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Giantsis IA, Antonopoulou D, Dekolis N, Zaralis K, Avdi M. Origin, demographics, inbreeding, phylogenetics, and phenogenetics of Karamaniko breed, a major common ancestor of the autochthonous Greek sheep. Trop Anim Health Prod 2022; 54:73. [PMID: 35072809 DOI: 10.1007/s11250-022-03081-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/20/2022] [Indexed: 11/24/2022]
Abstract
Greece has a long history in autochthonous sheep, the genetic ancestry of which has been associated with four subtypes known to inhabit Greece at the end of the nineteenth century. Among them, the Karamaniko breed is still surviving, however endangered. This study was designed in order to (a) determine the phylogenetic status, (b) to evaluate the levels of inbreeding, and (c) to assess the genetic basis of coat color of Karamaniko breed. For these purposes, the mitochondrial cyt b gene was sequenced, the AFLP methodology was applied, and the MC1R was genotyped, respectively, in 72 female sheep from the Karamaniko breed. Four different novel cyt b haplotypes were defined and three MC1R genotypes were scored, whereas inbreeding levels estimated using AFLPs by the means of relatedness coefficient (r) were 0.287, with gene diversity at the levels of 0.105. Phylogenetic analysis indicated an eastern Asian tropical and subtropical origin of the Karamaniko breed, close with breeds originating from central Turkey, or a clustering within western European or Mediterranean sheep, mirroring a recent genetic divergence, with a non-random spread towards the formation of lowland breeds. The MC1R genotypes were all associated with the white coat color, in which selective breeding has probably been based on traditional morphological characters. Finally, levels of inbreeding do not constitute an indication for a particular mating plan to prevent unpleasant phenomena such as inbreeding depression, probably because of the special attention paid by the farmers towards the avoidance of relative recurrent mating.
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Affiliation(s)
- Ioannis A Giantsis
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Florina, Greece.
| | - Danai Antonopoulou
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Florina, Greece.,Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikolaos Dekolis
- Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Zaralis
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Florina, Greece
| | - Melpomeni Avdi
- Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Ben-Jemaa S, Senczuk G, Ciani E, Ciampolini R, Catillo G, Boussaha M, Pilla F, Portolano B, Mastrangelo S. Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle. Front Genet 2021; 12:675569. [PMID: 33995500 PMCID: PMC8113768 DOI: 10.3389/fgene.2021.675569] [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: 03/03/2021] [Accepted: 04/07/2021] [Indexed: 12/31/2022] Open
Abstract
The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six relevant candidate regions were identified by at least two approaches. We found genomic signatures of selective sweeps spanning genes related to mitochondrial function, muscle development, growth, and meat traits (SCIN, THSD7A, ETV1, UCHL1, and MYOD1), which reflects the different breeding schemes between Maremmana (semi-wild conditions) and the other Podolian-derived Italian breeds (semi-extensive). We also identified several genes linked to Maremmana adaptation to the environment of the western-central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C-C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (HEATR9, MMP28, and ASIC2) or strongly associated with malaria resistance/susceptibility (AP2B1). Our results provide a glimpse into diverse selection signatures in Maremmana cattle and can be used to enhance our understanding of the genomic basis of environmental adaptation in cattle.
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Affiliation(s)
- Slim Ben-Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, University of Carthage, Ariana, Tunisia
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro”, Bari, Italy
| | | | - Gennaro Catillo
- Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), Centro di Ricerca Zootecnia e Acquacoltura, Lodi, Italy
| | - Mekki Boussaha
- INRAE, AgroParisTech, University of Paris Saclay, Saint Aubin, France
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
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Tripathi SB, Jatav G, Malik AA, Joshi S, Singh VK, Negi MS, Chauhan L, Sharma SS. AFLP markers based genetic diversity and population structure analysis of Kadaknath: an indigenous black meat poultry breed of India. Anim Biotechnol 2021; 33:1045-1055. [PMID: 33427028 DOI: 10.1080/10495398.2020.1865390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The current study is the first worldwide to assess the genetic diversity of Kadaknath poultry using amplified fragment length polymorphism (AFLP) markers. Out of total 96 accessions, four were outliers and 92 were Kadaknath accessions of which 30 were males, 62 were females. Of these, 74 were jet black, 7 penciled and 11 were golden feather color type of Kadaknath. High level of polymorphism (23.94%) was observed in 387 loci amplified using six AFLP primer combinations. The Jaccard's similarity coefficient ranged from 0.211 to 0.754 with an average dissimilarity of 0.517. Based on the neighbor-joining method of clustering, all accessions were clustered into seven major clusters which were not consistent with their respective geographical locations. The mean values of effective multiplex ratio, polymorphic information content, resolving power and marker index were 15.16, 0.38, 9.87 and 5.85 respectively. Further, the high log-likelihood score was produced when the number of populations (K) was set at 7 while carrying out the population STRUCTURE analysis, which was also congruent with clustering analysis based on genetic diversity. The extent of genetic diversity detected in this study could be used for germplasm selection and developing conservation strategies of pure breed of Kadaknath.
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Affiliation(s)
| | - Gayaprasad Jatav
- College of Veterinary Sciences and Animal Husbandry Mhow, Nanaji Deshmukh Veterinary Science University (NDVSU), Jabalpur, India
| | - Anoop Anand Malik
- Department of Biotechnology, TERI School of Advanced Studies, Vasant Kunj, New Delhi, India
| | - Shrikant Joshi
- College of Veterinary Sciences and Animal Husbandry Mhow, Nanaji Deshmukh Veterinary Science University (NDVSU), Jabalpur, India
| | - Vivek Kumar Singh
- Department of Biotechnology, TERI School of Advanced Studies, Vasant Kunj, New Delhi, India
| | - Madan Singh Negi
- TERI-Deakin Nano-Biotechnology Centre, The Energy and Resources Institute, Gurugram, India
| | - Laxmi Chauhan
- College of Veterinary Sciences and Animal Husbandry Mhow, Nanaji Deshmukh Veterinary Science University (NDVSU), Jabalpur, India
| | - Shyam Sundar Sharma
- TERI-Deakin Nano-Biotechnology Centre, The Energy and Resources Institute, Gurugram, India
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Malik M, Moaeen-ud-Din M, Bilal G, Ghaffar A, Muner R, Raja G, Khan W. Development of amplified fragment length polymorphism (AFLP) markers for the identification of Cholistani cattle. Arch Anim Breed 2018; 61:387-394. [PMID: 32175445 PMCID: PMC7065403 DOI: 10.5194/aab-61-387-2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 09/27/2018] [Indexed: 11/17/2022] Open
Abstract
The identification issue of livestock can be resolved by using molecular identification tools that are acceptable to preserve and maintain pure breeds worldwide. The application of a molecular identification methodology is more important for developing nations, e.g., Pakistan, where uncontrolled crossbreeding has become a common practice and the import of exotic animals and germplasm is ever increasing. This presents a risk to local breeds as also stated by the FAO. Therefore, the current study was designed to develop standard molecular markers for Cholistani cattle to ascertain their purity for breeding purpose. In this study 50 and 48 unrelated males were sampled for Cholistani and each crossbred cattle, respectively. Candidate molecular markers present in Cholistani but absent in crossbred cattle and vice versa were detected using the amplified fragment length polymorphism (AFLP) method. Eleven markers were developed and were converted to single nucleotide polymorphism (SNP) markers for genotyping. The allele frequencies in both breeds were determined for discrimination ability using polymerase-chain-reaction-restriction-fragment-polymorphism (PCR-AFLP). The probability of identifying the Cholistani breed was 0.905 and the probability of misjudgment was 0.073 using a panel of markers. The identified markers can ascertain the breed purity and are likely to extend the facility for breed purity testing before entering into a genetic improvement program in the country.
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Affiliation(s)
- Muhammad Haseeb Malik
- University Institute of Biochemistry & Biotechnology, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
- These authors contributed equally to this work
| | - Muhammad Moaeen-ud-Din
- National Center for Livestock Breeding, Genetics & Genomics, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
- Department of Animal Breeding & Genetics, Faculty of Veterinary & Animal Sciences, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
- These authors contributed equally to this work
| | - Ghulam Bilal
- Department of Animal Breeding & Genetics, Faculty of Veterinary & Animal Sciences, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - Abdul Ghaffar
- Animal Science Institute, National Agriculture Research Council, Islamabad, Pakistan
| | - Raja Danish Muner
- Department of Animal Breeding & Genetics, Faculty of Veterinary & Animal Sciences, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - Ghazala Kaukab Raja
- University Institute of Biochemistry & Biotechnology, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - Waqas Ahmad Khan
- Department of Biotechnology, Faculty of Sciences, University of Sargodha, Sargodha, Pakistan
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Rodríguez-Clark KM, Davidson B, Kingston S, Coyle BJ, Duchesne P, Braun MJ. Evaluating a potential source of founders for ex situ conservation efforts: genetic differentiation between disjunct populations of the Endangered red siskin Spinus cucullatus. ENDANGER SPECIES RES 2018. [DOI: 10.3354/esr00898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Muñoz LJ, Carballosa-Gautam MM, Yanowsky K, García-Atarés N, López DE. The genetic audiogenic seizure hamster from Salamanca: The GASH:Sal. Epilepsy Behav 2017; 71:181-192. [PMID: 27072920 DOI: 10.1016/j.yebeh.2016.03.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 03/01/2016] [Accepted: 03/04/2016] [Indexed: 12/17/2022]
Abstract
The hamster has been previously described as a paroxysmal dystonia model, but our strain is currently recognized as a model of audiogenic seizures (AGS). The original first epileptic hamster appeared spontaneously at the University of Valladolid, where it was known as the GPG:Vall line, and was transferred to the University of Salamanca where a new strain was developed, named GASH:Sal. By testing auditory brainstem responses, the GASH:Sal exhibits elevated auditory thresholds that indicate a hearing impairment. Moreover, amplified fragment length polymorphism analysis distinguished genetic differences between the susceptible GASH:Sal hamster strain and the control Syrian hamsters. The GASH:Sal constitutes an experimental model of reflex epilepsy of audiogenic origin derived from an autosomal recessive disorder. Thus, the GASH:Sal exhibits generalized tonic-clonic seizures, characterized by a short latency period after auditory stimulation, followed by wild running, a convulsive phase, and finally stupor, with origin in the brainstem. The seizure profile of the GASH:Sal is similar to those exhibited by other models of inherited AGS susceptibility, which decreases after six months of age, but the proneness across generations is maintained. The GASH:Sal can be considered a reliable model of audiogenic seizures, suitable to investigate current antiepileptic pharmaceutical treatments as well as novel therapeutic drugs. This article is part of a Special Issue entitled "Genetic and Reflex Epilepsies, Audiogenic Seizures and Strains: From Experimental Models to the Clinic".
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Affiliation(s)
- Luis J Muñoz
- Animal Research Service, University of Salamanca, 37007 Salamanca, Spain.
| | - Melissa M Carballosa-Gautam
- Institute for Neuroscience of Castilla y León/IBSAL, C/ Pintor Fernando Gallego, No. 1, 37007 Salamanca, Spain; The Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, 1095 NW 14thTerrace, Room 2-34, Miami, FL 33136, USA
| | - Kira Yanowsky
- Institute for Neuroscience of Castilla y León/IBSAL, C/ Pintor Fernando Gallego, No. 1, 37007 Salamanca, Spain
| | - Natividad García-Atarés
- Department of Anatomy and Radiology, School of Medicine, University of Valladolid, 47007, Spain
| | - Dolores E López
- Institute for Neuroscience of Castilla y León/IBSAL, C/ Pintor Fernando Gallego, No. 1, 37007 Salamanca, Spain; Department of Cell Biology and Pathology, University of Salamanca, Spain
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Liu YL, Cheng M, Jiang MF, Wang Y, Wang J, Fu XH. Genetic diversity analysis of eight indigenous goat breeds (groups) in China using AFLP markers. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414120060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Utsunomiya YT, Bomba L, Lucente G, Colli L, Negrini R, Lenstra JA, Erhardt G, Garcia JF, Ajmone-Marsan P. Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle. BMC Genet 2014; 15:47. [PMID: 24739206 PMCID: PMC4021504 DOI: 10.1186/1471-2156-15-47] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 04/09/2014] [Indexed: 11/18/2022] Open
Abstract
Background Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas. Results We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy. Conclusions The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle populations, which is essential for an effective conservation of the bovine genetic resources.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Paolo Ajmone-Marsan
- Institute of Zootechnics, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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Yang W, Kang X, Yang Q, Lin Y, Fang M. Review on the development of genotyping methods for assessing farm animal diversity. J Anim Sci Biotechnol 2013; 4:2. [PMID: 23343204 PMCID: PMC3563493 DOI: 10.1186/2049-1891-4-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 01/21/2013] [Indexed: 11/10/2022] Open
Abstract
Advances in molecular biotechnology have introduced new generations of molecular markers for use in the genetic improvement of farm animals. Consequently, more accurate genetic information can be obtained to better understand existing animal genetic resources. This review gives a brief summary on the development of genetic markers including both the classical genetic markers and more advanced DNA-based molecular markers. This review will help us better understand the characteristics of different genetic markers and the genetic diversity of animal genetic resources.
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Affiliation(s)
- Wanjie Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P, R, China.
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Genetic differentiation in populations of the yellow-necked mouse, Apodemus flavicollis, harbouring B chromosomes in different frequencies. POPUL ECOL 2012. [DOI: 10.1007/s10144-012-0333-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Piras D, Doro MG, Casu G, Melis PM, Vaccargiu S, Piras I, Parracciani D, Stradoni R, Frongia B, Lai G, Sale S, Cattari W, Piras R, Querci O, Demuro P, Cui S, Atzori F, Mancosu M, Marchiori F, Cammelli R, Spiga A, Loddo PP, Pili G, Boi R, Argiolas G, Mereu P, Leoni GG, Naitana S, Pirastu M, Novelletto A. Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock. PLoS One 2012; 7:e30785. [PMID: 22363488 PMCID: PMC3281868 DOI: 10.1371/journal.pone.0030785] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 12/28/2011] [Indexed: 11/18/2022] Open
Abstract
Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3) to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591) which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity.We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia.
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Affiliation(s)
- Daniela Piras
- Institute of Population Genetics, National Research Council, Sassari, Italy
| | - Maria Grazia Doro
- Institute of Population Genetics, National Research Council, Sassari, Italy
| | - Giuseppina Casu
- Institute of Population Genetics, National Research Council, Sassari, Italy
| | - Paola Maria Melis
- Institute of Population Genetics, National Research Council, Sassari, Italy
| | - Simona Vaccargiu
- Institute of Population Genetics, National Research Council, Sassari, Italy
| | | | | | | | | | | | - Salvatore Sale
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Walter Cattari
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Roberto Piras
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Ombretta Querci
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | | | - Sandro Cui
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Franco Atzori
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Marco Mancosu
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | | | - Rossana Cammelli
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Alessandra Spiga
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Pier Paolo Loddo
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Gianfranco Pili
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | - Roberto Boi
- ARAS, Regional Association of Sardinian Farmers, Cagliari, Italy
| | | | - Paolo Mereu
- Department of Physiological, Biochemical and Cell Sciences, University of Sassari, Sassari, Italy
| | | | - Salvatore Naitana
- Faculty of Veterinary Sciences, University of Sassari, Sassari, Italy
| | - Mario Pirastu
- Institute of Population Genetics, National Research Council, Sassari, Italy
- Genetic Park of Ogliastra, Perdasdefogu, Italy
| | - Andrea Novelletto
- Department of Biology, University “Tor Vergata”, Rome, Italy
- * E-mail:
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Withen KB, Brüniche-Olsen A, Pedersen BV, Gravlund P. The Agersoe cattle: the last remnants of the Danish island cattle (Bos taurus)? J Anim Breed Genet 2011; 128:141-52. [PMID: 21385229 DOI: 10.1111/j.1439-0388.2010.00883.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A phenotypically interesting strain of cattle existed on the small island of Agersoe, on the west coast of Zealand, Denmark, in the beginning of the last decade. The cattle share a great resemblance to the extinct Danish breed, the Island cattle. The objective of this study was to genetically characterize the Agersoe cattle, using microsatellites, amplified fragment length polymorphism (AFLP) and mtDNA markers, and analyse the genetic variability within the breed and the genetic relationship to 14 European breeds with focus on the Red Danish and Jutland breed. The results show diversity in nuclear markers comparable to that of modern breeds and that the Agersoe cattle are separable from the two native breeds. The absence of inbreeding and the degree of genetic diversity are taken as a sign of recent admixture. The Agersoe cattle did not exhibit a consistent association with any of the European breeds. Several arguments based on this survey have been put forward in favour of characterizing the Agersoe cattle as being the last remnants of the Danish Island Cattle.
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Affiliation(s)
- K B Withen
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark
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Bonin A, Ehrich D, Manel S. Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Mol Ecol 2007; 16:3737-58. [PMID: 17850542 DOI: 10.1111/j.1365-294x.2007.03435.x] [Citation(s) in RCA: 300] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Recently, the amplified fragment length polymorphism (AFLP) technique has gained a lot of popularity, and is now frequently applied to a wide variety of organisms. Technical specificities of the AFLP procedure have been well documented over the years, but there is on the contrary little or scattered information about the statistical analysis of AFLPs. In this review, we describe the various methods available to handle AFLP data, focusing on four research topics at the population or individual level of analysis: (i) assessment of genetic diversity; (ii) identification of population structure; (iii) identification of hybrid individuals; and (iv) detection of markers associated with phenotypes. Two kinds of analysis methods can be distinguished, depending on whether they are based on the direct study of band presences or absences in AFLP profiles ('band-based' methods), or on allelic frequencies estimated at each locus from these profiles ('allele frequency-based' methods). We investigate the characteristics and limitations of these statistical tools; finally, we appeal for a wider adoption of methodologies borrowed from other research fields, like for example those especially designed to deal with binary data.
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Affiliation(s)
- A Bonin
- Diversity Arrays Technology P/L, Yarralumla, ACT 2600, Australia
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Sechi T, Usai MG, Miari S, Mura L, Casu S, Carta A. Identifying native animals in crossbred populations: the case of the Sardinian goat population. Anim Genet 2007; 38:614-20. [DOI: 10.1111/j.1365-2052.2007.01655.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Negrini R, Nijman IJ, Milanesi E, Moazami-Goudarzi K, Williams JL, Erhardt G, Dunner S, Rodellar C, Valentini A, Bradley DG, Olsaker I, Kantanen J, Ajmone-Marsan P, Lenstra JA. Differentiation of European cattle by AFLP fingerprinting. Anim Genet 2007; 38:60-6. [PMID: 17257190 DOI: 10.1111/j.1365-2052.2007.01554.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Neolithic introduction of domestic cattle into Europe was followed by differential adaptation, selection, migration and genetic isolation, leading ultimately to the emergence of specialized breeds. We have studied the differentiation of European cattle by amplified fragment length polymorphism (AFLP) fingerprinting. Combining AFLP data sets from two laboratories yielded 81 biallelic polymorphic markers scored in 19-22 individual animals from 51 breeds. Model-based clustering differentiated Podolian cattle as well as French and Alpine breeds from other European cattle. AFLP genetic distances correlated well with microsatellite-based genetic distances calculated for the same breeds. However, the AFLP data emphasized the divergence of taurine and indicine cattle relative to the variation among European breeds and indicated an Eastern influence on Italian and Hungarian Podolian breeds. This probably reflects import from the East after the original introduction of domestic cattle into Europe. Our data suggest that Italian cattle breeds are relatively diverse at the DNA sequence level.
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Affiliation(s)
- R Negrini
- Institute of Zootechnics, Catholic University of Sacred Heart, Piacenza, Italy
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Negrini R, Milanesi E, Bozzi R, Pellecchia M, Ajmone-Marsan P. Tuscany autochthonous cattle breeds: an original genetic resource investigated by AFLP markers. J Anim Breed Genet 2006; 123:10-6. [PMID: 16420260 DOI: 10.1111/j.1439-0388.2006.00554.x] [Citation(s) in RCA: 13] [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 aim of this study was to assess the genetic diversity of four autochthonous cattle breeds of Tuscany and their relationships in comparison with Italian Friesian and Italian Brown, using amplified fragment length polymorphism markers. A total of 212 individuals were genotyped with three primer combinations generating 102 polymorphic markers. Average expected heterozygosity ranged from 0.23 in Mucca Pisana to 0.26 in Chianina, Italian Friesian, Italian Brown and Maremmana. The differences resulted not significant (Kruskall-Wallis test, p = 0.416). Gst-B index revealed that 86% of the total genetic variance is retained within population and only 14% is accounted by the between populations component. Multivariate analysis at individual and population level indicated that: (i) Calvana and Chianina are quite separate from the other breeds as an effect of the bottleneck experienced or as a signature of different origin; (ii) Podolian, Maremmana and Italian Brown clustered with the double purpose Mucca Pisana, revealing their contribution to its admixed genetic make up; (iii) Italian Friesian behaved always as out group. The 'analysis of molecular variance' recovered a significant subdivision clustering the six populations into three groups: Italian Friesian and Italian Brown versus Maremmana and Mucca Pisana versus Chianina and Calvana (6% of the total variance).
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Affiliation(s)
- R Negrini
- Istituto di Zootecnica, UCSC, Via Emilia Parmense, Piacenza, Italy.
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De Marchi M, Dalvit C, Targhetta C, Cassandro M. Assessing genetic diversity in indigenous Veneto chicken breeds using AFLP markers. Anim Genet 2006; 37:101-5. [PMID: 16573523 DOI: 10.1111/j.1365-2052.2005.01390.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Genetic variation in four indigenous chicken breeds from the Veneto region of Italy was assessed using amplified fragment length polymorphism (AFLP) markers. A total of 99 individuals were analysed using three AFLP primer combinations that produced 70 polymorphisms. Four indigenous Veneto chicken breeds (Ermellinata, Padovana, Pépoi and Robusta) and a reference broiler line were included in the analysis. Breed-specific markers were identified in each breed. The expected heterozygosity did not differ significantly among the indigenous Veneto chicken breeds and the broiler line. The coefficient of gene variation (Gst) value across loci indicated that almost half of the total variability was observed among breeds. Nei's standard genetic distance between pairs of breeds showed that the distance between the broiler line and the Pépoi breed was greater than the distances between the broiler line and the other three chicken breeds. Cluster analysis based on standard genetic distances between breeds indicated that the Padovana and Pépoi breeds were closely related. Factorial analysis based on a binary matrix of the AFLP data showed a clear distinction of all breeds.
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Affiliation(s)
- M De Marchi
- Department of Animal Science, University of Padova, Agripolis, Italy.
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Baus E, Darrock DJ, Bruford MW. Gene-flow patterns in Atlantic and Mediterranean populations of the Lusitanian sea star Asterina gibbosa. Mol Ecol 2005; 14:3373-82. [PMID: 16156809 DOI: 10.1111/j.1365-294x.2005.02681.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, the population structure of the Lusitanian sea star Asterina gibbosa was assessed using amplified fragment length polymorphism (AFLP). One hundred and twenty-two AFLP loci were analysed in 159 individuals from eight populations from across the species' range and revealed high levels of genetic diversity, with all individuals but two harbouring a unique banding pattern. As reported for other marine invertebrates, we found high levels of genetic differentiation between the Atlantic and Mediterranean basins, suggesting that the Strait of Gibraltar represents a major barrier to dispersal for this sea star. Our assignment studies suggest that, in the Atlantic, a measurable degree of gene flow occurs between populations, which could result in the isolation-by-distance pattern of differentiation observed in this basin. In contrast, no evidence of contemporary gene flow was found in the Mediterranean, suggesting contrasting patterns of dispersal of Asterina gibbosa in the Atlantic and Mediterranean basins.
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Affiliation(s)
- E Baus
- Biodiversity and Ecological Processes Group, Cardiff University, Main Building, Park Place, PO Box 915, Cardiff CF10 3TL, UK
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Bonin A, Pompanon F, Taberlet P. Use of amplified fragment length polymorphism (AFLP) markers in surveys of vertebrate diversity. Methods Enzymol 2005; 395:145-61. [PMID: 15865966 DOI: 10.1016/s0076-6879(05)95010-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The amplified fragment length polymorphism (AFLP) technique is one of the most informative and cost-effective fingerprinting methods. It produces polymerase chain reaction (PCR)-based multi-locus genotypes helpful in many areas of population genetics. This chapter focuses on technical laboratory information to successfully develop the AFLP technique for vertebrates. Several AFLP protocols are described, as well as recommendations about important factors of the procedure such as the choice of enzyme and primer combinations, the choice and scoring of markers, the influence of the genome size on the AFLP procedure, and the control and estimation of genotyping errors. Finally, this chapter proposes a troubleshooting guide to help resolve the main technical difficulties encountered during the AFLP procedure.
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Affiliation(s)
- Aurélie Bonin
- Laboratoire d'Ecologie Alpine, Université Joseph Fourier, F-38041 Grenoble Cedex 9, France
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de Gruijter JM, Gasser RB, Polderman AM, Asigri V, Dijkshoorn L. High resolution DNA fingerprinting by AFLP to study the genetic variation among Oesophagostomum bifurcum (Nematoda) from human and non-human primates from Ghana. Parasitology 2005; 130:229-37. [PMID: 15727072 DOI: 10.1017/s0031182004006249] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
An AFLP approach was established to investigate genetic diversity within Oesophagostomum bifurcum (order Strongylida) from human and non-human primates. Evaluation of different combinations of restriction enzymes (n = 8) and primers (n = 29) demonstrated that the use of HindIII/BglII digested templates and primers with the selective nucleotides + AG/ +AC, respectively, was the most effective for the analysis of O. bifurcum DNA. A total of 63 O. bifurcum adults from human, Patas monkey, Mona monkey and Olive baboon hosts from different geographical regions in Ghana were subjected to analysis using this method. Cluster analysis revealed 4 genetically distinct groups, namely O. bifurcum from the Patas monkey (I), from the Mona monkey (II), from humans (III) and from the Olive baboon (IV). These findings were concordant with those achieved previously using RAPD analysis and supports population genetic substructuring within O. bifurcum according to host species. The results demonstrated the effectiveness of the present AFLP method for establishing genetic variation within O. bifurcum, and indicates its applicability to other parasitic nematodes of human and/or veterinary health importance.
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Affiliation(s)
- J M de Gruijter
- Department of Parasitology, Leiden University Medical Center, University of Leiden, PO Box 9600, 2300 RC Leiden, The Netherlands.
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Development of breed identification markers derived from AFLP in beef cattle. Meat Sci 2004; 67:275-80. [DOI: 10.1016/j.meatsci.2003.10.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2003] [Accepted: 10/22/2003] [Indexed: 11/23/2022]
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Roos MH, Otsen M, Hoekstra R, Veenstra JG, Lenstra JA. Genetic analysis of inbreeding of two strains of the parasitic nematode Haemonchus contortus. Int J Parasitol 2004; 34:109-15. [PMID: 14711596 DOI: 10.1016/j.ijpara.2003.10.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Haemonchus contortus is a sheep parasitic nematode that causes severe economic losses. Previous studies have indicated a high degree of genetic heterogeneity, which is hardly affected by selection for drug resistance. As a tool for the analysis of the population dynamics of H. contortus and its response to drug resistance, we designed a strategy to study the inbreeding of a benzimidazole-sensitive and a benzimidazole-resistant strain. After 15 generations, a theoretical inbreeding coefficient of 0.87 was achieved. The different stages of inbreeding were analysed using restriction fragment polymorphism, microsatellite variability and amplified fragment length polymorphism. Model-based clustering of the amplified fragment length polymorphism genotypes showed that the allele frequencies of the benzimidazole-resistant strain were stable during the last eight generations. In the sensitive strain a gradual shift of allele frequencies was observed, which led to a temporary increase of the genetic diversity around the eight generations.
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Affiliation(s)
- Marleen H Roos
- Department of Molecular Recognition, Institute for Animal Science and Health (ID-Lelystad), Lelystad, The Netherlands.
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Adin A, Weber JC, Sotelo Montes C, Vidaurre H, Vosman B, Smulders MJM. Genetic differentiation and trade among populations of peach palm ( Bactris gasipaes Kunth) in the Peruvian Amazon-implications for genetic resource management. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:1564-1573. [PMID: 14985969 DOI: 10.1007/s00122-003-1581-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2003] [Accepted: 12/12/2003] [Indexed: 05/24/2023]
Abstract
Peach palm ( Bactris gasipaes Kunth) is cultivated for fruit and 'heart of palm', and is an important component of agroforestry systems in the Peruvian Amazon. In this study, AFLP was used to compare genetic diversity among domesticated populations along the Paranapura and Cuiparillo rivers, which are managed by indigenous and colonist farming communities, respectively. Gene diversity was 0.2629 for the populations in indigenous communities and 0.2534 in colonist communities. Genetic differentiation among populations ( G(st)) was 0.0377-0.0416 ( P<0.01) among populations along both rivers. There was no relation between genetic differentiation and the geographical location of populations along the rivers. Since natural seed dispersal by birds and rodents is thought to occur only across relatively short distances (100-200 m), it is likely that exchange of material by farmers and commercial traders is responsible for most of the 'long-distance' (over more than 20 km) gene flow among populations along the two rivers studied. This exchange of material may be important to counteract the effects of selection as well as genetic drift in small groups of trees in farmers' fields, much as in a metapopulation, and may account for the weak genetic differentiation between the two rivers ( G(st)=0.0249, P<0.01). A comparison with samples from other landraces in Peru and Brazil showed the existence of an isolation-by-distance structure up to 3,000 km, consistent with gene flow on a regional scale, likely mediated by trade in the Amazon Basin. Results are discussed with regard to practical implications for the management of genetic resources with farming communities.
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Affiliation(s)
- A Adin
- Plant Research International, Wageningen UR, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
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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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