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Yaro M, Munyard KA, Stear MJ, Groth DM. Molecular identification of livestock breeds: a tool for modern conservation biology. Biol Rev Camb Philos Soc 2016; 92:993-1010. [DOI: 10.1111/brv.12265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 02/14/2016] [Accepted: 02/18/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Mohammed Yaro
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Kylie A. Munyard
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Michael J. Stear
- Institute of Biodiversity, Animal Health and Comparative Medicine; University of Glasgow; Bearsden Road Glasgow G61 1QH U.K
| | - David M. Groth
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
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Colli L, Lancioni H, Cardinali I, Olivieri A, Capodiferro MR, Pellecchia M, Rzepus M, Zamani W, Naderi S, Gandini F, Vahidi SMF, Agha S, Randi E, Battaglia V, Sardina MT, Portolano B, Rezaei HR, Lymberakis P, Boyer F, Coissac E, Pompanon F, Taberlet P, Ajmone Marsan P, Achilli A. Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Genomics 2015; 16:1115. [PMID: 26714643 PMCID: PMC4696231 DOI: 10.1186/s12864-015-2342-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/22/2015] [Indexed: 01/31/2023] Open
Abstract
Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12–10 ka ago. Conclusions Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2342-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Licia Colli
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy.
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy.
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Marco Rosario Capodiferro
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. .,Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Marco Pellecchia
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Marcin Rzepus
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Institute of Food Science and Nutrition - ISAN, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Wahid Zamani
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. .,Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Mazandaran, 46414-356, Iran.
| | - Saeid Naderi
- Natural Resources Faculty, University of Guilan, Guilan, 41335-1914, Iran.
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. .,School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK.
| | | | - Saif Agha
- Department of Animal Production, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt.
| | - Ettore Randi
- Laboratorio di Genetica, Istituto per la Protezione e la Ricerca Ambientale (ISPRA), Bologna, 40064, Italy. .,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, DK-9000, Denmark.
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy.
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy.
| | - Hamid Reza Rezaei
- Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Gorgan, 49138-15739, Iran.
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Iraklio, Crete, 71409, Greece.
| | - Frédéric Boyer
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Eric Coissac
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - François Pompanon
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Pierre Taberlet
- Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France.
| | - Paolo Ajmone Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. .,Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy.
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. .,Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy.
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Kibegwa F, Githui K, Jung'a J, Badamana M, Nyamu M. Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya. J Anim Breed Genet 2015; 133:238-47. [DOI: 10.1111/jbg.12182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 02/01/2015] [Indexed: 11/30/2022]
Affiliation(s)
- F.M. Kibegwa
- Department of Animal Production; University of Nairobi; Nairobi Kenya
| | - K.E. Githui
- Molecular Genetics Laboratory; National Museums of Kenya; Nairobi Kenya
| | - J.O. Jung'a
- Department of Animal Production; University of Nairobi; Nairobi Kenya
| | - M.S. Badamana
- Department of Animal Production; University of Nairobi; Nairobi Kenya
| | - M.N. Nyamu
- Molecular Genetics Laboratory; National Museums of Kenya; Nairobi Kenya
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Orozco-terWengel P, Barbato M, Nicolazzi E, Biscarini F, Milanesi M, Davies W, Williams D, Stella A, Ajmone-Marsan P, Bruford MW. Revisiting demographic processes in cattle with genome-wide population genetic analysis. Front Genet 2015; 6:191. [PMID: 26082794 PMCID: PMC4451420 DOI: 10.3389/fgene.2015.00191] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/12/2015] [Indexed: 11/23/2022] Open
Abstract
The domestication of the aurochs took place approximately 10,000 years ago giving rise to the two main types of domestic cattle known today, taurine (Bos taurus) domesticated somewhere on or near the Fertile Crescent, and indicine (Bos indicus) domesticated in the Indus Valley. However, although cattle have historically played a prominent role in human society the exact origin of many extant breeds is not well known. Here we used a combination of medium and high-density Illumina Bovine SNP arrays (i.e., ~54,000 and ~770,000 SNPs, respectively), genotyped for over 1300 animals representing 56 cattle breeds, to describe the relationships among major European cattle breeds and detect patterns of admixture among them. Our results suggest modern cross-breeding and ancient hybridisation events have both played an important role, including with animals of indicine origin. We use these data to identify signatures of selection reflecting both domestication (hypothesized to produce a common signature across breeds) and local adaptation (predicted to exhibit a signature of selection unique to a single breed or group of related breeds with a common history) to uncover additional demographic complexity of modern European cattle.
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Affiliation(s)
| | - Mario Barbato
- School of Biosciences, Cardiff University Cardiff, UK
| | | | | | - Marco Milanesi
- Faculty of Agriculture, Università Cattolica del Sacro Cuore Piacenza, Italy
| | | | | | | | - Paolo Ajmone-Marsan
- Faculty of Agriculture, Università Cattolica del Sacro Cuore Piacenza, Italy
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56
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Scheu A, Powell A, Bollongino R, Vigne JD, Tresset A, Çakırlar C, Benecke N, Burger J. The genetic prehistory of domesticated cattle from their origin to the spread across Europe. BMC Genet 2015; 16:54. [PMID: 26018295 PMCID: PMC4445560 DOI: 10.1186/s12863-015-0203-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/20/2015] [Indexed: 11/25/2022] Open
Abstract
Background Cattle domestication started in the 9th millennium BC in Southwest Asia. Domesticated cattle were then introduced into Europe during the Neolithic transition. However, the scarcity of palaeogenetic data from the first European domesticated cattle still inhibits the accurate reconstruction of their early demography. In this study, mitochondrial DNA from 193 ancient and 597 modern domesticated cattle (Bos taurus) from sites across Europe, Western Anatolia and Iran were analysed to provide insight into the Neolithic dispersal process and the role of the local European aurochs population during cattle domestication. Results Using descriptive summary statistics and serial coalescent simulations paired with approximate Bayesian computation we find: (i) decreasing genetic diversity in a southeast to northwest direction, (ii) strong correlation of genetic and geographical distances, iii) an estimated effective size of the Near Eastern female founder population of 81, iv) that the expansion of cattle from the Near East and Anatolia into Europe does not appear to constitute a significant bottleneck, and that v) there is evidence for gene-flow between the Near Eastern/Anatolian and European cattle populations in the early phases of the European Neolithic, but that it is restricted after 5,000 BCE. Conclusions The most plausible scenario to explain these results is a single and regionally restricted domestication process of cattle in the Near East with subsequent migration into Europe during the Neolithic transition without significant maternal interbreeding with the endogenous wild stock. Evidence for gene-flow between cattle populations from Southwestern Asia and Europe during the earlier phases of the European Neolithic points towards intercontinental trade connections between Neolithic farmers. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0203-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amelie Scheu
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Palaeogenetics Group, 55099, Mainz, Germany. .,German Archaeological Institute, Scientific Department, Im Dol 2-6, Haus 2, 14195, Berlin, Germany.
| | - Adam Powell
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Palaeogenetics Group, 55099, Mainz, Germany.
| | - Ruth Bollongino
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Palaeogenetics Group, 55099, Mainz, Germany. .,Muséum National d'Histoire Naturelle, UMR7209, "Archéozoologie, archéobotanique: sociétés, pratiques et environnements", InEE, Département d'Ecologie et Gestion de la Biodiversité, CP 56, 55 rue Buffon, 75005, Paris, Cedex 05, France.
| | - Jean-Denis Vigne
- Muséum National d'Histoire Naturelle, UMR7209, "Archéozoologie, archéobotanique: sociétés, pratiques et environnements", InEE, Département d'Ecologie et Gestion de la Biodiversité, CP 56, 55 rue Buffon, 75005, Paris, Cedex 05, France.
| | - Anne Tresset
- Muséum National d'Histoire Naturelle, UMR7209, "Archéozoologie, archéobotanique: sociétés, pratiques et environnements", InEE, Département d'Ecologie et Gestion de la Biodiversité, CP 56, 55 rue Buffon, 75005, Paris, Cedex 05, France.
| | - Canan Çakırlar
- University of Groningen, Institute of Archaeology, Poststraat 6, NL-9712 ER, Groningen, Netherlands.
| | - Norbert Benecke
- German Archaeological Institute, Scientific Department, Im Dol 2-6, Haus 2, 14195, Berlin, Germany.
| | - Joachim Burger
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Palaeogenetics Group, 55099, Mainz, Germany.
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Bomba L, Nicolazzi EL, Milanesi M, Negrini R, Mancini G, Biscarini F, Stella A, Valentini A, Ajmone-Marsan P. Relative extended haplotype homozygosity signals across breeds reveal dairy and beef specific signatures of selection. Genet Sel Evol 2015; 47:25. [PMID: 25888030 PMCID: PMC4383072 DOI: 10.1186/s12711-015-0113-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 03/19/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND A number of methods are available to scan a genome for selection signatures by evaluating patterns of diversity within and between breeds. Among these, "extended haplotype homozygosity" (EHH) is a reliable approach to detect genome regions under recent selective pressure. The objective of this study was to use this approach to identify regions that are under recent positive selection and shared by the most representative Italian dairy and beef cattle breeds. RESULTS A total of 3220 animals from Italian Holstein (2179), Italian Brown (775), Simmental (493), Marchigiana (485) and Piedmontese (379) breeds were genotyped with the Illumina BovineSNP50 BeadChip v.1. After standard quality control procedures, genotypes were phased and core haplotypes were identified. The decay of linkage disequilibrium (LD) for each core haplotype was assessed by measuring the EHH. Since accurate estimates of local recombination rates were not available, relative EHH (rEHH) was calculated for each core haplotype. Genomic regions that carry frequent core haplotypes and with significant rEHH values were considered as candidates for recent positive selection. Candidate regions were aligned across to identify signals shared by dairy or beef cattle breeds. Overall, 82 and 87 common regions were detected among dairy and beef cattle breeds, respectively. Bioinformatic analysis identified 244 and 232 genes in these common genomic regions. Gene annotation and pathway analysis showed that these genes are involved in molecular functions that are biologically related to milk or meat production. CONCLUSIONS Our results suggest that a multi-breed approach can lead to the identification of genomic signatures in breeds of cattle that are selected for the same production goal and thus to the localisation of genomic regions of interest in dairy and beef production.
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Affiliation(s)
- Lorenzo Bomba
- Istituto di Zootecnica, UCSC, via Emilia Parmense 84, Piacenza, 29122, Italy.
| | - Ezequiel L Nicolazzi
- Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900, Italy.
| | - Marco Milanesi
- Istituto di Zootecnica, UCSC, via Emilia Parmense 84, Piacenza, 29122, Italy.
| | - Riccardo Negrini
- Associazione Italiana Allevatori (AIA), Via Tomassetti 9, Rome, 00161, Italy.
| | - Giordano Mancini
- Center for Computational Chemistry and Cosmology, Scuola Normale Superiore, Via Consoli del Mare 2, Pisa, 56126, Italy.
| | - Filippo Biscarini
- Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900, Italy.
| | - Alessandra Stella
- Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900, Italy. .,Istituto di biologia e biotecnologia Agraria (IBBA-CNR), Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
| | - Alessio Valentini
- Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), via de Lellis, Viterbo, 01100, Italy.
| | - Paolo Ajmone-Marsan
- Istituto di Zootecnica, UCSC, via Emilia Parmense 84, Piacenza, 29122, Italy.
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Kristensen TN, Hoffmann AA, Pertoldi C, Stronen AV. What can livestock breeders learn from conservation genetics and vice versa? Front Genet 2015; 6:38. [PMID: 25713584 PMCID: PMC4322732 DOI: 10.3389/fgene.2015.00038] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/26/2015] [Indexed: 11/17/2022] Open
Abstract
The management of livestock breeds and threatened natural population share common challenges, including small effective population sizes, high risk of inbreeding, and the potential benefits and costs associated with mixing disparate gene pools. Here, we consider what has been learnt about these issues, the ways in which the knowledge gained from one area might be applied to the other, and the potential of genomics to provide new insights. Although there are key differences stemming from the importance of artificial versus natural selection and the decreased level of environmental heterogeneity experienced by many livestock populations, we suspect that information from genetic rescue in natural populations could be usefully applied to livestock. This includes an increased emphasis on maintaining substantial population sizes at the expense of genetic uniqueness in ensuring future adaptability, and on emphasizing the way that environmental changes can influence the relative fitness of deleterious alleles and genotypes in small populations. We also suspect that information gained from cross-breeding and the maintenance of unique breeds will be increasingly important for the preservation of genetic variation in small natural populations. In particular, selected genes identified in domestic populations provide genetic markers for exploring adaptive evolution in threatened natural populations. Genomic technologies in the two disciplines will be important in the future in realizing genetic gains in livestock and maximizing adaptive capacity in wildlife, and particularly in understanding how parts of the genome may respond differently when exposed to population processes and selection.
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Affiliation(s)
- Torsten N. Kristensen
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Ary A. Hoffmann
- Department of Zoology and Department of Genetics, Bio21 Institute, The University of MelbourneMelbourne, VIC, Australia
| | - Cino Pertoldi
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
- Aalborg ZooAalborg, Denmark
| | - Astrid V. Stronen
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
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Avila F, Baily MP, Perelman P, Das PJ, Pontius J, Chowdhary R, Owens E, Johnson WE, Merriwether DA, Raudsepp T. A comprehensive whole-genome integrated cytogenetic map for the alpaca (Lama pacos). Cytogenet Genome Res 2015; 144:196-207. [PMID: 25662411 DOI: 10.1159/000370329] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2014] [Indexed: 11/19/2022] Open
Abstract
Genome analysis of the alpaca (Lama pacos, LPA) has progressed slowly compared to other domestic species. Here, we report the development of the first comprehensive whole-genome integrated cytogenetic map for the alpaca using fluorescence in situ hybridization (FISH) and CHORI-246 BAC library clones. The map is comprised of 230 linearly ordered markers distributed among all 36 alpaca autosomes and the sex chromosomes. For the first time, markers were assigned to LPA14, 21, 22, 28, and 36. Additionally, 86 genes from 15 alpaca chromosomes were mapped in the dromedary camel (Camelus dromedarius, CDR), demonstrating exceptional synteny and linkage conservation between the 2 camelid genomes. Cytogenetic mapping of 191 protein-coding genes improved and refined the known Zoo-FISH homologies between camelids and humans: we discovered new homologous synteny blocks (HSBs) corresponding to HSA1-LPA/CDR11, HSA4-LPA/CDR31 and HSA7-LPA/CDR36, and revised the location of breakpoints for others. Overall, gene mapping was in good agreement with the Zoo-FISH and revealed remarkable evolutionary conservation of gene order within many human-camelid HSBs. Most importantly, 91 FISH-mapped markers effectively integrated the alpaca whole-genome sequence and the radiation hybrid maps with physical chromosomes, thus facilitating the improvement of the sequence assembly and the discovery of genes of biological importance.
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Affiliation(s)
- Felipe Avila
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Tex., USA
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Dispersal of an ancient retroposon in the TP53 promoter of Bovidae: phylogeny, novel mechanisms, and potential implications for cow milk persistency. BMC Genomics 2015; 16:53. [PMID: 25653076 PMCID: PMC4324840 DOI: 10.1186/s12864-015-1235-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 01/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years, the perception of transposable genetic elements has changed from "junk DNA" to a focus of interest when appearing near or inside genes. Bov-A2 is a short interspersed nuclear element (SINE) that was first found in Bovidae and later in other ruminants. This retroposon is mostly used as a marker for phylogenetic analysis. RESULTS We describe insertions of Bov-A2 in the promoter region of TP53, a key tumor suppressor gene that is indispensable for diverse developmental processes, in Antilopinae and Tragelaphini (belonging to the Bovinae subfamily). In Tragelaphini two Bov-A2 elements were inserted sequentially, whereas in 5 tribes of Antilopinae only one Bov-A2 element was inserted, in a different site and reverse orientation. The entrance site in both cases employed short palindromes that can form hairpin secondary structures. Interestingly, mutations that create or disrupt base pairing in the palindrome sequence dictated the presence or absence of Bov-A2, such as in the domestic cow and buffalo, which lack Bov-A2. Transcription factor binding site analysis revealed unique binding sites for STAT3 and NFκB within the Bov-A2 sequence, which together with TP53 itself are known to play a crucial role in mammary involution. CONCLUSIONS This report demonstrates how short palindromes serve as hot spots for Bov-A2 retroposon insertion into the mammalian genome. The strict correlation between point mutation in the palindromes and the presence/absence of Bov-A2 retroposon insertions, questions the use of singular insertion events as valid phylogenetic markers inside families. Bov-A2 insertion into the TP53 promoter in Antilopinae and Tragelaphini may not only provide a genetic network that regulates mammary involution, but can also answer the need for rapid mammary involution in Savanna antelopes after weaning, partially in response to predation stress. The absence of Bov-A2 in domestic bovids may constitute the molecular background for greater lactation persistency.
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Sawaimul AD, Sahare MG, Ali SZ, Sirothia AR, Kumar S. Assessment of genetic variability among Indian sheep breeds using mitochondrial DNA cytochrome-b region. Vet World 2014. [DOI: 10.14202/vetworld.2014.852-855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Ruiz-Fons F, González-Barrio D, Aguilar-Ríos F, Soler AJ, Garde JJ, Gortázar C, Fernández-Santos MDR. Infectious pathogens potentially transmitted by semen of the black variety of the Manchega sheep breed: Health constraints for conservation purposes. Anim Reprod Sci 2014; 149:152-7. [PMID: 25066603 DOI: 10.1016/j.anireprosci.2014.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/30/2014] [Accepted: 07/07/2014] [Indexed: 11/27/2022]
Abstract
Conservation of genetic resources from endangered breeds may be conducted through germinal banks. Preservation of healthy samples is paramount to avoid preserving pathogens shed with germinal products. The black variety of Manchega sheep (BMS), and endangered breed endemic to south-central Spain, is the subject of a conservation program; a germinal bank has been recently established. However, several pathogens circulating in BMS flocks may be shed with semen and threaten BMS preservation. Therefore, we investigated the sanitary status of BMS flocks and semen samples from 4 of the 17 flocks in which this variety is bred worldwide. A serological screening for Maedi-Visna virus, bluetongue virus, Pestivirus spp., Brucella spp., Coxiella burnetii, Chlamydophila spp., Mycobacterium tuberculosis complex, Mycobacterium avium paratuberculosis, Anaplasma spp., Mycoplasma agalactiae, Toxoplasma gondii and Neospora caninum was performed to assess for pathogens potentially shed by semen. Semen samples from 11 of the 35 BMS rams and 4 samples from coexisting rams of the white variety (WMS) were analyzed by PCR to detect Maedi-Visna virus, C. burnetii, Anaplasma marginale, Anaplasma phagocytophilum and T. gondii. Maedi-Visna virus RNA was detected in 3 semen samples (2 BMS and 1 WMS) while C. burnetii DNA was detected in 3 samples from WMS rams. Pathogens that can be transmitted by semen were present in BMS flocks, and Maedi-Visna virus and C. burnetii showed the highest potential for transmission by artificial insemination. Our results point to the need of testing semen samples kept for conservation purposes of BMS before using them for artificial insemination.
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Affiliation(s)
- Francisco Ruiz-Fons
- Health & Biotechnology (SaBio) Group, IREC (CSIC-UCLM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain.
| | - David González-Barrio
- Health & Biotechnology (SaBio) Group, IREC (CSIC-UCLM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain
| | - Fernando Aguilar-Ríos
- Health & Biotechnology (SaBio) Group, IREC (CSIC-UCLM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain
| | - Ana J Soler
- Health & Biotechnology (SaBio) Group, IREC (CSIC-UCLM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain
| | - José Julián Garde
- Health & Biotechnology (SaBio) Group, IREC (CSIC-UCLM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain
| | - Christian Gortázar
- Health & Biotechnology (SaBio) Group, IREC (CSIC-UCLM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain
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Doro MG, Piras D, Leoni GG, Casu G, Vaccargiu S, Parracciani D, Naitana S, Pirastu M, Novelletto A. Phylogeny and patterns of diversity of goat mtDNA haplogroup A revealed by resequencing complete mitogenomes. PLoS One 2014; 9:e95969. [PMID: 24763315 PMCID: PMC3999278 DOI: 10.1371/journal.pone.0095969] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/01/2014] [Indexed: 11/18/2022] Open
Abstract
We sequenced to near completion the entire mtDNA of 28 Sardinian goats, selected to represent the widest possible diversity of the most widespread mitochondrial evolutionary lineage, haplogroup (Hg) A. These specimens were reporters of the diversity in the island but also elsewhere, as inferred from their affiliation to each of 11 clades defined by D-loop variation. Two reference sequences completed the dataset. Overall, 206 variations were found in the full set of 30 sequences, of which 23 were protein-coding non-synonymous single nucleotide substitutions. Many polymorphic sites within Hg A were informative for the reconstruction of its internal phylogeny. Bayesian and network clustering revealed a general similarity over the entire molecule of sequences previously assigned to the same D-loop clade, indicating evolutionarily meaningful lineages. Two major sister groupings emerged within Hg A, which parallel distinct geographical distributions of D-loop clades in extant stocks. The pattern of variation in protein-coding genes revealed an overwhelming role of purifying selection, with the quota of surviving variants approaching neutrality. However, a simple model of relaxation of selection for the bulk of variants here reported should be rejected. Non-synonymous diversity of Hg's A, B and C denoted that a proportion of variants not greater than that allowed in the wild was given the opportunity to spread into domesticated stocks. Our results also confirmed that a remarkable proportion of pre-existing Hg A diversity became incorporated into domestic stocks. Our results confirm clade A11 as a well differentiated and ancient lineage peculiar of Sardinia.
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Affiliation(s)
- Maria Grazia Doro
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
| | - Daniela Piras
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
- Experimental Zoo-prophylactic Institute of Sardinia, Sassari, Italy
| | | | - Giuseppina Casu
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
| | - Simona Vaccargiu
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
| | | | - Salvatore Naitana
- Faculty of Veterinary Sciences, University of Sassari, Sassari, Italy
| | - Mario Pirastu
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
- Genetic Park of Ogliastra, Perdasdefogu, Italy
| | - Andrea Novelletto
- Department of Biology, University “Tor Vergata”, Rome, Italy
- * E-mail:
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Abstract
The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50–60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.
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Mancini G, Gargani M, Chillemi G, Nicolazzi EL, Marsan PA, Valentini A, Pariset L. Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel. Mol Biol Rep 2014; 41:957-65. [PMID: 24442315 PMCID: PMC3929051 DOI: 10.1007/s11033-013-2940-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 12/20/2013] [Indexed: 01/16/2023]
Abstract
In this study we used a medium density panel of SNP markers to perform population genetic analysis in five Italian cattle breeds. The BovineSNP50 BeadChip was used to genotype a total of 2,935 bulls of Piedmontese, Marchigiana, Italian Holstein, Italian Brown and Italian Pezzata Rossa breeds. To determine a genome-wide pattern of positive selection we mapped the F st values against genome location. The highest F st peaks were obtained on BTA6 and BTA13 where some candidate genes are located. We identified selection signatures peculiar of each breed which suggest selection for genes involved in milk or meat traits. The genetic structure was investigated by using a multidimensional scaling of the genetic distance matrix and a Bayesian approach implemented in the STRUCTURE software. The genotyping data showed a clear partitioning of the cattle genetic diversity into distinct breeds if a number of clusters equal to the number of populations were given. Assuming a lower number of clusters beef breeds group together. Both methods showed all five breeds separated in well defined clusters and the Bayesian approach assigned individuals to the breed of origin. The work is of interest not only because it enriches the knowledge on the process of evolution but also because the results generated could have implications for selective breeding programs.
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Affiliation(s)
- Giordano Mancini
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, 01100, Viterbo, Italy
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Mariotti M, Valentini A, Marsan PA, Pariset L. Mitochondrial DNA of seven Italian sheep breeds shows faint signatures of domestication and suggests recent breed formation. ACTA ACUST UNITED AC 2013; 24:577-83. [DOI: 10.3109/19401736.2013.770493] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Abstract
Agroecology and industrial ecology can be viewed as complementary means for reducing the environmental footprint of animal farming systems: agroecology mainly by stimulating natural processes to reduce inputs, and industrial ecology by closing system loops, thereby reducing demand for raw materials, lowering pollution and saving on waste treatment. Surprisingly, animal farming systems have so far been ignored in most agroecological thinking. On the basis of a study by Altieri, who identified the key ecological processes to be optimized, we propose five principles for the design of sustainable animal production systems: (i) adopting management practices aiming to improve animal health, (ii) decreasing the inputs needed for production, (iii) decreasing pollution by optimizing the metabolic functioning of farming systems, (iv) enhancing diversity within animal production systems to strengthen their resilience and (v) preserving biological diversity in agroecosystems by adapting management practices. We then discuss how these different principles combine to generate environmental, social and economic performance in six animal production systems (ruminants, pigs, rabbits and aquaculture) covering a long gradient of intensification. The two principles concerning economy of inputs and reduction of pollution emerged in nearly all the case studies, a finding that can be explained by the economic and regulatory constraints affecting animal production. Integrated management of animal health was seldom mobilized, as alternatives to chemical drugs have only recently been investigated, and the results are not yet transferable to farming practices. A number of ecological functions and ecosystem services (recycling of nutrients, forage yield, pollination, resistance to weed invasion, etc.) are closely linked to biodiversity, and their persistence depends largely on maintaining biological diversity in agroecosystems. We conclude that the development of such ecology-based alternatives for animal production implies changes in the positions adopted by technicians and extension services, researchers and policymakers. Animal production systems should not only be considered holistically, but also in the diversity of their local and regional conditions. The ability of farmers to make their own decisions on the basis of the close monitoring of system performance is most important to ensure system sustainability.
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Agaviezor BO, Peters SO, Adefenwa MA, Yakubu A, Adebambo OA, Ozoje MO, Ikeobi CO, Wheto M, Ajayi OO, Amusan SA, Ekundayo OJ, Sanni TM, Okpeku M, Onasanya GO, De Donato M, Ilori BM, Kizilkaya K, Imumorin IG. Morphological and microsatellite DNA diversity of Nigerian indigenous sheep. J Anim Sci Biotechnol 2012; 3:38. [PMID: 23176051 PMCID: PMC3563600 DOI: 10.1186/2049-1891-3-38] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 11/01/2012] [Indexed: 11/10/2022] Open
Abstract
Background Sheep is important in the socio-economic lives of people around the world. It is estimated that more than half of our once common livestock breeds are now endangered. Since genetic characterization of Nigerian sheep is still lacking, we analyzed ten morphological traits on 402 animals and 15 microsatellite DNA markers in 384 animals of the 4 Nigerian sheep breeds to better understand genetic diversity for breeding management and germplasm conservation. Results Morphological traits of Uda and Balami were significantly (P < 0.05) higher than Yankasa, which were both higher than West African Dwarf (WAD) sheep. Stepwise discriminant analysis showed tail length, rump height, chest girth, ear length and chest depth as the most discriminating variables for classification. Mahalanobis distances show the least differentiation between Uda and Balami and the largest between WAD and Balami sheep. While 93.3% of WAD sheep were correctly assigned to their source genetic group, 63.9% of Yankasa, 61.2% of Balami and 45.2% of Uda were classified correctly by nearest neighbour discriminant analysis. The overall high Polymorphism Information Content (PIC) of all microsatellite markers ranged from 0.751 to 0.927 supporting their use in genetic characterization. Expected heterozygosity was high for all loci (0.783 to 0.93). Mean heterozygote deficiency across all populations (0.171 to 0.534) possibly indicate significant inbreeding (P < 0.05). Mean values for FST, FIT and FIS statistics across all loci were 0.088, 0.394 and 0.336 respectively. Yankasa and Balami are the most closely related breeds (DA = 0.184) while WAD and Balami are the farthest apart breeds (DA = 0.665), which is coincident with distance based on morphological analysis and population structure assessed by STRUCTURE. Conclusions These results suggest that within-breed genetic variation in Nigerian sheep is higher than between-breeds and may be a valuable tool for genetic improvement and conservation. The higher genetic variability in Yankasa suggests the presence of unique ancestral alleles reflecting the presence of certain functional genes which may result in better adaptability in more agro-ecological zones of Nigeria. These genetic characteristics are potentially useful in planning improvement and conservation strategies in Nigerian indigenous sheep.
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Avila F, Das PJ, Kutzler M, Owens E, Perelman P, Rubes J, Hornak M, Johnson WE, Raudsepp T. Development and application of camelid molecular cytogenetic tools. J Hered 2012; 105:858-69. [PMID: 23109720 DOI: 10.1093/jhered/ess067] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cytogenetic chromosome maps offer molecular tools for genome analysis and clinical cytogenetics and are of particular importance for species with difficult karyotypes, such as camelids (2n = 74). Building on the available human-camel zoo-fluorescence in situ hybridization (FISH) data, we developed the first cytogenetic map for the alpaca (Lama pacos, LPA) genome by isolating and identifying 151 alpaca bacterial artificial chromosome (BAC) clones corresponding to 44 specific genes. The genes were mapped by FISH to 31 alpaca autosomes and the sex chromosomes; 11 chromosomes had 2 markers, which were ordered by dual-color FISH. The STS gene mapped to Xpter/Ypter, demarcating the pseudoautosomal region, whereas no markers were assigned to chromosomes 14, 21, 22, 28, and 36. The chromosome-specific markers were applied in clinical cytogenetics to identify LPA20, the major histocompatibility complex (MHC)-carrying chromosome, as a part of an autosomal translocation in a sterile male llama (Lama glama, LGL; 2n = 73,XY). FISH with LPAX BACs and LPA36 paints, as well as comparative genomic hybridization, were also used to investigate the origin of the minute chromosome, an abnormally small LPA36 in infertile female alpacas. This collection of cytogenetically mapped markers represents a new tool for camelid clinical cytogenetics and has applications for the improvement of the alpaca genome map and sequence assembly.
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Affiliation(s)
- Felipe Avila
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Pranab J Das
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Michelle Kutzler
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Elaine Owens
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Polina Perelman
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Jiri Rubes
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Miroslav Hornak
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Warren E Johnson
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak)
| | - Terje Raudsepp
- From the Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843 (Avila, Das, and Raudsepp); Department of Animal Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331 (Kutzler); Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 (Owens); Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 (Perelman and Johnson); Laboratory of Cytogenetics of Animals, Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Perelman); and Veterinary Research Institute, Brno, Czech Republic (Rubes and Hornak).
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Yang H, Cuevas-Uribe R, Savage MG, Walter RB, Tiersch TR. Sperm cryopreservation in live-bearing Xiphophorus fishes: offspring production from Xiphophorus variatus and strategies for establishment of sperm repositories. Zebrafish 2012; 9:126-34. [PMID: 22924335 DOI: 10.1089/zeb.2012.0737] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cryopreservation of sperm from Xiphophorus fishes has produced live young in three species: X. hellerii, X. couchianus, and X. maculatus. In this study, the goal was to establish protocols for sperm cryopreservation and artificial insemination to produce live young in X. variatus, and to identify needs for repository development. The objectives were to: 1) collect basic biological characteristics of males; 2) cryopreserve sperm from X. variatus, 3) harvest live young from cryopreserved sperm, and 4) discuss the requirements for establishment of sperm repositories. The 35 males used in this study had a body weight of 0.298±0.096 g (mean±SD), body length of 2.5±0.2 cm, and testis weight of 6.4±3.4 mg. The sperm production per gram of testis was 2.33±1.32×10(9) cells. After freezing, the post-thaw motility decreased significantly to 37%±17% (ranging from 5% to 70%) (p=0.000) from 57%±14% (40%-80%) of fresh sperm (N=20). Artificial insemination of post-thaw sperm produced confirmed offspring from females of X. hellerii and X. variatus. This research, taken together with previous studies, provides a foundation for development of strategies for sperm repositories of Xiphophorus fishes. This includes: 1) the need for breeding strategies for regeneration of target populations, 2) identification of minimum fertilization capacity of frozen samples, 3) identification of fish numbers necessary for sampling and their genetic relationships, 4) selection of packaging containers for labeling and biosecurity, 5) assurance of quality control and standardization of procedures, 6) information systems that can manage the data associated with cryopreserved samples, including the genetic data, 7) biological data of sampled fish, 8) inventory data associated with frozen samples, and 9) data linking germplasm samples with other related materials such as body tissues or cells saved for DNA and RNA analyses.
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Affiliation(s)
- Huiping Yang
- Aquaculture Research Station, Louisiana State University Agricultural Center, Baton Rouge, LA 70820, USA.
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Berthouly-Salazar C, Thévenon S, Van TN, Nguyen BT, Pham LD, Chi CV, Maillard JC. Uncontrolled admixture and loss of genetic diversity in a local Vietnamese pig breed. Ecol Evol 2012; 2:962-75. [PMID: 22837841 PMCID: PMC3399162 DOI: 10.1002/ece3.229] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 01/18/2012] [Indexed: 12/25/2022] Open
Abstract
The expansion of intensive livestock production systems in developing countries has increased the introduction of highly productive exotic breeds facilitating indiscriminate crossbreeding with local breeds. In this study, we set out to investigate the genetic status of the Vietnamese Black H'mong pig breed by evaluating (1) genetic diversity and (2) introgression from exotic breeds. Two exotic breeds, namely Landrace and Yorkshire used for crossbreeding, and the H'mong pig population from Ha Giang (HG) province were investigated using microsatellite markers. Within the province, three phenotypes were observed: a White, a Spotted and a Black phenotype. Genetic differentiation between phenotypes was low (0.5-6.1%). The White phenotypes showed intermediate admixture values between exotic breeds and the Black HG population (0.53), indicating a crossbreed status. Management practices were used to predict the rate of private diversity loss due to exotic gene introgressions. After 60 generations, 100% of Black private alleles will be lost. This loss is accelerated if the admixture rate is increased but can be slowed down if the mortality rate (e.g., recruitment rate) is decreased. Our study showed that a large number of markers are needed for accurately identifying hybrid classes for closely related populations. While our estimate of admixture still seems underestimated, genetic erosion can occur very fast even through indiscriminate crossbreeding.
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Affiliation(s)
- Cécile Berthouly-Salazar
- Department of Botany & Zoology, DST-NRF Centre of Excellence for Invasion Biology (C·I·B), University of StellenboschMatieland 7602, South Africa
| | - Sophie Thévenon
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)UMR INTERTRYP, 34398 Montpellier, France
| | - Thu Nhu Van
- National Institute of Animal Husbandry (NIAH)Tu Liem, Hanoi, Vietnam
| | - Binh Trong Nguyen
- National Institute of Animal Husbandry (NIAH)Tu Liem, Hanoi, Vietnam
| | - Lan Doan Pham
- National Institute of Animal Husbandry (NIAH)Tu Liem, Hanoi, Vietnam
| | - Cuong Vu Chi
- National Institute of Animal Husbandry (NIAH)Tu Liem, Hanoi, Vietnam
| | - Jean-Charles Maillard
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)UPR AGIRs, 34398 Montpellier, France
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Rodenburg T, Turner S. The role of breeding and genetics in the welfare of farm animals. Anim Front 2012. [DOI: 10.2527/af.2012-0044] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- T.B. Rodenburg
- Animal Breeding and Genomics Centre, Wageningen University, P.O. Box 338, 6700 AH Wageningen, The Netherlands
| | - S.P. Turner
- Scottish Agricultural College, West Mains Road, Edinburgh EH9 3JG, United Kingdom
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73
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Genetic diversity analysis of the mitochondrial D-loop of Nigerian indigenous sheep. ACTA ACUST UNITED AC 2012. [DOI: 10.1017/s2078633612000070] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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74
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DEBES PAULV, NORMANDEAU ERIC, FRASER DYLANJ, BERNATCHEZ LOUIS, HUTCHINGS JEFFREYA. Differences in transcription levels among wild, domesticated, and hybrid Atlantic salmon (Salmo salar) from two environments. Mol Ecol 2012; 21:2574-87. [DOI: 10.1111/j.1365-294x.2012.05567.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Phylogenetic position of a copper age sheep (Ovis aries) mitochondrial DNA. PLoS One 2012; 7:e33792. [PMID: 22457789 PMCID: PMC3311544 DOI: 10.1371/journal.pone.0033792] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 02/17/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Sheep (Ovis aries) were domesticated in the Fertile Crescent region about 9,000-8,000 years ago. Currently, few mitochondrial (mt) DNA studies are available on archaeological sheep. In particular, no data on archaeological European sheep are available. METHODOLOGY/PRINCIPAL FINDINGS Here we describe the first portion of mtDNA sequence of a Copper Age European sheep. DNA was extracted from hair shafts which were part of the clothes of the so-called Tyrolean Iceman or Ötzi (5,350-5,100 years before present). Mitochondrial DNA (a total of 2,429 base pairs, encompassing a portion of the control region, tRNA(Phe), a portion of the 12S rRNA gene, and the whole cytochrome B gene) was sequenced using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products. We have compared the sequence with the corresponding sequence of 334 extant lineages. CONCLUSIONS/SIGNIFICANCE A phylogenetic network based on a new cladistic notation for the mitochondrial diversity of domestic sheep shows that the Ötzi's sheep falls within haplogroup B, thus demonstrating that sheep belonging to this haplogroup were already present in the Alps more than 5,000 years ago. On the other hand, the lineage of the Ötzi's sheep is defined by two transitions (16147, and 16440) which, assembled together, define a motif that has not yet been identified in modern sheep populations.
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Canavez FC, Luche DD, Stothard P, Leite KRM, Sousa-Canavez JM, Plastow G, Meidanis J, Souza MA, Feijao P, Moore SS, Camara-Lopes LH. Genome sequence and assembly of Bos indicus. J Hered 2012; 103:342-8. [PMID: 22315242 DOI: 10.1093/jhered/esr153] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cattle are divided into 2 groups referred to as taurine and indicine, both of which have been under strong artificial selection due to their importance for human nutrition. A side effect of this domestication includes a loss of genetic diversity within each specialized breed. Recently, the first taurine genome was sequenced and assembled, allowing for a better understanding of this ruminant species. However, genetic information from indicine breeds has been limited. Here, we present the first genome sequence of an indicine breed (Nellore) generated with 52X coverage by SOLiD sequencing platform. As expected, both genomes share high similarity at the nucleotide level for all autosomes and the X chromosome. Regarding the Y chromosome, the homology was considerably lower, most likely due to uncompleted assembly of the taurine Y chromosome. We were also able to cover 97% of the annotated taurine protein-coding genes.
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Affiliation(s)
- Flavio C Canavez
- Department of Molecular Biology, Genoa Biotecnologia SA, São Paulo, SP 04004-030, Brazil
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Ducrot C, Bed'Hom B, Béringue V, Coulon JB, Fourichon C, Guérin JL, Krebs S, Rainard P, Schwartz-Cornil I, Torny D, Vayssier-Taussat M, Zientara S, Zundel E, Pineau T. Issues and special features of animal health research. Vet Res 2011; 42:96. [PMID: 21864344 PMCID: PMC3170600 DOI: 10.1186/1297-9716-42-96] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 08/24/2011] [Indexed: 11/10/2022] Open
Abstract
In the rapidly changing context of research on animal health, INRA launched a collective discussion on the challenges facing the field, its distinguishing features, and synergies with biomedical research. As has been declared forcibly by the heads of WHO, FAO and OIE, the challenges facing animal health, beyond diseases transmissible to humans, are critically important and involve food security, agriculture economics, and the ensemble of economic activities associated with agriculture. There are in addition issues related to public health (zoonoses, xenobiotics, antimicrobial resistance), the environment, and animal welfare.Animal health research is distinguished by particular methodologies and scientific questions that stem from the specific biological features of domestic species and from animal husbandry practices. It generally does not explore the same scientific questions as research on human biology, even when the same pathogens are being studied, and the discipline is rooted in a very specific agricultural and economic context.Generic and methodological synergies nevertheless exist with biomedical research, particularly with regard to tools and biological models. Certain domestic species furthermore present more functional similarities with humans than laboratory rodents.The singularity of animal health research in relation to biomedical research should be taken into account in the organization, evaluation, and funding of the field through a policy that clearly recognizes the specific issues at stake. At the same time, the One Health approach should facilitate closer collaboration between biomedical and animal health research at the level of research teams and programmes.
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Affiliation(s)
- Christian Ducrot
- INRA, UR346 Epidémiologie animale, 63122 Saint Genès Champanelle, France
| | - Bertrand Bed'Hom
- INRA, UMR1313 Génétique Animale et Biologie Intégrative, 78352 Jouy-en-Josas Cedex, France
| | - Vincent Béringue
- INRA, UR892 Virologie et Immunologie Moléculaires, 78352 Jouy-en-Josas, France
| | | | - Christine Fourichon
- ONIRIS-INRA, UMR1300 Bioagression, Épidémiologie et Analyse de risque, Atlanpole La Chantrerie, BP 40706, 44307 Nantes Cedex 3, France
| | - Jean-Luc Guérin
- ENVT-INRA, UMR1225 IHAP Interactions hôtes-agents pathogènes, 23 chemin des Capelles, 31076 Toulouse Cedex, France
| | - Stéphane Krebs
- ONIRIS-INRA, UMR1300 Bioagression, Épidémiologie et Analyse de risque, Atlanpole La Chantrerie, BP 40706, 44307 Nantes Cedex 3, France
| | - Pascal Rainard
- INRA, UR1282 IASP Infectiologie animale et santé publique, 37380 Nouzilly, France
| | | | - Didier Torny
- INRA, UMR1323 RiTME, 65 Boulevard de Brandebourg, 94205 Ivry-sur-Seine, France
| | - Muriel Vayssier-Taussat
- INRA, USC Bartonella et Tiques, ANSES, 23 Avenue du Général de Gaulle, F-94700 Maisons-Alfort, France
| | - Stephan Zientara
- ENVA-ANSES-INRA, UMR1161 Virologie, 7 avenue du Général de Gaulle, 94704 Maisons Alfort Cedex, France
| | - Etienne Zundel
- INRA, Département de santé animale, 37380 Nouzilly, France
| | - Thierry Pineau
- INRA, Département de santé animale, BP 93173, 31027 Toulouse Cedex 3, France
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Joost S, Colli L, Bonin A, Biebach I, Allendorf FW, Hoffmann I, Hanotte O, Taberlet P, Bruford MW. Promoting collaboration between livestock and wildlife conservation genetics communities. CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-011-9457-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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