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Hanslik S, Harr B, Brem G, Schlötterer C. Microsatellite analysis reveals substantial genetic differentiation between contemporary New World and Old World Holstein Friesian populations. Anim Genet 2000; 31:31-8. [PMID: 10690359 DOI: 10.1046/j.1365-2052.2000.00569.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genotypic data from 39 microsatellite loci typed in 211 animals were used to assess the genetic differentiation between Old World and New World Holstein Friesian cattle populations. Gene diversities were similar in all five Holstein Friesian populations surveyed, ranging from 0.43 to 0.48. A tree of individuals based on the proportion of shared alleles indicated a clear distinction between Old World and New World Holstein Friesian populations. Similarly, genetic differentiation between populations, as measured by FST, was highly significant. Using the split decomposition method, we were able to visualize the significant introgression of New World Holstein Friesian into European Holstein Friesian populations.
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Affiliation(s)
- S Hanslik
- Institut für Tierzucht und Genetik, Veterinärmedizinische Universität Wien, Austria
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40
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Crouau-Roy B. Trans-speciation maintenance in the MHC region of a polymorphism which includes a polymorphic dinucleotide locus, and the de novo arisal of a polymorphic tetranucleotide microsatellite. TISSUE ANTIGENS 1999; 54:560-4. [PMID: 10674969 DOI: 10.1034/j.1399-0039.1999.540604.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Alleles and the surrounding regions of DQCAR, a dinucleotide repeat tightly linked to HLA-DQB1, were sequenced in a range of primate species including man. Three polymorphic regions can usefully be defined in the description of these sequences: the dinucleotide GT repeat itself, the anonymous region 5' of this repeat, and a variable CTGT repeat in the 3' region. The 5' sequence displayed six alleles in the individuals studied. One of these alleles was invariably associated with substitutions in the GT repeat and absence of the CTGT repeat, the others with pure, polymorphic GT repeats and variation in the numbers of CTGT repeats. Haplotypes can be classified by the allele in the 5' region. Those carrying allele 1 were only found in man, those with allele 2 in man, chimpanzee and gorilla. The third haplotype (indicated by the presence of allele 3) was found in chimpanzee, gorilla and orang-utan, the fourth in chimpanzee and gibbon, the fifth in baboon, guenon and mangabey and the sixth in guenon and macaque. The alleles in the 5' region, but from different species, are thus often more similar than alleles from the same species, a phenomenon already shown for some HLA genes. This suggests that major histocompatibility sequences and surrounding sequences shared a correlated evolutionary history. The new polymorphic tetranucleotide microsatellite (CTGT, 3rd region) has possibly arisen de novo from the pre-existing dinucleotide GT. This study provides information not only on the molecular evolution of this particular microsatellite but also of the trans-speciation maintenance of polymorphism of its surrounding sequences.
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Affiliation(s)
- B Crouau-Roy
- CNRS, CIGH, UPR 8291, CHU Purpan, Toulouse, France.
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41
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Martín-Burriel I, García-Muro E, Zaragoza P. Genetic diversity analysis of six Spanish native cattle breeds using microsatellites. Anim Genet 1999; 30:177-82. [PMID: 10442978 DOI: 10.1046/j.1365-2052.1999.00437.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Six native Spanish cattle breeds have been characterized by using 30 microsatellite markers. The studied populations can be divided into three groups: Brown orthoid (Asturian Mountain, Asturian Lowland and the Nord-west Brown Group), Red convex (Pyrenean and Menorquina) and the Iberian bovine (Fighting bull). Allele frequencies were calculated and used for the characterization of the breeds and the study of their genetic relationships. Different genetic distance measures were calculated and used for dendogram construction. The closest populations were those representing Asturian breeds, the most divergent being Menorquina and Fighting Bull. The latter also showed the lowest diversity values (mean number of alleles per locus and heterozygosity). Genetic distances obtained between the other populations under analysis were similar to those reported for different European cattle breeds. This work analyzes the recent origin of these populations and contributes to the knowledge and genetic characterization of European native breeds.
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Affiliation(s)
- I Martín-Burriel
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza Miguel Servet, Spain
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42
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MacHugh DE, Troy CS, McCormick F, Olsaker I, Eythórsdóttir E, Bradley DG. Early medieval cattle remains from a Scandinavian settlement in Dublin: genetic analysis and comparison with extant breeds. Philos Trans R Soc Lond B Biol Sci 1999; 354:99-108; discussion 108-9. [PMID: 10091250 PMCID: PMC1692458 DOI: 10.1098/rstb.1999.0363] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A panel of cattle bones excavated from the 1000-year-old Viking Fishamble Street site in Dublin was assessed for the presence of surviving mitochondrial DNA (mtDNA). Eleven of these bones gave amplifiable mtDNA and a portion of the hypervariable control region was determined for each specimen. A comparative analysis was performed with control region sequences from five extant Nordic and Irish cattle breeds. The medieval population displayed similar levels of mtDNA diversity to modern European breeds. However, a number of novel mtDNA haplotypes were also detected in these bone samples. In addition, the presence of a putative ancestral sequence at high frequency in the medieval population supports an early post-domestication expansion of cattle in Europe.
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Affiliation(s)
- D E MacHugh
- Department of Genetics, Trinity College, Dublin 2, Ireland
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43
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Vanhala T, Tuiskula-Haavisto M, Elo K, Vilkki J, Mäki-Tanila A. Evaluation of genetic variability and genetic distances between eight chicken lines using microsatellite markers. Poult Sci 1998; 77:783-90. [PMID: 9628523 DOI: 10.1093/ps/77.6.783] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The genetic variability and divergence of eight chicken lines were evaluated using nine microsatellite markers. The chicken lines included three White Leghorn hybrids, three Finnish Landrace lines, a Rhode Island Red line, and a broiler hybrid line. All the microsatellite loci were found to be polymorphic, the number of alleles varying from 4 to 13 per locus and 1 to 10 per line, respectively. Observed heterozygosities ranged from 0.00 to 0.91. The highest (0.67) and lowest (0.29) mean heterozygosity per line was observed in the broiler and in White Leghorn of Mäkelä, respectively. Three of the microsatellite loci deviated from the Hardy-Weinberg equilibrium in some populations. F statistics indicated clearly the subdivision of the total population into different lines. The genetic distances confirmed the classification of Finnish Landraces into different lines. A phylogenetic consensus tree was constructed from resampled data (1,000 times) using the neighbor-joining method. According to the phylogenetic tree, the lines were grouped into three clusters, in which the White Leghorns formed one group, two Landraces a second group, and a Landrace, the Rhode Island Red, and the broiler lines a third group. Allele distribution at the loci does not support either the stepwise or the infinite alleles mutation model, but the distribution pattern was quite irregular at different loci.
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Affiliation(s)
- T Vanhala
- Agricultural Research Centre MTT, Animal Production Research, Animal Breeding, Jokioinen, Finland
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Arranz JJ, Bayón Y, San Primitivo F. Comparison of protein markers and microsatellites in differentiation of cattle populations. Anim Genet 1996; 27:415-9. [PMID: 9022156 DOI: 10.1111/j.1365-2052.1996.tb00508.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Five cattle populations, representing four breeds, were analysed for 14 protein markers and five microsatellite loci. The breeds studied were Brown Swiss and three autochthonous Spanish cattle: Avileña-Negra Ibérica (A-NI), two populations (A-NI 1 and A-NI 2) from different, reproductively isolated, locations; Sayaguesa; and Morucha. A total of 752 animals were examined for biochemical polymorphisms, of which 488 were also DNA typed. Genetic parameters and phylogenetic trees were obtained separately for each group of markers and results were compared. Estimates of heterozygosity and genetic distances from microsatellites were greater than those obtained using protein markers. The overall topology of the two dendrograms was similar. A-NI 1 and A-NI 2 populations were grouped together, related to Morucha, and the three of them related to Sayaguesa. Brown Swiss appeared in a separate branch from Spanish cattle. These results support the usefulness of microsatellites in the study of genetic relationships among closely related populations and breeds.
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Affiliation(s)
- J J Arranz
- Departamento de Producción Animal, Universidad de León, Spain
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Goldstein DB, Ruiz Linares A, Cavalli-Sforza LL, Feldman MW. Genetic absolute dating based on microsatellites and the origin of modern humans. Proc Natl Acad Sci U S A 1995; 92:6723-7. [PMID: 7624310 PMCID: PMC41401 DOI: 10.1073/pnas.92.15.6723] [Citation(s) in RCA: 451] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We introduce a new genetic distance for microsatellite loci, incorporating features of the stepwise mutation model, and test its performance on microsatellite polymorphisms in humans, chimpanzees, and gorillas. We find that it performs well in determining the relations among the primates, but less well than other distance measures (not based on the stepwise mutation model) in determining the relations among closely related human populations. However, the deepest split in the human phylogeny seems to be accurately reconstructed by the new distance and separates African and non-African populations. The new distance is independent of population size and therefore allows direct estimation of divergence times if the mutation rate is known. Based on 30 microsatellite polymorphisms and a recently reported average mutation rate of 5.6 x 10(-4) at 15 dinucleotide microsatellites, we estimate that the deepest split in the human phylogeny occurred about 156,000 years ago. Unlike most previous estimates, ours requires no external calibration of the rate of molecular evolution. We can use such calibrations, however, to test our estimate.
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Affiliation(s)
- D B Goldstein
- Department of Biological Sciences, Stanford University, CA 94305, USA
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Usha AP, Simpson SP, Williams JL. Probability of random sire exclusion using microsatellite markers for parentage verification. Anim Genet 1995; 26:155-61. [PMID: 7793682 DOI: 10.1111/j.1365-2052.1995.tb03155.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Many microsatellite sequences have been described in the bovine genome. Being highly polymorphic these have been suggested as markers for parentage verification and individual identification in cattle. We have evaluated the use of five highly polymorphic microsatellite markers for parentage verification in 14 breeds of cattle in the UK. Three of the microsatellite loci occur within introns in genes: BoLA DRB3, steroid 21-hydroxylase, and the beta subunit of the follicle-stimulating hormone. The other two are anonymous sites ETH131 and HEL6. Results were analysed by a statistical approach that takes in to account deviations from Hardy-Wienberg equilibrium and linkage disequilibrium for multiple loci. The method of determining the probability of random sire exclusion uses observed genotype frequencies instead of allele frequencies. Independently, the markers used have a probability of between 0.72 and 0.62 of identifying a parentage error, while used together the five markers give, on average across breeds, a probability of 0.99 of excluding an incorrect sire.
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Affiliation(s)
- A P Usha
- Roslin Institute, Edinburgh Research Station, Midlothian, UK
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Loftus RT, MacHugh DE, Ngere LO, Balain DS, Badi AM, Bradley DG, Cunningham EP. Mitochondrial genetic variation in European, African and Indian cattle populations. Anim Genet 1994; 25:265-71. [PMID: 7985843 DOI: 10.1111/j.1365-2052.1994.tb00203.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Mitochondrial DNA from representative animals of 13 different cattle breeds was assayed for restriction fragment length polymorphisms (RFLP) to determine phylogenetic relationships and levels of variation among breeds; 16 different mitotypes were found, described by 20 polymorphisms. Within these 16 mitotypes two major lineages were apparent: an Afro-European and an Asian type. These were found to differ at over 2.3% of sites surveyed. None of the mitotypes found in the Asian lineage was detectable in the Afro-European lineage and vice versa. Within each of the major mitotypes there were no further significant differences within or among breeds. Using rates of mitochondrial evolution estimated from other species, the two lineages were estimated to have diverged between 575,000 and 1,150,000 years ago; well outside the 10,000 years bp timeframe postulated by a single domestication hypothesis. The results presented are concordant with those generated in other studies and provide strong evidence for an independent domestication of Asian Bos indicus. Furthermore, the grouping of all African indicine populations within the clade containing all Bos taurus lineages points to the hybrid origins of the humped cattle of that continent.
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Affiliation(s)
- R T Loftus
- Department of Genetics, Trinity College, Dublin, Ireland
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