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Senczuk G, Mastrangelo S, Ajmone-Marsan P, Becskei Z, Colangelo P, Colli L, Ferretti L, Karsli T, Lancioni H, Lasagna E, Marletta D, Persichilli C, Portolano B, Sarti FM, Ciani E, Pilla F. On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data. Genet Sel Evol 2021; 53:48. [PMID: 34078254 PMCID: PMC8173809 DOI: 10.1186/s12711-021-00639-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022] Open
Abstract
Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00639-w.
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Affiliation(s)
- Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy.
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Paolo Ajmone-Marsan
- Department of Animal Science Food and Nutrition, DIANA, Nutrigenomics and Proteomics Research Centre, PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre, BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Zsolt Becskei
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine, Bulevar Oslobodjenja street 18, 11000, Belgrade, Serbia
| | - Paolo Colangelo
- National Council of Research (CNR), Research Institute On Terrestrial Ecosystems (IRET), Via Salaria km 29.300, Montelibretti, 00015, Rome, Italy
| | - Licia Colli
- Department of Animal Science Food and Nutrition, DIANA, Nutrigenomics and Proteomics Research Centre, PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre, BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Luca Ferretti
- Department of Biology and Biotechnology, University of Pavia, Italy, Pavia
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di sotto, 06123, Perugia, Italy
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Donata Marletta
- Department of Agriculture, Food and Environment, University of Catania, 95125, Catania, Italy
| | - Christian Persichilli
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Baldassare Portolano
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Francesca M Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Elena Ciani
- Department of Bioscience, Biotechnology and Biopharmaceuticals, University of Bari, 70124, Bari, Italy
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
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Patra AK, Kwon YM, Kang SG, Fujiwara Y, Kim SJ. The complete mitochondrial genome sequence of the tubeworm Lamellibrachia satsuma and structural conservation in the mitochondrial genome control regions of Order Sabellida. Mar Genomics 2016; 26:63-71. [PMID: 26776396 DOI: 10.1016/j.margen.2015.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/30/2015] [Accepted: 12/30/2015] [Indexed: 11/18/2022]
Abstract
The control region of the mitochondrial genomes shows high variation in conserved sequence organizations, which follow distinct evolutionary patterns in different species or taxa. In this study, we sequenced the complete mitochondrial genome of Lamellibrachia satsuma from the cold-seep region of Kagoshima Bay, as a part of whole genome study and extensively studied the structural features and patterns of the control region sequences. We obtained 15,037 bp of mitochondrial genome using Illumina sequencing and identified the non-coding AT-rich region or control region (354 bp, AT=83.9%) located between trnH and trnR. We found 7 conserved sequence blocks (CSB), scattered throughout the control region of L. satsuma and other taxa of Annelida. The poly-TA stretches, which commonly form the stem of multiple stem-loop structures, are most conserved in the CSB-I and CSB-II regions. The mitochondrial genome of L. satsuma encodes a unique repetitive sequence in the control region, which forms a unique secondary structure in comparison to Lamellibrachia luymesi. Phylogenetic analyses of all protein-coding genes indicate that L. satsuma forms a monophyletic clade with L. luymesi along with other tubeworms found in cold-seep regions (genera: Lamellibrachia, Escarpia, and Seepiophila). In general, the control region sequences of Annelida could be aligned with certainty within each genus, and to some extent within the family, but with a higher rate of variation in conserved regions.
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Affiliation(s)
- Ajit Kumar Patra
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea.
| | - Yong Min Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea.
| | - Sung Gyun Kang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea.
| | - Yoshihiro Fujiwara
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Japan.
| | - Sang-Jin Kim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea; National Marine Biodiversity Institute of Korea, Seocheon 325-902, Republic of Korea.
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Beja-Pereira A, Caramelli D, Lalueza-Fox C, Vernesi C, Ferrand N, Casoli A, Goyache F, Royo LJ, Conti S, Lari M, Martini A, Ouragh L, Magid A, Atash A, Zsolnai A, Boscato P, Triantaphylidis C, Ploumi K, Sineo L, Mallegni F, Taberlet P, Erhardt G, Sampietro L, Bertranpetit J, Barbujani G, Luikart G, Bertorelle G. The origin of European cattle: evidence from modern and ancient DNA. Proc Natl Acad Sci U S A 2006; 103:8113-8. [PMID: 16690747 PMCID: PMC1472438 DOI: 10.1073/pnas.0509210103] [Citation(s) in RCA: 228] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cattle domestication from wild aurochsen was among the most important innovations during the Neolithic agricultural revolution. The available genetic and archaeological evidence points to at least two major sites of domestication in India and in the Near East, where zebu and the taurine breeds would have emerged independently. Under this hypothesis, all present-day European breeds would be descended from cattle domesticated in the Near East and subsequently spread during the diffusion of herding and farming lifestyles. We present here previously undescribed genetic evidence in contrast with this view, based on mtDNA sequences from five Italian aurochsen dated between 7,000 and 17,000 years B.P. and >1,000 modern cattle from 51 breeds. Our data are compatible with local domestication events in Europe and support at least some levels of introgression from the aurochs in Italy. The distribution of genetic variation in modern cattle suggest also that different south European breeds were affected by introductions from northern Africa. If so, the European cattle may represent a more variable and valuable genetic resource than previously realized, and previous simple hypotheses regarding the domestication process and the diffusion of selected breeds should be revised.
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Affiliation(s)
- Albano Beja-Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP) and Secção Autónoma de Engenharia de Ciências Agrárias, Universidade do Porto, 4485-661 Vairão, Portugal
- Laboratoire d’Ecologie Alpine–Génomique des Populations et Biodiversité, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5553, Université Joseph Fourier, B.P. 53, 38041 Grenoble Cedex 9, France
| | - David Caramelli
- Dipartimento di Biologia Animale e Genetica, Laboratorio di Antropologia, Università di Firenze, Via del Proconsolo, 12-50122 Firenze, Italy
| | - Carles Lalueza-Fox
- Secció Antropologia, Departament Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal, 645-08028 Barcelona, Spain
| | - Cristiano Vernesi
- Centro di Ecologia Alpina, Viote del Monte Bondone, 38040 Trento, Italy
| | - Nuno Ferrand
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP) and Secção Autónoma de Engenharia de Ciências Agrárias, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Zoologia/Antropologia da Faculdade de Ciências Praça Gomes Teixeira, Campus Agrario de Vairao, 4099-002 Porto, Portugal
| | - Antonella Casoli
- Dipartimento di Chimica Generale e Inorganica, Chimica Analitica, Chimica Fisica, Università di Parma, Parco Area delle Scienze 17/A, 43100 Parma, Italy
| | - Felix Goyache
- Servicio Regional de Investigación y Desarrollo Agroalimentario–Centro De Seleccion Y Reproduccion Animal-Somió, Área de Genética y Reproducción Animal, 33203 Gijón, Spain
| | - Luis J. Royo
- Servicio Regional de Investigación y Desarrollo Agroalimentario–Centro De Seleccion Y Reproduccion Animal-Somió, Área de Genética y Reproducción Animal, 33203 Gijón, Spain
| | - Serena Conti
- Dipartimento di Biologia Animale e Genetica, Laboratorio di Antropologia, Università di Firenze, Via del Proconsolo, 12-50122 Firenze, Italy
- Dipartimento di Scienze Zootecniche, Università di Firenze, Via delle Cascine, 5-50144 Firenze, Italy
| | - Martina Lari
- Dipartimento di Biologia Animale e Genetica, Laboratorio di Antropologia, Università di Firenze, Via del Proconsolo, 12-50122 Firenze, Italy
| | - Andrea Martini
- Dipartimento di Scienze Zootecniche, Università di Firenze, Via delle Cascine, 5-50144 Firenze, Italy
| | - Lahousine Ouragh
- Département de Pathologie Médicale et Chirurgicale des Equidés et Carnivores, Institut Agronomique et Vétérinaire Hassan II, 10101 Rabat, Morocco
| | - Ayed Magid
- Animal Production Department, University of Al-Fateh, 13538 Tripoli, Libya
| | - Abdulkarim Atash
- Animal Production Department, University of Al-Fateh, 13538 Tripoli, Libya
| | - Attila Zsolnai
- Research Institute for Animal Breeding and Nutrition, 2053 Herceghalom, Hungary
| | - Paolo Boscato
- Dipartimento di Dipartimento di Scienze Ambientali, Università di Siena, Via delle Cerchia, 5-53100 Siena, Italy
| | - Costas Triantaphylidis
- Department of Genetics, Development and Molecular Biology, Aristotle University of Thessalonica, 54124 Thessalonica, Greece
| | | | - Luca Sineo
- Dipartimento di Biologia Animale, Università di Palermo, Via Archirafi, 18-90123 Palermo, Italy
| | - Francesco Mallegni
- Dipartimento di Scienze Archeologiche, Università di Pisa, Via Santa Maria, 53-56126 Pisa, Italy
| | - Pierre Taberlet
- Laboratoire d’Ecologie Alpine–Génomique des Populations et Biodiversité, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5553, Université Joseph Fourier, B.P. 53, 38041 Grenoble Cedex 9, France
| | - Georg Erhardt
- Institut für Tierzucht und Haustiergenetik, Justus-Liebig-Universität Gieben, Ludwigstrasse 21b, 35390 Gieben, Germany
| | - Lourdes Sampietro
- Unitat de Biologia Evolutiva, Departament di Ciències Experimentals e de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain; and
| | - Jaume Bertranpetit
- Unitat de Biologia Evolutiva, Departament di Ciències Experimentals e de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain; and
| | - Guido Barbujani
- Dipartimento di Biologia, Università di Ferrara, Via Borsari 46, I-44100 Ferrara, Italy
| | - Gordon Luikart
- Laboratoire d’Ecologie Alpine–Génomique des Populations et Biodiversité, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5553, Université Joseph Fourier, B.P. 53, 38041 Grenoble Cedex 9, France
| | - Giorgio Bertorelle
- Dipartimento di Biologia, Università di Ferrara, Via Borsari 46, I-44100 Ferrara, Italy
- To whom correspondence should be addressed. E-mail:
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