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Belay S, Belay G, Nigussie H, Ahbara AM, Tijjani A, Dessie T, Tarekegn GM, Jian-Lin H, Mor S, Woldekiros HS, Dobney K, Lebrasseur O, Hanotte O, Mwacharo JM. Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats. Sci Rep 2024; 14:14908. [PMID: 38942813 DOI: 10.1038/s41598-024-65303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/19/2024] [Indexed: 06/30/2024] Open
Abstract
Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We analyzed 57 Ethiopian indigenous domestic goat genomes alongside 67 equivalents of east, west, and north-west African, European, South Asian, Middle East, and wild Bezoar goats. Cluster, ADMIXTURE (K = 4) and phylogenetic analysis revealed four genetic groups comprising African, European, South Asian, and wild Bezoar goats. The Middle Eastern goats had an admixed genome of these four genetic groups. At K = 5, the West African Dwarf and Moroccan goats were separated from East African goats demonstrating a likely historical legacy of goat arrival and dispersal into Africa via the coastal Mediterranean Sea and the Horn of Africa. FST, XP-EHH, and Hp analysis revealed signatures of selection in Ethiopian goats overlaying genes for thermo-sensitivity, oxidative stress response, high-altitude hypoxic adaptation, reproductive fitness, pathogen defence, immunity, pigmentation, DNA repair, modulation of renal function and integrated fluid and electrolyte homeostasis. Notable examples include TRPV1 (a nociception gene); PTPMT1 (a critical hypoxia survival gene); RETREG (a regulator of reticulophagy during starvation), and WNK4 (a molecular switch for osmoregulation). These results suggest that human-mediated translocations and adaptation to contrasting environments are shaping indigenous African goat genomes.
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Affiliation(s)
- Shumuye Belay
- Tigray Agricultural Research Institute, Mekelle, Ethiopia.
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia.
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Helen Nigussie
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abulgasim M Ahbara
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Department of Zoology, Misurata University, Misurata, Libya
| | - Abdulfatai Tijjani
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Getinet M Tarekegn
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Institute of Biotechnology (IoB), Addis Ababa University, Addis Ababa, Ethiopia
| | - Han Jian-Lin
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Beijing, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Siobhan Mor
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Helina S Woldekiros
- Department of Anthropology, Washington University in St. Louis, St. Louis, USA
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- University of Sydney, Sydney, Australia
| | - Ophelie Lebrasseur
- Palaeogenomics and Bioarchaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Joram M Mwacharo
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia.
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2
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Chessari G, Criscione A, Marletta D, Crepaldi P, Portolano B, Manunza A, Cesarani A, Biscarini F, Mastrangelo S. Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds. Sci Rep 2024; 14:3. [PMID: 38168531 PMCID: PMC10762050 DOI: 10.1038/s41598-023-49125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north-south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction.
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Affiliation(s)
- Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy.
| | - Donata Marletta
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Paola Crepaldi
- Dipartimento Scienze Agrarie e Ambientali, Produzione, Territorio, Agroenergia, University of Milan, Via Giovanni Celoria 2, 20133, Milan, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
| | - Arianna Manunza
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
- Animal and Dairy Science Department, University of Georgia, 425 River Road, 30602, Athens, GA, USA
| | - Filippo Biscarini
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
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3
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Pogorevc N, Dotsev A, Upadhyay M, Sandoval-Castellanos E, Hannemann E, Simčič M, Antoniou A, Papachristou D, Koutsouli P, Rahmatalla S, Brockmann G, Sölkner J, Burger P, Lymberakis P, Poulakakis N, Bizelis I, Zinovieva N, Horvat S, Medugorac I. Whole-genome SNP genotyping unveils ancestral and recent introgression in wild and domestic goats. Mol Ecol 2024; 33:e17190. [PMID: 37909668 DOI: 10.1111/mec.17190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/04/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome-wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus, C. pyrenaica, C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus, C. a. cretica, C. h. dorcas, C. caucasica caucasica, C. c. severtzovi, C. c. cylindricornis, C. falconeri, C. sibirica sibirica, C. s. alaiana and C. nubiana, as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar-type and ibex-type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats.
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Affiliation(s)
- Neža Pogorevc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Arsen Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, Russia
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Edson Sandoval-Castellanos
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Elisabeth Hannemann
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
| | - Mojca Simčič
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Crete, Greece
| | - Dimitris Papachristou
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Panagiota Koutsouli
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Siham Rahmatalla
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gudrun Brockmann
- Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Pamela Burger
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Irakleio, Greece
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio, Greece
| | - Iosif Bizelis
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Natalia Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, Russia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University of Munich, Martinsried/Planegg, Germany
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4
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Benjelloun B, Leempoel K, Boyer F, Stucki S, Streeter I, Orozco-terWengel P, Alberto FJ, Servin B, Biscarini F, Alberti A, Engelen S, Stella A, Colli L, Coissac E, Bruford MW, Ajmone-Marsan P, Negrini R, Clarke L, Flicek P, Chikhi A, Joost S, Taberlet P, Pompanon F. Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints. Mol Ecol 2023:e17257. [PMID: 38149334 DOI: 10.1111/mec.17257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/18/2023] [Accepted: 12/05/2023] [Indexed: 12/28/2023]
Abstract
The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.
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Affiliation(s)
- Badr Benjelloun
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Florian J Alberto
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Castanet-Tolosan, France
| | - Filippo Biscarini
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stefan Engelen
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Eric Coissac
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- AIA Associazione Italiana Allevatori, Roma, Italy
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Abdelkader Chikhi
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pierre Taberlet
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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5
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Havaš Auguštin D, Šarac J, Reidla M, Tamm E, Grahovac B, Kapović M, Novokmet N, Rudan P, Missoni S, Marjanović D, Korolija M. Refining the Global Phylogeny of Mitochondrial N1a, X, and HV2 Haplogroups Based on Rare Mitogenomes from Croatian Isolates. Genes (Basel) 2023; 14:1614. [PMID: 37628665 PMCID: PMC10454736 DOI: 10.3390/genes14081614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) has been used for decades as a predominant tool in population genetics and as a valuable addition to forensic genetic research, owing to its unique maternal inheritance pattern that enables the tracing of individuals along the maternal lineage across numerous generations. The dynamic interplay between evolutionary forces, primarily genetic drift, bottlenecks, and the founder effect, can exert significant influence on genetic profiles. Consequently, the Adriatic islands have accumulated a subset of lineages that exhibits remarkable absence or rarity within other European populations. This distinctive genetic composition underscores the islands' potential as a significant resource in phylogenetic research, with implications reaching beyond regional boundaries to contribute to a global understanding. In the initial attempt to expand the mitochondrial forensic database of the Croatian population with haplotypes from small isolated communities, we sequenced mitogenomes of rare haplogroups from different Croatian island and mainland populations using next-generation sequencing (NGS). In the next step and based on the obtained results, we refined the global phylogeny of haplogroup N1a, HV2, and X by analyzing rare haplotypes, which are absent from the current phylogenetic tree. The trees were based on 16 novel and 52 previously published samples, revealing completely novel branches in the X and HV2 haplogroups and a new European cluster in the ancestral N1a variant, previously believed to be an exclusively African-Asian haplogroup. The research emphasizes the importance of investigating geographically isolated populations and their unique characteristics within a global context.
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Affiliation(s)
- Dubravka Havaš Auguštin
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Jelena Šarac
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Maere Reidla
- Institute of Genomics, University of Tartu, 50090 Tartu, Estonia
| | - Erika Tamm
- Institute of Genomics, University of Tartu, 50090 Tartu, Estonia
| | | | | | | | - Pavao Rudan
- Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Saša Missoni
- Institute for Anthropological Research, 10000 Zagreb, Croatia
- Faculty of Dental Medicine and Health, J. J. Strossmayer University, 31000 Osijek, Croatia
| | - Damir Marjanović
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
- Genetics and Bioengineering Department, International Burch University, 71000 Sarajevo, Bosnia and Herzegovina
| | - Marina Korolija
- Forensic Science Centre “Ivan Vučetić”, Ministry of the Interior, 10000 Zagreb, Croatia
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6
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Rannamäe E, Saarma U, Kantanen J, Bläuer A. Maternal genetic diversity of ancient goats in Finland and Estonia and comparison with extant northern European goat breeds. Anim Genet 2023; 54:177-188. [PMID: 36514938 DOI: 10.1111/age.13281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 12/15/2022]
Abstract
Countries in the northern Baltic Sea region have been historically linked for thousands of years, and animal husbandry is one of the many information sources that enables the study of historical connections. Although goat husbandry in this part of Europe has been evidenced by scant archaeological materials, zooarchaeological and historical evidence has revealed its continuity, at least since the Late Iron Age. To explore the historical relationship between goat lineages and investigate affinities between the past and present-day populations in the Baltic Sea region, we analysed a 476-bp fragment of the mitochondrial DNA control region in 14 ancient goats from Finland and Estonia and 10 extant goats from Finland. The results revealed high mitochondrial diversity among the ancient goats. Two maternal lineages were shared between the Late Iron Age and medieval individuals from Finland and Estonia. Moreover, ancient Finnish and Estonian goats showed maternal affinity to extant Finngoat and Swedish Landrace breeds. Overall, the analysis of maternal goat lineages confirmed tight historical connections in the region.
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Affiliation(s)
- Eve Rannamäe
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu, Estonia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Juha Kantanen
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Auli Bläuer
- Archaeology, University of Turku, Turku, Finland
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7
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Arslan M. Whole-genome sequencing and genomic analysis of Norduz goat (Capra hircus). Mamm Genome 2023:10.1007/s00335-023-09990-3. [PMID: 37004528 DOI: 10.1007/s00335-023-09990-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/21/2023] [Indexed: 04/04/2023]
Abstract
Artificial and natural selective breeding of goats has resulted in many different goat breeds all around the world. Norduz goat is one of these breeds, and it is a local goat breed of Turkey. The goats are favorable due to pre-weaning viability and reproduction values compared to the regional breeds. Development in sequencing technologies has let to understand huge genomic structures and complex phenotypes. Until now, such a comprehensive study has not been carried out to understand the genomic structure of the Norduz goats, yet. In the study, the next-generation sequencing was carried out to understand the genomic structure of Norduz goat. Real-time PCR was used to evaluate prominent CNVs in the Norduz goat individuals. Whole genome of the goat was constructed with an average of 33.1X coverage level. In the stringent filtering condition, 9,757,980 SNPs, 1,536,715 InDels, and 290 CNVs were detected in the Norduz goat genome. Functional analysis of high-impact SNP variations showed that the classical complement activation biological process was affected significantly in the goat. CNVs in the goat genome were found in genes related to defense against viruses, immune response, and cell membrane transporters. It was shown that GBP2, GBP5, and mammalian ortholog GBP1, which are INF-stimulated GTPases, were found to be high copy numbers in the goats. To conclude, genetic variations mainly in immunological response processes suggest that Norduz goat is an immunologically improved goat breed and natural selection could take an important role in the genetical improvements of the goats.
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Affiliation(s)
- Mevlüt Arslan
- Department of Genetics, Faculty of Veterinary Medicine, Van Yüzüncü Yıl University, Tuşba, 65080, Van, Turkey.
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8
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De AK, Sawhney S, Sunder J, Muthiyan R, Ponraj P, Sujatha T, Malakar D, Mondal S, Bera AK, Kumar A, Chakurkar EB, Bhattacharya D. Peeping into Mitochondrial Diversity of Andaman Goats: Unveils Possibility of Maritime Transport with Diversified Geographic Signaling. Genes (Basel) 2023; 14:genes14040784. [PMID: 37107542 PMCID: PMC10138289 DOI: 10.3390/genes14040784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/22/2023] [Accepted: 03/14/2023] [Indexed: 04/29/2023] Open
Abstract
Andaman and Nicobar Islands, a part of South-East Asia, is enriched with the presence of native breeds of livestock (cattle, pig, goat) and poultry. There are two native goat breeds, viz., Andaman local goat and Teressa goat in Andaman and Nicobar Islands. However, to date, the origin and genetic makeup of these two breeds have not been detailed. Therefore, the present study describes the genetic makeup of Andaman goats through analysis of mitochondrial D-loop sequence for sequence polymorphism, phylogeographical signaling and population expansion events. The genetic diversity of the Teressa goat was less compared to the Andaman local goat due to its sole presence on Teressa Island. Out of 38 well-defined haplotypes of Andaman goats, the majority of haplotypes belonged to haplogroup A followed by haplogroup B and haplogroup D. The result of mismatch distribution and neutrality tests indicated no population expansion event of haplogroup A and B. Finally, based on poor geographical signaling, we hypothesize that Andaman goats have been imported to these Islands either through multidirectional diffusion or unidirectional diffusion. We justify our hypothesis of multidirectional diffusion on the basis of observation of the haplotype and nucleotide diversity of Andaman goats. Simultaneously, the probability of unidirectional diffusion of goats in these islands from the Indian subcontinent in different spells of domestication events through maritime routes cannot be ignored.
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Affiliation(s)
- Arun Kumar De
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Sneha Sawhney
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Jai Sunder
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Ramachandran Muthiyan
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Perumal Ponraj
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Tamilvanan Sujatha
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Dhruba Malakar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Samiran Mondal
- Department of Veterinary Pathology, West Bengal University of Animal and Fishery Sciences, Kolkata 700037, West Bengal, India
| | - Asit Kumar Bera
- Reservoir and Wetland Fisheries Division, ICAR-Central Inland Fishery Research Institute, Barrackpore 700120, West Bengal, India
| | - Ashish Kumar
- Centre for Technology Alternatives for Rural Areas, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Eaknath Bhanudasrao Chakurkar
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
| | - Debasis Bhattacharya
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman and Nicobar Islands, India
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9
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Salim B, Alasmari S, Mohamed NS, Ahmed MKA, Nakao R, Hanotte O. Genetic variation and demographic history of Sudan desert sheep reveal two diversified lineages. BMC Genomics 2023; 24:118. [PMID: 36927331 PMCID: PMC10018940 DOI: 10.1186/s12864-023-09231-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
More than 400 million sheep are raised on the African continent, the majority of which are indigenous and are primarily reared for sustenance. They have effectively adapted to various climatic and production environments, surviving and flourishing. The genetic relationships among these sheep populations remain understudied. Herein, we sequenced the entire mitochondrial DNA control region of 120 animals from Hamary and Kabashi and their crossbreed (Hamary x Kabashi) of Sudan desert sheep (SDS) to understand their maternal-inherited genetic variation and demographic history profiles and relate those to the history of sheep pastoralism on the African continent. The results show a diversified and predominant D- loop haplogroup B (n = 102, 85%), with all other sequences belonging to haplogroup A. Most of the maternal genetic variation was partitioned between haplogroup (76.3%) while within haplogroup accounted for 23.7% of the variation. However, little genetic differentiation was observed among the two breeds and their crosses, with our results supporting a Hamari maternal origin for the crossbreed. Bayesian coalescent-based analysis reveals distinct demographic history between the two haplogroups, two breeds and their crosses. Comparison of the two haplogroup showed that haplogroup B experienced an earlier expansion than haplogroup A. Unlike the breed-based comparison, the expansion of the two breeds started roughly at the same time, around 6500 years ago, with Kabashi having a slightly greater effective population size. The maternal ancestors of SDS may have diverged before their introduction to the African continent. This study provides novel insights into the early history of these two main breeds of Sudan desert sheep and their crosses.
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Affiliation(s)
- Bashir Salim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, P.O Box 32, Khartoum-North, Sudan.
| | - Saeed Alasmari
- Department of Biology, Faculty of Arts and Sciences, Najran University, 1988, Najran, Kingdom of Saudi Arabia
| | - Nouh Saad Mohamed
- Molecular Biology Unit, Sirius Training and Research Center, Khartoum, Sudan
| | - Mohamed-Khair A Ahmed
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK.,LiveGene - CTLGH, International Livestock Research Institute, Addis Ababa, Ethiopia
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10
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Transcriptomics and Selection Pressure Analysis Reveals the Influence Mechanism of PLIN1 Protein on the Development of Small Size in Min Pigs. Int J Mol Sci 2023; 24:ijms24043947. [PMID: 36835359 PMCID: PMC9960057 DOI: 10.3390/ijms24043947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Body size is an important biological phenotypic trait that has attracted substantial attention. Small domestic pigs can serve as excellent animal models for biomedicine and also help meet sacrificial culture needs in human societies. Although the mechanisms underlying vertebral development regulating body size variation in domestic pigs during the embryonic period have been well described, few studies have examined the genetic basis of body size variation in post embryonic developmental stages. In this study, seven candidate genes-PLIN1, LIPE, PNPLA1, SCD, FABP5, KRT10 and IVL-significantly associated with body size were identified in Min pigs, on the basis of weighted gene co-expression network analysis (WGCNA), and most of their functions were found to be associated with lipid deposition. Six candidate genes except for IVL were found to have been subjected to purifying selection. PLIN1 had the lowest ω value (0.139) and showed heterogeneous selective pressure among domestic pig lineages with different body sizes (p < 0.05). These results suggested that PLIN1 is an important genetic factor regulating lipid deposition and consequently affecting body size variation in pigs. The culture of whole pig sacrifice in Manchu during the Qing Dynasty in China might have contributed to the strong artificial domestication and selection of Hebao pigs.
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11
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Ben Sassi-Zaidy Y, Mohamed-Brahmi A, Chaouch M, Maretto F, Cendron F, Charfi-Cheikhrouha F, Ben Abderrazak S, Djemali M, Cassandro M. Historical Westward Migration Phases of Ovis aries Inferred from the Population Structure and the Phylogeography of Occidental Mediterranean Native Sheep Breeds. Genes (Basel) 2022; 13:genes13081421. [PMID: 36011332 PMCID: PMC9408117 DOI: 10.3390/genes13081421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 08/04/2022] [Indexed: 01/18/2023] Open
Abstract
In this study, the genetic relationship and the population structure of western Mediterranean basin native sheep breeds are investigated, analyzing Maghrebian, Central Italian, and Venetian sheep with a highly informative microsatellite markers panel. The phylogeographical analysis, between breeds’ differentiation level (Wright’s fixation index), gene flow, ancestral relatedness measured by molecular coancestry, genetic distances, divergence times estimates and structure analyses, were revealed based on the assessment of 975 genotyped animals. The results unveiled the past introduction and migration history of sheep in the occidental Mediterranean basin since the early Neolithic. Our findings provided a scenario of three westward sheep migration phases fitting properly to the westward Neolithic expansion argued by zooarcheological, historical and human genetic studies.
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Affiliation(s)
- Yousra Ben Sassi-Zaidy
- Laboratory of Diversity, Management and Conservation of Biological Systems, LR18ES06, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
- Laboratory of Animal Genetic and Feed Resources Research, Department of Animal Science, Institut National Agronomique de Tunis (INAT), University of Carthage, Tunis-Mahragène Tunis 2078, Tunisia
- Correspondence: (Y.B.S.-Z.); (F.C.); Tel.: +39-049-8272871 (F.C.); Fax: +39-049-8272633 (F.C.)
| | - Aziza Mohamed-Brahmi
- Laboratory of Agricultural Production Systems Sustainability in the North Western Region of Tunisia, Department of Animal Production, Ecole Supérieure d’Agriculture du Kef Boulifa, University of Jendouba, Le Kef 7119, Tunisia
| | - Melek Chaouch
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (LR11IPT06), Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Fabio Maretto
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
| | - Filippo Cendron
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
- Correspondence: (Y.B.S.-Z.); (F.C.); Tel.: +39-049-8272871 (F.C.); Fax: +39-049-8272633 (F.C.)
| | - Faouzia Charfi-Cheikhrouha
- Laboratory of Diversity, Management and Conservation of Biological Systems, LR18ES06, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia
| | - Souha Ben Abderrazak
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (LR11IPT06), Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Mnaour Djemali
- Laboratory of Animal Genetic and Feed Resources Research, Department of Animal Science, Institut National Agronomique de Tunis (INAT), University of Carthage, Tunis-Mahragène Tunis 2078, Tunisia
| | - Martino Cassandro
- Department of Agronomy, Animal, Food, Natural Resources and Environment, University of Padova, 35020 Legnaro Padova, Italy
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12
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Consortium VG, Nijman IJ, Rosen BD, Bardou P, Faraut T, Cumer T, Daly KG, Zheng Z, Cai Y, Asadollahpour H, Kul BÇ, Zhang WY, Guangxin E, Ayin A, Baird H, Bakhtin M, Bâlteanu VA, Barfield D, Berger B, Blichfeldt T, Boink G, Bugiwati SRA, Cai Z, Carolan S, Clark E, Cubric-Curik V, Dagong MIA, Dorji T, Drew L, Guo J, Hallsson J, Horvat S, Kantanen J, Kawaguchi F, Kazymbet P, Khayatzadeh N, Kim N, Shah MK, Liao Y, Martínez A, Masangkay JS, Masaoka M, Mazza R, McEwan J, Milanesi M, Faruque MO, Nomura Y, Ouchene-Khelifi NA, Pereira F, Sahana G, Salavati M, Sasazaki S, Da Silva A, Simčič M, Sölkner J, Sutherland A, Tigchelaar J, Zhang H, Consortium E, Ajmone-Marsan P, Bradley DG, Colli L, Drögemüller C, Jiang Y, Lei C, Mannen H, Pompanon F, Tosser-Klopp G, Lenstra JA. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions. Mol Ecol 2022; 31:4364-4380. [PMID: 35751552 DOI: 10.1111/mec.16579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/12/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022]
Abstract
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and 7 wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during the migrations into northern Europe, eastern and southern Asia and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographic range.
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Affiliation(s)
| | - Isaäc J Nijman
- Utrecht Univ., Netherlands.,Univ. Medical Center Utrecht, Utrecht Univ, The Netherlands
| | | | - Philippe Bardou
- GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Thomas Faraut
- GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Tristan Cumer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | | | - Zhuqing Zheng
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | - Yudong Cai
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | | | | | | | | | | | - Hayley Baird
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | - Valentin A Bâlteanu
- Inst. of Life SciencesUniv. Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | | | - Beate Berger
- Univ. Natural Resources and Life Sciences Vienna (BOKU)
| | - Thor Blichfeldt
- Norwegian Association of Sheep and Goat Breeders, Aas, Norway
| | - Geert Boink
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands
| | | | | | | | | | | | | | - Tashi Dorji
- International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | | | | | | | - Simon Horvat
- Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | | | | | - Namshin Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | | | - Yuying Liao
- Guangxi Key Laboratory of Livestock Genetic Improvement, Guangxi, China
| | | | | | | | - Raffaele Mazza
- Laboratorio Genetica e Servizi, Agrotis srl, Cremona, Italy
| | - John McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | | | | | | | - Filipe Pereira
- IDENTIFICA Genetic Testing Maia & Centre for Functional Ecology, Porto, Portugal
| | | | | | | | | | - Mojca Simčič
- Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | | | | | | | | | | | - Paolo Ajmone-Marsan
- Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy.,UCSC PRONUTRIGEN Nutrigenomics Res. Centre, Piacenza, Italy
| | | | - Licia Colli
- Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy.,UCSC BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy
| | | | - Yu Jiang
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | - Chuzhao Lei
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | | | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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13
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Kandoussi A, Badaoui B, Boujenane I, Piro M, Petit D. How have sheep breeds differentiated from each other in Morocco? Genetic structure and geographical distribution patterns. Genet Sel Evol 2021; 53:83. [PMID: 34736399 PMCID: PMC8567669 DOI: 10.1186/s12711-021-00679-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
Background Based on the relatively homogeneous origin of the sheep breeds in Morocco that originate mainly from Iberia, it is highly relevant to address the question of how these very diverse sheep populations differentiated from each other. The Mountains of the High Atlas and Middle Atlas are expected to constitute North–South and West–East geographical barriers, respectively, which could have shaped the history of the differentiation of sheep breeds. The aim of this study was to test this hypothesis by considering the genetic structure and the spatial distribution of five major breeds (Sardi, Timahdite, Beni Guil, Boujaad and D’man) and one minor breed (Blanche de Montagne), by analysing the mtDNA control region, using 30 individuals per breed. Results Phylogenetic and network analyses did not indicate any clear separation among the studied breeds and discriminant component principal analysis showed some overlap between them, which indicates a common genetic background. The calculated pairwise FST values and Nei’s genetic distances revealed that most breeds showed a moderate genetic differentiation. The lowest and highest degrees of differentiation were retrieved in the Beni Guil and Boujaad breeds, respectively. Analysis of molecular variance (AMOVA) indicated that more than 95% of the genetic diversity occurs within individuals, while between- and within-population variabilities represent only 1.332% and 2.881%, respectively. Isolation-by-distance, spatial Principal Component Analysis (sPCA), and spatial AMOVA analyses evidenced clear examples of geographical structuration among the breeds, both between and within breeds. However, several enigmatic relationships remain, which suggest the occurrence of complex events leading to breed differentiation. Conclusions The approaches used here resulted in a convergent view on the hypothetic events that could have led to the progressive differentiation between the Moroccan breeds. The major split seems to be linked to the West–East barrier of the Middle Atlas, whereas the influence of the High Atlas is less obvious and incompletely resolved. The study of additional breeds that have settled near the High Atlas should clarify the relationships between the breeds of the West part of the country, in spite of their small population size. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00679-2.
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Affiliation(s)
- Asmae Kandoussi
- Department of Animal Production and Biotechnology, Institut Agronomique et Vétérinaire Hassan II, Rabat-Instituts, PO Box 6202, 10101, Rabat, Morocco.,Glycosylation et Différenciation Cellulaire, EA 7500, Laboratoire Peirene, Université de Limoges, 123 av. A. Thomas, 87060, Limoges Cedex, France
| | - Bouabid Badaoui
- Laboratory of Biodiversity, Ecology and Genome, Mohammed V University, 4 Avenue Ibn Battouta, B.P. 1014 RP, Rabat, Morocco
| | - Ismaïl Boujenane
- Department of Animal Production and Biotechnology, Institut Agronomique et Vétérinaire Hassan II, Rabat-Instituts, PO Box 6202, 10101, Rabat, Morocco
| | - Mohammed Piro
- Department of Medicine, Surgery and Reproduction, Institut Agronomique et Vétérinaire Hassan II, Rabat-Instituts, PO Box 6202, 10101, Rabat, Morocco
| | - Daniel Petit
- Glycosylation et Différenciation Cellulaire, EA 7500, Laboratoire Peirene, Université de Limoges, 123 av. A. Thomas, 87060, Limoges Cedex, France.
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14
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Wanjala G, Bagi Z, Kusza S. Meta-Analysis of Mitochondrial DNA Control Region Diversity to Shed Light on Phylogenetic Relationship and Demographic History of African Sheep ( Ovis aries) Breeds. BIOLOGY 2021; 10:762. [PMID: 34439994 PMCID: PMC8389696 DOI: 10.3390/biology10080762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022]
Abstract
To improve sheep breeding and conservation of genetic resources, the mitochondrial DNA control region (mtDNA CR) of 399 sequences of African indigenous sheep breeds from previously published research articles were meta-analyzed to elucidate their phylogenetic relationship, diversity, and demographic history. A total of 272 haplotypes were found, of which 207 were unique and a high level of mtDNA CR variability was observed. Generally, the number of polymorphic sites, nucleotide and haplotype diversity were high (284, 0.254 ± 0.012 and 0.993 ± 0.002, respectively). The median-joining (MJ) network of haplotypes produced three major haplogroups (A, B and C), with haplogroup B being dominant. A mixture of populations suggests a common matrilineal origin and lack of and/or a weak phylogeographic structure. Mismatch analysis showed recent expansion of North African breeds, whereas East African and continental populations exhibited selection pressures for adaptation. A slight historical genetic difference was also observed between the fat tail and thin tail sheep breeds. However, further investigations are required using more samples and long sequence segments to achieve deeper levels of conclusions on the African sheep phylogenetic relationship. The present meta-analysis results contribute to the general understanding of African native sheep populations for improved management of sheep genetic resources.
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Affiliation(s)
- George Wanjala
- Centre for Agricultural Genomics and Biotechnology, H-4032 Egyetem tér 1, 4032 Debrecen, Hungary; (G.W.); (Z.B.)
- Doctoral School of Animal Science, University of Debrecen, H-4032 Böszörményi út 138, 4032 Debrecen, Hungary
| | - Zoltán Bagi
- Centre for Agricultural Genomics and Biotechnology, H-4032 Egyetem tér 1, 4032 Debrecen, Hungary; (G.W.); (Z.B.)
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, H-4032 Egyetem tér 1, 4032 Debrecen, Hungary; (G.W.); (Z.B.)
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15
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Deniskova TE, Dotsev AV, Selionova MI, Reyer H, Sölkner J, Fornara MS, Aybazov AMM, Wimmers K, Brem G, Zinovieva NA. SNP-Based Genotyping Provides Insight Into the West Asian Origin of Russian Local Goats. Front Genet 2021; 12:708740. [PMID: 34276802 PMCID: PMC8282346 DOI: 10.3389/fgene.2021.708740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Specific local environmental and sociocultural conditions have led to the creation of various goat populations in Russia. National goat diversity includes breeds that have been selected for down and mohair production traits as well as versatile local breeds for which pastoralism is the main management system. Effective preservation and breeding programs for local goat breeds are missing due to the lack of DNA-based data. In this work, we analyzed the genetic diversity and population structure of Russian local goats, including Altai Mountain, Altai White Downy, Dagestan Downy, Dagestan Local, Karachaev, Orenburg, and Soviet Mohair goats, which were genotyped with the Illumina Goat SNP50 BeadChip. In addition, we addressed genetic relationships between local and global goat populations obtained from the AdaptMap project. Russian goats showed a high level of genetic diversity. Although a decrease in historical effective population sizes was revealed, the recent effective population sizes estimated for three generations ago were larger than 100 in all studied populations. The mean runs of homozygosity (ROH) lengths ranged from 79.42 to 183.94 Mb, and the average ROH number varied from 18 to 41. Short ROH segments (<2 Mb) were predominant in all breeds, while the longest ROH class (>16 Mb) was the least frequent. Principal component analysis, Neighbor-Net graph, and Admixture clustering revealed several patterns in Russian local goats. First, a separation of the Karachaev breed from other populations was observed. Moreover, genetic connections between the Orenburg and Altai Mountain breeds were suggested and the Dagestan breeds were found to be admixed with the Soviet Mohair breed. Neighbor-Net analysis and clustering of local and global breeds demonstrated the close genetic relations between Russian local and Turkish breeds that probably resulted from past admixture events through postdomestication routes. Our findings contribute to the understanding of the genetic relationships of goats originating in West Asia and Eurasia and may be used to design breeding programs for local goats to ensure their effective conservation and proper management.
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Affiliation(s)
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Marina I Selionova
- Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | | | - Ali-Magomed M Aybazov
- All-Russian Research Institute of Sheep and Goat Breeding - Branch of the Federal State Budgetary Scientific Institution, North Caucasian Agrarian Center, Stavropol, Russia
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
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16
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Ressaissi Y, Amills M, Noce A, Ben Hamouda M. Characterizing the Mitochondrial Diversity of Arbi Goats from Tunisia. Biochem Genet 2021; 59:1225-1232. [PMID: 33743097 DOI: 10.1007/s10528-021-10058-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
Arbi is one of the main local goat breeds in Tunisia, representing an important economic resource in arid and hot areas where cattle and sheep cannot thrive successfully. In the current work, we have characterized the mitochondrial diversity of 26 Arbi goats by partially sequencing the mitochondrial D-loop region. These sequences plus 10 retrieved from GenBank were analyzed with the DnaSP v.5.10.1, evidencing the existence of 12 different haplotypes. Nucleotide and haplotype diversities were 0.02 and 0.96. Moreover, median-joining network analysis showed that all D-loop sequences from Arbi goats correspond to haplogroup A and that in general they do not cluster with sequences from other goat breeds. The high diversity that has been observed in North African goats is compatible with the maritime diffusion of the Neolithic package 10,000-7000 YBP. Moreover, there are evidences that local Tunisian breeds have been extensively crossed with highly productive transboundary breeds in order to improve meat and milk yields. These uncontrolled crossing practices may lead to the loss of alleles that play key roles in the adaptation of Tunisian local breeds to a harsh environment.
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Affiliation(s)
- Yosra Ressaissi
- Institut National Agronomique de La Tunisie (INAT), 43 Avenue Charles Nicolle, 1082, Tunis, Tunisia.
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antonia Noce
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Mohamed Ben Hamouda
- Institut National de La Recherche Agronomique de Tunisie (INRAT), Rue Hédi Karray, 2049, Ariana, Tunisie
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Tanaka K, Hoshi A, Nojima R, Suzuki K, Takiguchi H, Takatsuki S, Takizawa T, Hosoi E, Tamate HB, Hayashida M, Anezaki T, Fukue Y, Minami M. Genetic Variation in Y-Chromosome Genes of Sika Deer ( Cervus nippon) in Japan. Zoolog Sci 2021; 37:411-416. [PMID: 32972081 DOI: 10.2108/zs200043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/21/2020] [Indexed: 11/17/2022]
Abstract
Sika deer (Cervus nippon) in Japan are classified into southern and northern groups. However, previous studies primarily relied on maternally inherited mitochondrial DNA (mtDNA). The paternally inherited Y-chromosome is useful for analyzing the contribution of males to the population genetic history of sika deer. In total, approximately 16 kb of partial sequences of four Y-chromosomal genes, Y-linked, sex-determining region Y, DEAD-box helicase 3 Y-linked, and Zinc finger protein Y-linked, were sequenced to investigate intraspecific variation. As a result, we identified nine intronic single nucleotide polymorphisms (SNPs) in 478 sika deer samples collected over the entire Japanese archipelago from Hokkaido to Kyushu. SNP genotyping revealed 10 distinct haplotypes (SYH1-SYH10). The most common haplotype (SYH1) was present in all populations and was the most abundant haplotype, identified in 80.3% of the sampled individuals. The remaining haplotypes were unique to a single locality. SYH1 was also central to all other haplotypes that diverged by a SNP, resulting in this haplotype being the core of a star-like cluster topography. We found that contrary to mtDNA patterns, there was no clear differentiation of Y-chromosome markers between the southern and the northern populations. Due to the female philopatry of sika deer, mtDNA may provide a highly structured differentiation of populations. On the other hand, the male-biased gene flow may provide a reduced differentiation of populations. Our findings revealed that the genetic structure of the Japanese sika deer is more complex than previously thought based on mtDNA-based phylogeographic studies.
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Affiliation(s)
- Kazuaki Tanaka
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan,
| | - Asuka Hoshi
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
| | - Rai Nojima
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
| | - Kaho Suzuki
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
| | - Harutaka Takiguchi
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
| | - Seiki Takatsuki
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
| | - Tatsuya Takizawa
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
| | - Eiji Hosoi
- Faculty of Agriculture, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Hidetoshi B Tamate
- Department of Biology, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Maki Hayashida
- Department of Animal Science Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Kanagawa 243-0034, Japan
| | - Tomoko Anezaki
- Gunma Museum of Natural History, Tomioka, Gunma 370-2345, Japan
| | - Yuko Fukue
- NPO Institute for Biodiversity Research and Education "Earthworm," Karuizawa, Nagano 389-0115, Japan
| | - Masato Minami
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
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Diversity Analysis and Genetic Relationships among Local Brazilian Goat Breeds Using SSR Markers. Animals (Basel) 2020; 10:ani10101842. [PMID: 33050450 PMCID: PMC7600759 DOI: 10.3390/ani10101842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 01/08/2023] Open
Abstract
Simple Summary This study aimed to evaluate the genetic diversity of six groups of native Brazilian goats using a panel of single sequence repeats (SSRs). Results indicated a definite genetic differentiation among the Brazilian goat herd, which indicates the existence of at least four breeds according to the international concepts (Moxotó and Repartida; the Grauna and Serrana Azul; Canindé and Marota breeds). Abstract The genetic diversity of six Brazilian native goats was reported using molecular markers. Hair samples of 332 animals were collected from different goat breeds (Moxotó, Canindé, Serrana Azul, Marota, Repartida, and Graúna) from five states of Northeast Brazil (Paraíba, Pernambuco, Rio Grande do Norte, Bahia, and Piauí). A panel of 27 microsatellites or single sequence repeats (SSRs) were selected and amplified using a polymerase chain reaction (PCR) technique. All populations showed an average allele number of over six. The mean observed heterozygosity for Brazilian breeds was superior to 0.50. These results demonstrated the high genetic diversity in the studied populations with values ranging from 0.53 (Serrana Azul) to 0.62 (Repartida). The expected average heterozygosity followed the same trend ranging from 0.58 (Serrana Azul) to 0.65 (Repartida), and the values obtained are very similar for all six breeds. The fixation index (Fis) had values under 10% except for the Moxotó breed (13%). The mean expected heterozygosity of all Brazilian populations was over 0.50. Results indicated a within-breed genetic variability in the Brazilian breeds based on the average number of alleles and the average observed heterozygosity. The interbreed genetic diversity values showed proper genetic differentiation among local Brazilian goat breeds.
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Deng J, Xie XL, Wang DF, Zhao C, Lv FH, Li X, Yang J, Yu JL, Shen M, Gao L, Yang JQ, Liu MJ, Li WR, Wang YT, Wang F, Li JQ, Hehua EE, Liu YG, Shen ZQ, Ren YL, Liu GJ, Chen ZH, Gorkhali NA, Rushdi HE, Salehian-Dehkordi H, Esmailizadeh A, Nosrati M, Paiva SR, Caetano AR, Štěpánek O, Olsaker I, Weimann C, Erhardt G, Curik I, Kantanen J, Mwacharo JM, Hanotte O, Bruford MW, Ciani E, Periasamy K, Amills M, Lenstra JA, Han JL, Zhang HP, Li L, Li MH. Paternal Origins and Migratory Episodes of Domestic Sheep. Curr Biol 2020; 30:4085-4095.e6. [PMID: 32822607 DOI: 10.1016/j.cub.2020.07.077] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/14/2020] [Accepted: 07/27/2020] [Indexed: 01/22/2023]
Abstract
The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.
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Affiliation(s)
- Juan Deng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Life Science, Hebei University, Baoding 071002, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xin Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jia-Lin Yu
- Station for Breeding and Improvement of Animal and Poultry of Changshou District, Chongqing 401220, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi 830001, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi 830001, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashi University, Kashi 844000, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010000, China
| | - EEr Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750000, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650000, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou 256600, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou 256600, China
| | - Guang-Jian Liu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Neena A Gorkhali
- Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council (NARC), Kathmandu, Nepal
| | - Hossam E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Samuel R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Avenida W5 Norte (Final), Caixa Postal 02372, CEP 70770-917 Brasília, DF, Brazil
| | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Avenida W5 Norte (Final), Caixa Postal 02372, CEP 70770-917 Brasília, DF, Brazil
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Rantirovska 93, 58601, Jihlava, Czech Republic
| | - Ingrid Olsaker
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - Joram M Mwacharo
- International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia; CTLGH and SRUC, the Roslin Institute Building, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - Olivier Hanotte
- LiveGene, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia; School of Life Sciences, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff CF10 3AX, Wales, United Kingdom; Sustainable Places Research Institute, Cardiff University CF10 3BA, Wales, United Kingdom
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24 Moro, Bari, Italy
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Hong-Ping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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20
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Kandoussi A, Boujenane I, Auger C, Serranito B, Germot A, Piro M, Maftah A, Badaoui B, Petit D. The origin of sheep settlement in Western Mediterranean. Sci Rep 2020; 10:10225. [PMID: 32576960 PMCID: PMC7311441 DOI: 10.1038/s41598-020-67246-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 05/21/2020] [Indexed: 11/25/2022] Open
Abstract
The arrival of Neolithic culture in North Africa, especially domestic animals has been essentially documented from archaeological records. As the data relative to sheep are scarce, we studied the genetic relationship between Moroccan sheep breeds and Mediterranean ones using the sequencing of 628 bp of the mitochondrial DNA control region in 193 Moroccan individuals, belonging to six breeds, and 652 sequences from other breeds in Europe and Middle East. Through Network analysis and an original phylogenetically derived method, the connection proportions of each Moroccan breed to foreign ones were estimated, highlighting the strong links between Moroccan and Iberian breeds. The first founders of Moroccan sheep population were issued at 79% from Iberia and 21% from a territory between Middle East and Africa. Their calculated expansion times were respectively 7,100 and 8,600 years B.P. This suggests that Neolithization was introduced by a double influence, from Iberia and from another route, maybe Oriental or Sub-Saharan. The consequence of the environmental changes encountered by founders from Iberia was tested using different neutrality tests. There are significant selection signatures at the level of Moroccan and European breeds settled in elevated altitudes, and an erosion of nucleotide diversity in Moroccan breeds living in arid areas.
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Affiliation(s)
- Asmae Kandoussi
- Department of Animal Production and Biotechnology, Institut Agronomique et Vétérinaire Hassan II, PO Box 6202 Rabat-Instituts, 10101, Rabat, Morocco
- Glycosylation et différenciation cellulaire, EA 7500, Laboratoire Peirene, Université de Limoges, 123 av. A. Thomas, 87060, Limoges, Cedex, France
| | - Ismaïl Boujenane
- Department of Animal Production and Biotechnology, Institut Agronomique et Vétérinaire Hassan II, PO Box 6202 Rabat-Instituts, 10101, Rabat, Morocco
| | - Clément Auger
- Glycosylation et différenciation cellulaire, EA 7500, Laboratoire Peirene, Université de Limoges, 123 av. A. Thomas, 87060, Limoges, Cedex, France
| | - Bruno Serranito
- Glycosylation et différenciation cellulaire, EA 7500, Laboratoire Peirene, Université de Limoges, 123 av. A. Thomas, 87060, Limoges, Cedex, France
| | - Agnès Germot
- Glycosylation et différenciation cellulaire, EA 7500, Laboratoire Peirene, Université de Limoges, 123 av. A. Thomas, 87060, Limoges, Cedex, France
| | - Mohammed Piro
- Department of Medicine, Surgery and Reproduction, Institut Agronomique et Vétérinaire Hassan II, PO Box 6202 Rabat-Instituts, 10101, Rabat, Morocco
| | - Abderrahman Maftah
- Glycosylation et différenciation cellulaire, EA 7500, Laboratoire Peirene, Université de Limoges, 123 av. A. Thomas, 87060, Limoges, Cedex, France
| | - Bouabid Badaoui
- Laboratory of Biodiversity, Ecology and Genome, Mohammed V University, 4 Avenue Ibn Battouta, B.P, 1014 RP, Rabat, Morocco
| | - Daniel Petit
- Glycosylation et différenciation cellulaire, EA 7500, Laboratoire Peirene, Université de Limoges, 123 av. A. Thomas, 87060, Limoges, Cedex, France.
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21
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Organization and Management of Conservation Programs and Research in Domestic Animal Genetic Resources. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11120235] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Creating national committees for domestic animal genetic resources within genetic resource national commissions is recommended to organize in situ and ex situ conservation initiatives. In situ conservation is a high priority because it retains traditional zootechnical contexts and locations to ensure the long-term survival of breeds. In situ actions can be based on subsidies, technical support, structure creation, or trademark definition. Provisional or permanent relocation of breeds may prevent immediate extinction when catastrophes, epizootics, or social conflicts compromise in situ conservation. Ex situ in vivo (animal preservation in rescue or quarantine centers) and in vitro methods (germplasm, tissues/cells, DNA/genes storage) are also potential options. Alert systems must detect emergencies and summon the national committee to implement appropriate procedures. Ex situ coordinated centers must be prepared to permanently or provisionally receive extremely endangered collections. National germplasm banks must maintain sufficient samples of national breeds (duplicated) in their collections to restore extinct populations at levels that guarantee the survival of biodiversity. A conservation management survey, describing national and international governmental and non-governmental structures, was developed. Conservation research initiatives for international domestic animal genetic resources from consortia centralize the efforts of studies on molecular, genomic or geo-evolutionary breed characterization, breed distinction, and functional gene identification. Several consortia also consider ex situ conservation relying on socioeconomic or cultural aspects. The CONBIAND network (Conservation for the Biodiversity of Local Domestic Animals for Sustainable Rural Development) exemplifies conservation efficiency maximization in a low-funding setting, integrating several Latin American consortia with international cooperation where limited human, material, and economic resources are available.
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Tabata R, Kawaguchi F, Sasazaki S, Yamamoto Y, Rakotondraparany F, Ratsoavina FM, Yonezawa T, Mannen H. Phylogeographic Analysis of Madagascan Goats Using mtDNA Control Region and SRY Gene Sequences. Zoolog Sci 2019; 36:294-298. [DOI: 10.2108/zs180184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/21/2019] [Indexed: 11/17/2022]
Affiliation(s)
- Risa Tabata
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Yoshio Yamamoto
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Felix Rakotondraparany
- Mention Zoologie et Biodiversité Animale, Faculty of Sciences, Antananarivo University, BP 906 Ankatso, Antananarivo 101, Madagascar
| | - Fanomezana Mihaja Ratsoavina
- Mention Zoologie et Biodiversité Animale, Faculty of Sciences, Antananarivo University, BP 906 Ankatso, Antananarivo 101, Madagascar
| | - Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa 243-0034, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
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Silva-Jarquin JC, Román-Ponce SI, Durán-Aguilar M, Vera-Ávila HR, Cambrón-Sandoval VH, Andrade-Montemayor HM. Morphostructural Characterization of the Black Creole Goat Raised in Central Mexico, a Currently Threatened Zoogenetic Resource. Animals (Basel) 2019; 9:E459. [PMID: 31330979 PMCID: PMC6680401 DOI: 10.3390/ani9070459] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/13/2019] [Accepted: 07/15/2019] [Indexed: 11/16/2022] Open
Abstract
In order to evaluate the morphostructural variability of the Black Creole goat (BCG), the present study was carried out in a population of 226 animals from eight localities and 14 morphometric variables were taken. Descriptive statistics for the variables were obtained and 10 of these presented variation coefficients of less than 10%. The degree of harmony in the morphology of the population was determined by the number of positive correlations with significant differences (p < 0.05), including a correlation test using Spearman's method. In order to reduce the matrix of variables, a principal components analysis was performed, and it was evaluated based on Kaiser's criteria (eigenvalue > 1). Finally, a hierarchical analysis of conglomerates using Ward's method was performed using the Euclidean distance to evaluate the distances among localities. Morphometric variables were also included to visualize the relationship among the localities and their average per variable. The results showed that the animals evaluated presented a certain degree of homogeneity and maintained a highly harmonic model. The BCG population showed a high aptitude for milk production, which confirmed the zootechnical purpose of the breed. The BCG populations evaluated maintain similar morphostructural profiles specific to them that can distinguish this population from other animal breeds.
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Affiliation(s)
- Juan Carlos Silva-Jarquin
- Doctorado en Ciencias Biológicas, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro. Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro, C.P. 76230, México
| | - Sergio Iván Román-Ponce
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal. INIFAP-SADER. Km. 1 Carretera a Colón, Ajuchitlán, Querétaro, C.P. 76280, México
| | - Marina Durán-Aguilar
- Licenciatura en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro. Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro, C.P. 76230, México
| | - Héctor Raymundo Vera-Ávila
- Licenciatura en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro. Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro, C.P. 76230, México
| | - Víctor Hugo Cambrón-Sandoval
- Licenciatura en Horticultura Ambiental, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro. Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro, C.P. 76230, México
| | - Héctor Mario Andrade-Montemayor
- Licenciatura en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro. Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro, C.P. 76230, México.
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Tarekegn GM, Wouobeng P, Jaures KS, Mrode R, Edea Z, Liu B, Zhang W, Mwai OA, Dessie T, Tesfaye K, Strandberg E, Berglund B, Mutai C, Osama S, Wolde AT, Birungi J, Djikeng A, Meutchieye F. Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics. PLoS One 2019; 14:e0214843. [PMID: 31002664 PMCID: PMC6474588 DOI: 10.1371/journal.pone.0214843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 03/21/2019] [Indexed: 11/18/2022] Open
Abstract
Indigenous goats make significant contributions to Cameroon’s national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest HO (0.335±0.13) and HE (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest HO (0.401±0.12) and HE (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high FIS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average FST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.
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Affiliation(s)
- Getinet Mekuriaw Tarekegn
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
- * E-mail: (GMT); (FM)
| | - Patrick Wouobeng
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
- Faculty of Agronomy and Agriculture, University of Dschang, Dschang, Cameroon
| | - Kouam Simo Jaures
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
- Faculty of Agronomy and Agriculture, University of Dschang, Dschang, Cameroon
| | - Raphael Mrode
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju, Korea
| | - Bin Liu
- Nei Mongol BioNew Technology Co.Ltd, Hohhot, China
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Okeyo Ally Mwai
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Erling Strandberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Britt Berglund
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Collins Mutai
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Sarah Osama
- The University of Queensland, Queensland, Australia
| | - Asaminew Tassew Wolde
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Josephine Birungi
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Appolinaire Djikeng
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
- Centre for Tropical Livestock Genetics and Health, The University of Edinburgh, Scotland, United Kingdom
| | - Félix Meutchieye
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
- Faculty of Agronomy and Agriculture, University of Dschang, Dschang, Cameroon
- * E-mail: (GMT); (FM)
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New world goat populations are a genetically diverse reservoir for future use. Sci Rep 2019; 9:1476. [PMID: 30728441 PMCID: PMC6365549 DOI: 10.1038/s41598-019-38812-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/30/2018] [Indexed: 01/02/2023] Open
Abstract
Western hemisphere goats have European, African and Central Asian origins, and some local or rare breeds are reported to be adapted to their environments and economically important. By-in-large these genetic resources have not been quantified. Using 50 K SNP genotypes of 244 animals from 12 goat populations in United States, Costa Rica, Brazil and Argentina, we evaluated the genetic diversity, population structure and selective sweeps documenting goat migration to the "New World". Our findings suggest the concept of breed, particularly among "locally adapted" breeds, is not a meaningful way to characterize goat populations. The USA Spanish goats were found to be an important genetic reservoir, sharing genomic composition with the wild ancestor and with specialized breeds (e.g. Angora, Lamancha and Saanen). Results suggest goats in the Americas have substantial genetic diversity to use in selection and promote environmental adaptation or product driven specialization. These findings highlight the importance of maintaining goat conservation programs and suggest an awaiting reservoir of genetic diversity for breeding and research while simultaneously discarding concerns about breed designations.
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Tabata R, Kawaguchi F, Sasazaki S, Yamamoto Y, Bakhtin M, Kazymbet P, Meldevekob A, Suleimenov MZ, Nishibori M, Mannen H. The Eurasian Steppe is an important goat propagation route: A phylogeographic analysis using mitochondrial DNA and Y-chromosome sequences of Kazakhstani goats. Anim Sci J 2018; 90:317-322. [PMID: 30586684 DOI: 10.1111/asj.13144] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 11/28/2022]
Abstract
Goats (Capra hircus) were domesticated in the Fertile Crescent and propagated all over the world. The Silk Road through the Eurasian Steppe belt is a possible propagation route for domestic goats to Central Asia. Kazakhstan is in close geographical proximity to domestication centers and covers the majority of the Eurasian Steppe belt. In this study, we examined the genetic diversity and phylogeographic structure of Kazakhstani goats. The mtDNA sequences of 141 Kazakhstani goats were categorized into haplogroups A, C, and D, of which haplogroup A was predominant (97%), whereas haplogroups C and D were detected at low frequencies (1.4% each). The Kazakhstani haplotypes C were thzen categorized into Asian mtDNA type. Sequence analysis of the SRY gene on the Y-chromosome in 67 male Kazakhstani goats revealed two haplotypes: Y1A (64%) and Y2A (36%). Analysis of the distribution of mtDNA haplogroups and SRY haplotypes from Eurasia and Africa demonstrated genetic similarity among animals from Kazakhstan, Mongolia, and Northwest China located on the Eurasian Steppe belt. These phylogeographic results suggested that the Eurasian Steppe belt was an important propagation route for goats to Central Asia.
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Affiliation(s)
- Risa Tabata
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yoshio Yamamoto
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Meirat Bakhtin
- Radiobiology Scientific Center, Astana Medical University, Astana, Kazakhstan
| | - Polat Kazymbet
- Radiobiology Scientific Center, Astana Medical University, Astana, Kazakhstan
| | | | | | - Masahide Nishibori
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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Bertolini F, Cardoso TF, Marras G, Nicolazzi EL, Rothschild MF, Amills M. Genome-wide patterns of homozygosity provide clues about the population history and adaptation of goats. Genet Sel Evol 2018; 50:59. [PMID: 30449279 PMCID: PMC6241033 DOI: 10.1186/s12711-018-0424-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 10/15/2018] [Indexed: 01/15/2023] Open
Abstract
Background Patterns of homozygosity can be influenced by several factors, such as demography, recombination, and selection. Using the goat SNP50 BeadChip, we genotyped 3171 goats belonging to 117 populations with a worldwide distribution. Our objectives were to characterize the number and length of runs of homozygosity (ROH) and to detect ROH hotspots in order to gain new insights into the consequences of neutral and selection processes on the genome-wide homozygosity patterns of goats. Results The proportion of the goat genome covered by ROH is, in general, less than 15% with an inverse relationship between ROH length and frequency i.e. short ROH (< 3 Mb) are the most frequent ones. Our data also indicate that ~ 60% of the breeds display low FROH coefficients (< 0.10), while ~ 30 and ~ 10% of the goat populations show moderate (0.10 < FROH < 0.20) or high (> 0.20) FROH values. For populations from Asia, the average number of ROH is smaller and their coverage is lower in goats from the Near East than in goats from Central Asia, which is consistent with the role of the Fertile Crescent as the primary centre of goat domestication. We also observed that local breeds with small population sizes tend to have a larger fraction of the genome covered by ROH compared to breeds with tens or hundreds of thousands of individuals. Five regions on three goat chromosomes i.e. 11, 12 and 18, contain ROH hotspots that overlap with signatures of selection. Conclusions Patterns of homozygosity (average number of ROH of 77 and genome coverage of 248 Mb; FROH < 0.15) are similar in goats from different geographic areas. The increased homozygosity in local breeds is the consequence of their small population size and geographic isolation as well as of founder effects and recent inbreeding. The existence of three ROH hotspots that co-localize with signatures of selection demonstrates that selection has also played an important role in increasing the homozygosity of specific regions in the goat genome. Finally, most of the goat breeds analysed in this work display low levels of homozygosity, which is favourable for their genetic management and viability. Electronic supplementary material The online version of this article (10.1186/s12711-018-0424-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA. .,National Institute of Aquatic Resources, Technical University of Denmark (DTU), Lyngby, 2800, Denmark.
| | - Tainã Figueiredo Cardoso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus, Universitat Autonoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Gabriele Marras
- Fondazione Parco Tecnologico Padano (PTP), 26900, Lodi, Italy
| | | | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus, Universitat Autonoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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Colli L, Milanesi M, Talenti A, Bertolini F, Chen M, Crisà A, Daly KG, Del Corvo M, Guldbrandtsen B, Lenstra JA, Rosen BD, Vajana E, Catillo G, Joost S, Nicolazzi EL, Rochat E, Rothschild MF, Servin B, Sonstegard TS, Steri R, Van Tassell CP, Ajmone-Marsan P, Crepaldi P, Stella A. Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes. Genet Sel Evol 2018; 50:58. [PMID: 30449284 PMCID: PMC6240949 DOI: 10.1186/s12711-018-0422-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/15/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats. RESULTS A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows. CONCLUSIONS After domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.
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Affiliation(s)
- Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy. .,BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, Piacenza, Italy.
| | - Marco Milanesi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,School of Veterinary Medicine, Department of Support, Production and Animal Health, São Paulo State University (UNESP), Araçatuba, Brazil
| | - Andrea Talenti
- Dipartimento di Medicina Veterinaria, University of Milan, Milan, Italy
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, USA.,National Institute of Aquatic Resources, Technical University of Denmark, DTU, Lyngby, Denmark
| | - Minhui Chen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Århus, Denmark.,Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alessandra Crisà
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Kevin Gerard Daly
- Population Genetics Lab, Smurfit Institute of Genetics, Trinity College of Dublin, Dublin, Ireland
| | - Marcello Del Corvo
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Århus, Denmark
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Elia Vajana
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gennaro Catillo
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Bertrand Servin
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France
| | | | - Roberto Steri
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Paolo Ajmone-Marsan
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, University of Milan, Milan, Italy
| | - Alessandra Stella
- Fondazione Parco Tecnologico Padano, Lodi, Italy.,Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Milan, Italy
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Ouchene-Khelifi NA, Lafri M, Pompanon F, Ouhrouch A, Ouchene N, Blanquet V, Lenstra JA, Benjelloun B, Da Silva A. Genetic homogeneity of North-African goats. PLoS One 2018; 13:e0202196. [PMID: 30114267 PMCID: PMC6095539 DOI: 10.1371/journal.pone.0202196] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 07/30/2018] [Indexed: 11/18/2022] Open
Abstract
North Africa represents a rich and early reservoir of goat genetic diversity, from which the main African breeds have been derived. In this study, the genetic diversity of four indigenous Algerian goat breeds (i.e., Arabia, Makatia, M’Zabite and Kabyle, with n = 12 for each breed) has been investigated for the first time by genome-wide SNP genotyping; moreover in a broader context, genetic structuration of Algerian and Moroccan goats was explored (via FST, MDS, STRUCTURE, FineSTRUCTURE, BAPS, sPCA and DAPC analyses). At national level, the study revealed high level of genetic diversity and a significant phenomenon of admixture affecting all the Algerian breeds. At broader scale, clear global genetic homogeneity appeared considering both Algerian and Moroccan stocks. Indeed, genetic structuration was almost nonexistent among Arabia (from Algeria), Draa, Black and Nord (from Morocco), while the ancestral Kabyle and M’Zabite breeds, reared by Berber peoples, showed genetic distinctness. The study highlighted the threat to the Maghrebin stock, probably induced by unsupervised cross-breeding practices which have intensified in recent centuries. Moreover, it underlined the necessity to deepen our understanding of the genetic resources represented by the resilient North-African goat stock.
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Affiliation(s)
- Nadjet-Amina Ouchene-Khelifi
- Science Veterinary Institute, University of Blida, Blida, Algeria
- Laboratory of Biotechnology related to Animal Reproduction (LBRA), University of Blida, Blida, Algeria
| | - Mohamed Lafri
- Science Veterinary Institute, University of Blida, Blida, Algeria
- Laboratory of Biotechnology related to Animal Reproduction (LBRA), University of Blida, Blida, Algeria
| | - François Pompanon
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Abdessamad Ouhrouch
- National Institute of Agronomic Research (INRA Maroc), Regional Center of Agronomic Research, Beni Mellal, Morocco
- Laboratoire de Biotechnologies et Valorisation des Ressources Phytogénétiques (LBVRP), Université Sultan Moulay Slimane, Béni Mellal, Maroc
| | - Nassim Ouchene
- Science Veterinary Institute, University of Blida, Blida, Algeria
- Laboratory of Biotechnology related to Animal Reproduction (LBRA), University of Blida, Blida, Algeria
| | | | | | - Badr Benjelloun
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
- National Institute of Agronomic Research (INRA Maroc), Regional Center of Agronomic Research, Beni Mellal, Morocco
| | - Anne Da Silva
- Univ. Limoges, INRA, EA7500, USC1061 GAMAA, Limoges, France
- * E-mail:
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31
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El Moutchou N, González A, Chentouf M, Lairini K, Muñoz-Mejías ME, Rodero E. Exploring the genetic diversity and relationships between Spanish and Moroccan goats using microsatellite markers. Small Rumin Res 2018. [DOI: 10.1016/j.smallrumres.2018.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Fantazi K, Migliore S, Kdidi S, Racinaro L, Tefiel H, Boukhari R, Federico G, Di Marco Lo Presti V, Gaouar SBS, Vitale M. Analysis of differences in prion protein gene ( PRNP) polymorphisms between Algerian and Southern Italy's goats. ITALIAN JOURNAL OF ANIMAL SCIENCE 2018. [DOI: 10.1080/1828051x.2017.1420430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Khaled Fantazi
- National Institute of Agronomic Research, Animal Productions Division – INRA Algeria, Algiers, Algeria
| | - Sergio Migliore
- Istituto Zooprofilattico Sperimentale della Sicilia, Adelmo Mirri, Palermo, Italy
| | - Samia Kdidi
- Animal Molecular Genetics Livestock and Wildlife Laboratory, Arid Land Institute, Medenine, Tunisia
| | - Luca Racinaro
- Superior National Veterinary School, El-Harrach, Algiers, Algeria
| | - Hakim Tefiel
- Superior National Veterinary School, El-Harrach, Algiers, Algeria
| | - Rachid Boukhari
- Physiopathology and Biochemistry of Nutrition laboratory (PpBioNut), University Abou Bekr Belkaid, Tlemcen, Algeria
| | - Giovanni Federico
- Istituto Zooprofilattico Sperimentale of Mezzogiorno, sezione di Reggio Calabria, Catona, RC, Italy
| | | | - Semir Bechir Suheil Gaouar
- Physiopathology and Biochemistry of Nutrition laboratory (PpBioNut), University Abou Bekr Belkaid, Tlemcen, Algeria
| | - Maria Vitale
- Istituto Zooprofilattico Sperimentale della Sicilia, Adelmo Mirri, Palermo, Italy
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Genetic homogeneity of goat malaria parasites in Asia and Africa suggests their expansion with domestic goat host. Sci Rep 2018; 8:5827. [PMID: 29643434 PMCID: PMC5895593 DOI: 10.1038/s41598-018-24048-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/26/2018] [Indexed: 11/12/2022] Open
Abstract
Plasmodium was first identified in a goat in Angola in 1923, and only recently characterized by DNA isolation from a goat blood sample in Zambia. Goats were first domesticated in the Fertile Crescent approximately 10,000 years ago, and are now globally distributed. It is not known if the Plasmodium identified in African goats originated from parasites circulating in the local ungulates, or if it co-evolved in the goat before its domestication. To address this question, we performed PCR-based surveillance using a total of 1,299 goat blood samples collected from Sudan and Kenya in Africa, Iran in west Asia, and Myanmar and Thailand in southeast Asia. Plasmodium DNA was detected from all locations, suggesting that the parasite is not limited to Africa, but widely distributed. Whole mitochondrial DNA sequences revealed that there was only one nucleotide substitution between Zambian/Kenyan samples and others, supporting the existence of a goat-specific Plasmodium species, presumably Plasmodium caprae, rather than infection of goats by local ungulate malaria parasites. We also present the first photographic images of P. caprae, from one Kenyan goat sample.
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34
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Convergent genomic signatures of domestication in sheep and goats. Nat Commun 2018; 9:813. [PMID: 29511174 PMCID: PMC5840369 DOI: 10.1038/s41467-018-03206-y] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/29/2018] [Indexed: 12/15/2022] Open
Abstract
The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species. The sheep and goat were domesticated ~10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.
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35
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Onzima RB, Upadhyay MR, Mukiibi R, Kanis E, Groenen MAM, Crooijmans RPMA. Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds. Anim Genet 2018; 49:59-70. [PMID: 29344947 PMCID: PMC5838551 DOI: 10.1111/age.12631] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2017] [Indexed: 12/18/2022]
Abstract
Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium‐density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO) and expected (HE) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub‐structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within‐breed diversity and heterozygote advantage in crossbreeding schemes.
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Affiliation(s)
- R B Onzima
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands.,National Agricultural Research Organization (NARO), P O Box 295, Entebbe, Uganda
| | - M R Upadhyay
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - R Mukiibi
- Department of Agriculture, Food and Nutritional Sciences (AFNS), Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, 1416 College Plaza Edmonton, T6G 2C8, Alberta, Canada
| | - E Kanis
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands
| | - M A M Groenen
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands
| | - R P M A Crooijmans
- Wageningen University & Research, Animal Breeding and Genomics, P O Box 338, 6700AH, Wageningen, The Netherlands
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Abstract
Goats have played a key role as source of nourishment for humans in their expansion all over the world in long land and sea trips. This has guaranteed a place for this species in the important and rapid episode of livestock expansion triggered by Columbus' arrival in the Americas in the late 1400s. The aims of this study are to provide a comprehensive perspective on genetic diversity in American goat populations and to assess their origins and evolutionary trajectories. This was achieved by combining data from autosomal neutral genetic markers obtained in more than two thousand samples that encompass a wide range of Iberian, African and Creole goat breeds. In general, even though Creole populations differ clearly from each other, they lack a strong geographical pattern of differentiation, such that populations of different admixed ancestry share relatively close locations throughout the large geographical range included in this study. Important Iberian signatures were detected in most Creole populations studied, and many of them, particularly the Cuban Creole, also revealed an important contribution of African breeds. On the other hand, the Brazilian breeds showed a particular genetic structure and were clearly separated from the other Creole populations, with some influence from Cape Verde goats. These results provide a comprehensive characterisation of the present structure of goat genetic diversity, and a dissection of the Iberian and African influences that gave origin to different Creole caprine breeds, disentangling an important part of their evolutionary history. Creole breeds constitute an important reservoir of genetic diversity that justifies the development of appropriate management systems aimed at improving performance without loss of genomic diversity.
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Al-Araimi NA, Al-Atiyat RM, Gaafar OM, Vasconcelos R, Luzuriaga-Neira A, Eisa MO, Amir N, Benaissa MH, Alfaris AA, Aljumaah RS, Elnakhla SM, Salem MM, Ishag IA, El Khasmi M, Beja-Pereira A. Maternal genetic diversity and phylogeography of native Arabian goats. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.09.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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38
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Vidal O, Drögemüller C, Obexer-Ruff G, Reber I, Jordana J, Martínez A, Bâlteanu VA, Delgado JV, Eghbalsaied S, Landi V, Goyache F, Traoré A, Pazzola M, Vacca GM, Badaoui B, Pilla F, D'Andrea M, Álvarez I, Capote J, Sharaf A, Pons À, Amills M. Differential distribution of Y-chromosome haplotypes in Swiss and Southern European goat breeds. Sci Rep 2017; 7:16161. [PMID: 29170508 PMCID: PMC5701018 DOI: 10.1038/s41598-017-15593-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/27/2017] [Indexed: 11/09/2022] Open
Abstract
The analysis of Y-chromosome variation has provided valuable clues about the paternal history of domestic animal populations. The main goal of the current work was to characterize Y-chromosome diversity in 31 goat populations from Central Eastern (Switzerland and Romania) and Southern Europe (Spain and Italy) as well as in reference populations from Africa and the Near East. Towards this end, we have genotyped seven single nucleotide polymorphisms (SNPs), mapping to the SRY, ZFY, AMELY and DDX3Y Y-linked loci, in 275 bucks from 31 populations. We have observed a low level of variability in the goat Y-chromosome, with just five haplotypes segregating in the whole set of populations. We have also found that Swiss bucks carry exclusively Y1 haplotypes (Y1A: 24%, Y1B1: 15%, Y1B2: 43% and Y1C: 18%), while in Italian and Spanish bucks Y2A is the most abundant haplotype (77%). Interestingly, in Carpathian goats from Romania the Y2A haplotype is also frequent (42%). The high Y-chromosome differentiation between Swiss and Italian/Spanish breeds might be due to the post-domestication spread of two different Near Eastern genetic stocks through the Danubian and Mediterranean corridors. Historical gene flow between Southern European and Northern African goats might have also contributed to generate such pattern of genetic differentiation.
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Affiliation(s)
- Oriol Vidal
- Departament de Biologia, Universitat de Girona, 17003, Girona, Spain.
| | - Cord Drögemüller
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | | | - Irene Reber
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Valentin Adrian Bâlteanu
- Institute of Life Sciences, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine, 400372, Cluj-Napoca, Romania
| | | | - Shahin Eghbalsaied
- Transgenesis Center of Excellence, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
| | - Vincenzo Landi
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Felix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, Gijón, 33394, Spain
| | - Amadou Traoré
- Institut de l'Environnement et Recherches Agricoles, 04 BP 8645, Ouagadougou, 04, Burkina Faso
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
| | | | - Bouabid Badaoui
- University Mohammed V, Agdal, Faculty of Sciences, 4 Av. Ibn Battota, Rabat, Morocco
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università Degli Studi Del Molise, Campobasso, Italy
| | - Mariasilvia D'Andrea
- Dipartimento Agricoltura, Ambiente e Alimenti, Università Degli Studi Del Molise, Campobasso, Italy
| | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, Gijón, 33394, Spain
| | - Juan Capote
- Instituto Canario de Investigaciones Agrarias, Canary Islands, Tenerife, La Laguna 38108, Spain
| | - Abdoallah Sharaf
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czechia.,Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Àgueda Pons
- Unitat de Races Autòctones, Servei de Millora Agrària, (SEMILLA-SAU), Son Ferriol, 07198, Spain
| | - Marcel Amills
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
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Amills M, Capote J, Tosser-Klopp G. Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing pieces. Anim Genet 2017; 48:631-644. [PMID: 28872195 DOI: 10.1111/age.12598] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2017] [Indexed: 12/23/2022]
Abstract
Domestic goats (Capra hircus) are spread across the five continents with a census of 1 billion individuals. The worldwide population of goats descends from a limited number of bezoars (Capra aegagrus) domesticated 10 000 YBP (years before the present) in the Fertile Crescent. The extraordinary adaptability and hardiness of goats favoured their rapid spread over the Old World, reaching the Iberian Peninsula and Southern Africa 7000 YBP and 2000 YBP respectively. Molecular studies have revealed one major mitochondrial haplogroup A and five less frequent haplogroups B, C, D, F and G. Moreover, the analysis of autosomal and Y-chromosome markers has evidenced an appreciable geographic differentiation. The implementation of new molecular technologies, such as whole-genome sequencing and genome-wide genotyping, allows for the exploration of caprine diversity at an unprecedented scale, thus providing new insights into the evolutionary history of goats. In spite of a number of pitfalls, the characterization of the functional elements of the goat genome is expected to play a key role in understanding the genetic determination of economically relevant traits. Genomic selection and genome editing also hold great potential, particularly for improving traits that cannot be modified easily by traditional selection.
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Affiliation(s)
- M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - J Capote
- Instituto Canario de Investigaciones Agrarias, La Laguna, 38108, Tenerife, Spain
| | - G Tosser-Klopp
- INRA-GenPhySE-Génétique, Physiologie et Systèmes d'Elevage-UMR1388, 24 Chemin de Borde Rouge-Auzeville CS 52627, 31326, Castanet Tolosan Cedex, France
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40
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Martínez A, Manunza A, Delgado JV, Landi V, Adebambo A, Ismaila M, Capote J, El Ouni M, Elbeltagy A, Abushady AM, Galal S, Ferrando A, Gómez M, Pons A, Badaoui B, Jordana J, Vidal O, Amills M. Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach. Sci Rep 2016; 6:38935. [PMID: 27966592 PMCID: PMC5155231 DOI: 10.1038/srep38935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 11/16/2016] [Indexed: 12/23/2022] Open
Abstract
Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds.
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Affiliation(s)
- Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | - Arianna Manunza
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | | | - Vincenzo Landi
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | - Ayotunde Adebambo
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta PMB 2240, Nigeria
| | - Muritala Ismaila
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta PMB 2240, Nigeria
| | - Juan Capote
- Instituto Canario de Investigaciones Agrarias, La Laguna 38108, Tenerife, Spain
| | - Mabrouk El Ouni
- Livestock & Wildlife Laboratory, Arid Land Institute Medenine, 4119 Médenine, Tunisia
| | - Ahmed Elbeltagy
- Department of Animal Biotechnology, Animal Production Research Institute, Dokki, Giza, Egypt
| | - Asmaa M. Abushady
- Genetics Department, Faculty of Agriculture, Ain Shams University, Shubra 11241, Cairo, Egypt
| | - Salah Galal
- Animal Production Department, Faculty of Agriculture, Ain Shams University, Abbassia 11566, Cairo, Egypt
| | - Ainhoa Ferrando
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Mariano Gómez
- Servicio de Ganadería. Diputación Foral de Bizkaia. Avda. Lehendakari Aguirre n° 9-2°, 48014 Bilbao, Spain
| | - Agueda Pons
- Unitat de Races Autòctones, Servei de Millora Agrària, (SEMILLA-SAU), Son Ferriol 07198, Spain
| | - Bouabid Badaoui
- University Mohammed V, Agdal, Faculty of Sciences, 4 Av. Ibn Battota, Rabat, Morocco
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Oriol Vidal
- Departament de Biologia, Universitat de Girona, Girona 17071, Spain
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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41
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Manunza A, Noce A, Serradilla JM, Goyache F, Martínez A, Capote J, Delgado JV, Jordana J, Muñoz E, Molina A, Landi V, Pons A, Balteanu V, Traoré A, Vidilla M, Sánchez-Rodríguez M, Sànchez A, Cardoso TF, Amills M. A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds. Genet Sel Evol 2016; 48:52. [PMID: 27455838 PMCID: PMC4960707 DOI: 10.1186/s12711-016-0229-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/29/2016] [Indexed: 12/19/2022] Open
Abstract
Background The main goal of the current work was to infer the demographic history of seven Spanish goat breeds (Malagueña, Murciano-Granadina, Florida, Palmera, Mallorquina, Bermeya and Blanca de Rasquera) based on genome-wide diversity data generated with the Illumina Goat SNP50 BeadChip (population size, N = 176). Five additional populations from Europe (Saanen and Carpathian) and Africa (Tunisian, Djallonké and Sahel) were also included in this analysis (N = 80) for comparative purposes. Results Our results show that the genetic background of Spanish goats traces back mainly to European breeds although signs of North African admixture were detected in two Andalusian breeds (Malagueña and Murciano-Granadina). In general, observed and expected heterozygosities were quite similar across the seven Spanish goat breeds under analysis irrespective of their population size and conservation status. For the Mallorquina and Blanca de Rasquera breeds, which have suffered strong population declines during the past decades, we observed increased frequencies of large-sized (ROH), a finding that is consistent with recent inbreeding. In contrast, a substantial part of the genome of the Palmera goat breed comprised short ROH, which suggests a strong and ancient founder effect. Conclusions Admixture with African goats, genetic drift and inbreeding have had different effects across the seven Spanish goat breeds analysed in the current work. This has generated distinct patterns of genome-wide diversity that provide new clues about the demographic history of these populations. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0229-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arianna Manunza
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antonia Noce
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | | | - Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, Gijón, 33394, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Juan Capote
- Instituto Canario de Investigaciones Agrarias, 38108, La Laguna, Tenerife, Spain
| | | | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Eva Muñoz
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Vincenzo Landi
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Agueda Pons
- Unitat de Races Autòctones, Servei de Millora Agrària i Pesquera (SEMILLA), 07198, Son Ferriol, Spain
| | - Valentin Balteanu
- Faculty of Animal Science and Biotechnologies and Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine, 400372, Cluj-Napoca, Romania
| | - Amadou Traoré
- Institut de l'Environnement et Recherches Agricoles, 04 BP 8645, Ouagadougou 04, Burkina Faso
| | - Montse Vidilla
- Associació de Ramaders de Cabra Blanca de Rasquera, Rasquera, 43513, Spain
| | | | - Armand Sànchez
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Tainã Figueiredo Cardoso
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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42
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Visser C, Lashmar SF, Van Marle-Köster E, Poli MA, Allain D. Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data. PLoS One 2016; 11:e0154353. [PMID: 27171175 PMCID: PMC4865245 DOI: 10.1371/journal.pone.0154353] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/12/2016] [Indexed: 11/18/2022] Open
Abstract
The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations.
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Affiliation(s)
- Carina Visser
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
- * E-mail:
| | - Simon F. Lashmar
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | - Este Van Marle-Köster
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | - Mario A. Poli
- Instituto de Genética “Ewald Favret”, CICVyA-INTA, Hurlingham, Argentina
| | - Daniel Allain
- INRA, UMR1388 GenPhySe, CS52627, Castanet Tolosan, France
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43
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Zhang Y, Lu Y, Yindee M, Li K, Kuo H, Ju Y, Ye S, Faruque MO, Li Q, Wang Y, Cuong VC, Pham LD, Bouahom B, Yang B, Liang X, Cai Z, Vankan D, Manatchaiworakul W, Kowlim N, Duangchantrasiri S, Wajjwalku W, Colenbrander B, Zhang Y, Beerli P, Lenstra JA, Barker JSF. Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region. Mol Ecol 2016; 25:1530-50. [DOI: 10.1111/mec.13518] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 11/30/2015] [Accepted: 12/10/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Yi Zhang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Yongfang Lu
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Marnoch Yindee
- Department of Clinical Science and Public Health Faculty of Veterinary Science Mahidol University Kanchanaburi Campus Kanchanaburi 71150 Thailand
| | - Kuan‐Yi Li
- Department of Animal Science and Technology National Taiwan University Taipei 10673 Taiwan
| | - Hsiao‐Yun Kuo
- Livestock Research Institute Council of Agriculture Tainan 71246 Taiwan
| | - Yu‐Ten Ju
- Department of Animal Science and Technology National Taiwan University Taipei 10673 Taiwan
| | - Shaohui Ye
- College of Animal Science and Technology Yunnan Agricultural University Kunming 650201 China
| | - Md Omar Faruque
- Department of Animal Breeding and Genetics Bangladesh Agricultural University Mymensingh 2202 Bangladesh
| | - Qiang Li
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Vu Chi Cuong
- Key Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 Vietnam
| | - Lan Doan Pham
- Key Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 Vietnam
| | - Bounthong Bouahom
- National Agriculture and Forestry Research Institute P.O. Box 811 Vientiane Capital Lao P.D.R
| | - Bingzhuang Yang
- Guangxi Buffalo Research Institute Chinese Academy of Agriculture Sciences Nanning 530001 China
| | - Xianwei Liang
- Guangxi Buffalo Research Institute Chinese Academy of Agriculture Sciences Nanning 530001 China
| | - Zhihua Cai
- College of Animal Science Anhui Science and Technology University Fengyang 233100 China
| | - Dianne Vankan
- The School of Veterinary Science University of Queensland, Gatton Campus Gatton Qld 4343 Australia
| | - Wallaya Manatchaiworakul
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Nonglid Kowlim
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Somphot Duangchantrasiri
- Khao‐Nang‐Ram Wildlife Research Station Department of National Parks Wildlife and Plant Conservation Bangkok 10900 Thailand
| | - Worawidh Wajjwalku
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Ben Colenbrander
- Faculty of Veterinary Medicine Utrecht University Yalelaan 104 3584 CM Utrecht The Netherlands
| | - Yuan Zhang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Peter Beerli
- Department of Scientific Computing Florida State University Tallahassee FL 32306‐4120 USA
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine Utrecht University Yalelaan 104 3584 CM Utrecht The Netherlands
| | - J. Stuart F. Barker
- School of Environmental and Rural Science University of New England Armidale NSW 2351 Australia
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Resende A, Gonçalves J, Muigai AWT, Pereira F. Mitochondrial DNA variation of domestic sheep (Ovis aries) in Kenya. Anim Genet 2016; 47:377-81. [DOI: 10.1111/age.12412] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Adriana Resende
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR); University of Porto; Rua dos Bragas 289 Porto 4050-123 Portugal
| | - Joana Gonçalves
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP); Rua Dr. Roberto Frias s/n Porto 4200-465 Portugal
| | - Anne W. T. Muigai
- Jomo Kenyatta University of Agriculture and Technology; P.O. Box 62000 Nairobi 00200 Kenya
| | - Filipe Pereira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR); University of Porto; Rua dos Bragas 289 Porto 4050-123 Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP); Rua Dr. Roberto Frias s/n Porto 4200-465 Portugal
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45
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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: 51] [Impact Index Per Article: 5.7] [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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46
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Bruford MW, Ginja C, Hoffmann I, Joost S, Orozco-terWengel P, Alberto FJ, Amaral AJ, Barbato M, Biscarini F, Colli L, Costa M, Curik I, Duruz S, Ferenčaković M, Fischer D, Fitak R, Groeneveld LF, Hall SJG, Hanotte O, Hassan FU, Helsen P, Iacolina L, Kantanen J, Leempoel K, Lenstra JA, Ajmone-Marsan P, Masembe C, Megens HJ, Miele M, Neuditschko M, Nicolazzi EL, Pompanon F, Roosen J, Sevane N, Smetko A, Štambuk A, Streeter I, Stucki S, Supakorn C, Telo Da Gama L, Tixier-Boichard M, Wegmann D, Zhan X. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Front Genet 2015; 6:314. [PMID: 26539210 PMCID: PMC4612686 DOI: 10.3389/fgene.2015.00314] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022] Open
Abstract
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.
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Affiliation(s)
- Michael W Bruford
- School of Biosciences, Cardiff University Cardiff, UK ; Sustainable Places Research Institute, Cardiff University Cardiff, UK
| | - Catarina Ginja
- Faculdade de Ciências, Centro de Ecologia, Evolução e Alterações Ambientais (CE3C), Universidade de Lisboa Lisboa, Portugal ; Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão Portugal
| | - Irene Hoffmann
- Food and Agriculture Organization of the United Nations, Animal Genetic Resources Branch, Animal Production and Health Division Rome, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Florian J Alberto
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Andreia J Amaral
- Faculty of Sciences, BioISI- Biosystems and Integrative Sciences Institute, University of Lisbon Campo Grande, Portugal
| | - Mario Barbato
- School of Biosciences, Cardiff University Cardiff, UK
| | | | - Licia Colli
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Mafalda Costa
- School of Biosciences, Cardiff University Cardiff, UK
| | - Ino Curik
- Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - Solange Duruz
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Daniel Fischer
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland
| | - Robert Fitak
- Institut für Populationsgenetik Vetmeduni, Vienna, Austria
| | | | | | - Olivier Hanotte
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Faiz-Ul Hassan
- School of Life Sciences, University of Nottingham Nottingham, UK ; Department of Animal Breeding and Genetics, University of Agriculture Faisalabad, Pakistan
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp Antwerp, Belgium
| | - Laura Iacolina
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland ; Department of Biology, University of Eastern Finland Kuopio, Finland
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Paolo Ajmone-Marsan
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Charles Masembe
- Institute of the Environment and Natural Resources, Makerere University Kampala, Uganda
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands
| | - Mara Miele
- School of Planning and Geography, Cardiff University Cardiff, UK
| | | | | | - François Pompanon
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Jutta Roosen
- TUM School of Management, Technische Universität München Munich, Germany
| | - Natalia Sevane
- Department of Animal Production, Veterinary Faculty, Universidad Complutense de Madrid Madrid, Spain
| | | | - Anamaria Štambuk
- Department of Biology, Faculty of Science, University of Zagreb Zagreb, Croatia
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - China Supakorn
- School of Life Sciences, University of Nottingham Nottingham, UK ; School of Agricultural Technology, Walailak University Tha Sala, Thailand
| | - Luis Telo Da Gama
- Centre of Research in Animal Health (CIISA) - Faculty of Veterinary Medicine, University of Lisbon Lisbon, Portugal
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg Fribourg, Switzerland
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Beijing, China ; Cardiff University - Institute of Zoology, Joint Laboratory for Biocomplexity Research Beijing, China
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47
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Waki A, Sasazaki S, Kobayashi E, Mannen H. Paternal phylogeography and genetic diversity of East Asian goats. Anim Genet 2015; 46:337-9. [PMID: 25917305 DOI: 10.1111/age.12293] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2015] [Indexed: 11/28/2022]
Abstract
This study was a first analysis of paternal genetic diversity for extensive Asian domestic goats using SRY gene sequences. Sequencing comparison of the SRY 3'-untranslated region among 210 Asian goats revealed four haplotypes (Y1A, Y1B, Y2A and Y2B) derived from four variable sites including a novel substitution detected in this study. In Asian goats, the predominant haplotype was Y1A (62%) and second most common was Y2B (30%). Interestingly, the Y2B was a unique East Asian Y chromosomal variant, which differentiates eastern and western Eurasian goats. The SRY geographic distribution in Myanmar and Cambodia indicated predominant the haplotype Y1A in plains areas and a high frequency of Y2B in mountain areas. The results suggest recent genetic infiltration of modern breeds into South-East Asian goats and an ancestral SRY Y2B haplotype in Asian native goats.
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Affiliation(s)
- A Waki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
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48
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Benjelloun B, Alberto FJ, Streeter I, Boyer F, Coissac E, Stucki S, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Leempoel K, Alberti A, Engelen S, Chikhi A, Clarke L, Flicek P, Joost S, Taberlet P, Pompanon F. Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data. Front Genet 2015; 6:107. [PMID: 25904931 PMCID: PMC4387958 DOI: 10.3389/fgene.2015.00107] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/02/2015] [Indexed: 12/15/2022] Open
Abstract
Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extinction due to their substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial to characterize the neutral and adaptive genetic diversity of indigenous populations. A fine characterization of whole genome variation in farm animals is now possible by using new sequencing technologies. We sequenced the complete genome at 12× coverage of 44 goats geographically representative of the three phenotypically distinct indigenous populations in Morocco. The study of mitochondrial genomes showed a high diversity exclusively restricted to the haplogroup A. The 44 nuclear genomes showed a very high diversity (24 million variants) associated with low linkage disequilibrium. The overall genetic diversity was weakly structured according to geography and phenotypes. When looking for signals of positive selection in each population we identified many candidate genes, several of which gave insights into the metabolic pathways or biological processes involved in the adaptation to local conditions (e.g., panting in warm/desert conditions). This study highlights the interest of WGS data to characterize livestock genomic diversity. It illustrates the valuable genetic richness present in indigenous populations that have to be sustainably managed and may represent valuable genetic resources for the long-term preservation of the species.
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Affiliation(s)
- Badr Benjelloun
- Laboratoire d'Ecologie Alpine, Université Grenoble-Alpes Grenoble, France ; Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique Grenoble, France ; National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research Beni-Mellal, Morocco
| | - Florian J Alberto
- Laboratoire d'Ecologie Alpine, Université Grenoble-Alpes Grenoble, France ; Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique Grenoble, France
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute Hinxton, UK
| | - Frédéric Boyer
- Laboratoire d'Ecologie Alpine, Université Grenoble-Alpes Grenoble, France ; Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique Grenoble, France
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine, Université Grenoble-Alpes Grenoble, France ; Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique Grenoble, France
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Mohammed BenBati
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research Beni-Mellal, Morocco
| | - Mustapha Ibnelbachyr
- Regional Centre of Agronomic Research Errachidia, National Institute of Agronomic Research (INRA Maroc) Errachidia, Morocco
| | - Mouad Chentouf
- Regional Centre of Agronomic Research Tangier, National Institute of Agronomic Research (INRA Maroc) Tangier, Morocco
| | - Abdelmajid Bechchari
- Regional Centre of Agronomic Research Oujda, National Institute of Agronomic Research (INRA Maroc) Oujda, Morocco
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Adriana Alberti
- Centre National de Séquençage, CEA-Institut de Génomique Genoscope, Évry, France
| | - Stefan Engelen
- Centre National de Séquençage, CEA-Institut de Génomique Genoscope, Évry, France
| | - Abdelkader Chikhi
- Regional Centre of Agronomic Research Errachidia, National Institute of Agronomic Research (INRA Maroc) Errachidia, Morocco
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute Hinxton, UK
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, Université Grenoble-Alpes Grenoble, France ; Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique Grenoble, France
| | - François Pompanon
- Laboratoire d'Ecologie Alpine, Université Grenoble-Alpes Grenoble, France ; Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique Grenoble, France
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Cinar Kul B, Bilgen N, Lenstra JA, Korkmaz Agaoglu O, Akyuz B, Ertugrul O. Y-chromosomal variation of local goat breeds of Turkey close to the domestication centre. J Anim Breed Genet 2015; 132:449-53. [PMID: 25781056 DOI: 10.1111/jbg.12154] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/17/2015] [Indexed: 02/05/2023]
Abstract
Genetic variations in chromosome Y are enabling researchers to identify paternal lineages, which are informative for introgressions and migrations. In this study, the male-specific region markers, sex-determining region-Y (SRY), amelogenin (AMELY) and zinc finger (ZFY) were analysed in seven Turkish native goat breeds, Angora, Kilis, Hair, Honamlı, Norduz, Gürcü and Abaza. A SNP in the ZFY gene defined a new haplotype Y2C. All domestic haplogroups originate from Capra aegagrus, while the finding of Y1A, Y1B, Y2A and Y2C in 32, 4, 126 and 2 Turkish domestic goats, respectively, appears to indicate a predomestic origin of the major haplotypes. The occurrence of four haplotypes in the Hair goat and, in contrast, a frequency of 96% of Y1A in the Kilis breed illustrate that Y-chromosomal variants have a more breed-dependent distribution than mitochondrial or autosomal DNA. This probably reflects male founder effects, but a role in adaptation cannot be excluded.
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Affiliation(s)
- B Cinar Kul
- Department of Genetics, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
| | - N Bilgen
- Department of Genetics, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - O Korkmaz Agaoglu
- Department of Animal Science, Faculty of Veterinary Medicine, Mehmet Akif Ersoy University, Burdur, Turkey
| | - B Akyuz
- Department of Genetics, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - O Ertugrul
- Department of Genetics, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
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50
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Kim JH, Byun MJ, Choi SB, Suh S, Kim YS, Kim MJ, Ko YG, Cho CY. Detection of a distinct variation site for geographical classification of mitochondrial DNA haplogroup A in the domestic goat (Capra hircus). Genes Genomics 2014. [DOI: 10.1007/s13258-014-0204-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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