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Genome‐Wide Detection of Copy Number Variants in European
doi: 10.1111/age.12954 Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states † † ‡ § ¶ S. Bovo* , A. Ribani* ,M.Munoz~ , E. Alves , J. P. Araujo , R. Bozzi , R. Charneca , † † † †† F. Di Palma**, G. Etherington**, A. I. Fernandez , F. Garcıa , J. Garcıa-Casco , D. Karolyi , ‡‡ §§ ¶ ¶¶ † M. Gallo , K. Gvozdanovic , J. M. Martins , M. J. Mercat ,Y.Nunez~ , R. Quintanilla***, ††† ‡‡‡ §§§ ¶¶¶ †††† C. Radovic , V. Razmaite , J. Riquet , R. Savic , G. Schiavo* ,M.Skrlep****, G. Usai , ‡‡‡‡ † V. J. Utzeri* , C. Zimmer , C. Ovilo and L. Fontanesi* *Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna 40127, Italy. † ‡ Departamento Mejora Genetica Animal, INIA, Crta. de la Coruna,~ km. 7,5, Madrid 28040, Spain. Centro de Investigacßao~ de Montanha, § Instituto Politecnico de Viana do Castelo, Escola Superior Agraria, Refoios do Lima, Ponte de Lima 4990-706, Portugal. DAGRI – Animal ¶ Science Section, Universita di Firenze, Via delle Cascine 5, Firenze 50144, Italy. MED – Mediterranean Institute for Agriculture, Environment and Development, Universidade de Evora, Polo da Mitra, Apartado 94, Evora 7006-554, Portugal. **Earlham Institute, Norwich Research †† Park, Colney Lane, Norwich NR47UZ, UK. Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetosimunska c. ‡‡ §§ 25, Zagreb 10000, Croatia. Associazione Nazionale Allevatori Suini, Via Nizza 53, Roma 00198, Italy. Faculty of Agrobiotechnical ¶¶ Sciences Osijek, University of Osijek, Vladimira Preloga 1, Osijek 31000, Croatia. IFIP Institut Du Porc, La Motte au Vicomte, BP 35104, Le Rheu Cedex 35651, France. ***Programa de Genetica y Mejora Animal, IRTA, Torre Marimon, Caldes de Montbui, Barcelona 08140, Spain. -
Whole-Genome Sequencing of European Autochthonous and Commercial Pig Breeds Allows the Detection of Signatures of Selection
Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems Samuele Bovo, Anisa Ribani, Maria Muñoz, Estefania Alves, Jose P. Araujo, Riccardo Bozzi, Marjeta Čandek-Potokar, Rui Charneca, Federica Di Palma, Graham Etherington, et al. To cite this version: Samuele Bovo, Anisa Ribani, Maria Muñoz, Estefania Alves, Jose P. Araujo, et al.. Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems. Genetics Se- lection Evolution, BioMed Central, 2020, 52 (1), pp.33. 10.1186/s12711-020-00553-7. hal-02883278 HAL Id: hal-02883278 https://hal.archives-ouvertes.fr/hal-02883278 Submitted on 29 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Bovo et al. Genet Sel Evol (2020) 52:33 https://doi.org/10.1186/s12711-020-00553-7 Genetics Selection Evolution RESEARCH ARTICLE Open Access Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to diferent breeding and production systems Samuele Bovo1, Anisa Ribani1, Maria Muñoz2, Estefania Alves2, Jose P. -
Genomic Diversity, Linkage Disequilibrium and Selection Signatures in European Local Pig Breeds Assessed with a High Density
www.nature.com/scientificreports OPEN Genomic diversity, linkage disequilibrium and selection signatures in European local pig Received: 6 March 2019 Accepted: 30 August 2019 breeds assessed with a high density Published: xx xx xxxx SNP chip M. Muñoz 1, R. Bozzi 2, J. García-Casco1, Y. Núñez1, A. Ribani3, O. Franci2, F. García1, M. Škrlep4, G. Schiavo3, S. Bovo 3, V. J. Utzeri3, R. Charneca5, J. M. Martins 5, R. Quintanilla6, J. Tibau6, V. Margeta7, I. Djurkin-Kušec 7, M. J. Mercat8, J. Riquet9, J. Estellé 10, C. Zimmer11, V. Razmaite 12, J. P. Araujo13, Č. Radović14, R. Savić 15, D. Karolyi 16, M. Gallo17, M. Čandek-Potokar 4, A. I. Fernández1, L. Fontanesi 3 & C. Óvilo 1 Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population diferentiation and structure, genetic distances, linkage disequilibrium and efective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small efective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. -
Low Mitochondrial Diversity in Native Italian Pig Breeds Is Consistent with The
bioRxiv preprint doi: https://doi.org/10.1101/128751; this version posted April 19, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 RUNNING HEAD: Diversity of Italian pigs 2 3 4 Low mitochondrial diversity in native Italian pig breeds is consistent with the 5 occurrence of strong population bottlenecks 6 7 8 Joanna Kubejko1, Marcel Amills1*, Fabio Pilla2, Mariasilvia D’Andrea2 and Alex Clop1 9 10 1Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC- 11 IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 12 Spain; 2Dipartimento di Agricoltura, Ambiente e Alimenti, Università degli Studi del 13 Molise, Campobasso, Italy. 14 15 *Corresponding author: Marcel Amills, Department of Animal Genetics, Center for 16 Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat 17 Autònoma de Barcelona, Bellaterra, 08193 Spain. Tel. 34 93 5636600. E-mail: 18 [email protected]. 19 20 21 22 23 24 bioRxiv preprint doi: https://doi.org/10.1101/128751; this version posted April 19, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 25 ABSTRACT 26 27 In this study, we have analysed the variation of 81 Italian pigs from the Calabrese, 28 Casertana, Cinta Senese, Sarda and Nero Siciliano breeds as well as 54 Italian wild boars 29 by using a dataset of mitochondrial control region sequences generated by us and others. -
Whole-Genome Sequencing of European Autochthonous and Commercial Pig Breeds Allows the Detection of Signatures of Selection
Bovo et al. Genet Sel Evol (2020) 52:33 https://doi.org/10.1186/s12711-020-00553-7 Genetics Selection Evolution RESEARCH ARTICLE Open Access Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to diferent breeding and production systems Samuele Bovo1, Anisa Ribani1, Maria Muñoz2, Estefania Alves2, Jose P. Araujo3, Riccardo Bozzi4, Marjeta Čandek‑Potokar5, Rui Charneca6, Federica Di Palma7, Graham Etherington7, Ana I. Fernandez2, Fabián García2, Juan García‑Casco2, Danijel Karolyi8, Maurizio Gallo9, Vladimir Margeta10, José Manuel Martins6, Marie J. Mercat11, Giulia Moscatelli1, Yolanda Núñez2, Raquel Quintanilla12, Čedomir Radović13, Violeta Razmaite14, Juliette Riquet15, Radomir Savić16, Giuseppina Schiavo1, Graziano Usai17, Valerio J. Utzeri1, Christoph Zimmer18, Cristina Ovilo2 and Luca Fontanesi1* Abstract Background: Natural and artifcial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to diferent environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo‑Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow‑Bellied Mangalitsa, Schwäbisch‑Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European com‑ mercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole‑ genome sequencing data obtained by using a DNA‑pool sequencing approach. -
This Is the Peer Reviewed Version of the Following Article: Bovo, S., A
This is the peer reviewed version of the following article: Bovo, S., A. Ribani, M. Muñoz, E. Alves, J. P. Araujo, R. Bozzi, and R. Charneca et al. 2020. "Genome‐Wide Detection Of Copy Number Variants In European Autochthonous And Commercial Pig Breeds By Whole‐Genome Sequencing Of DNA Pools Identified Breed‐Characterising Copy Number States". Animal Genetics 51 (4): 541-556. doi:10.1111/age.12954, which has been published in final form at https://doi.org/10.1111/age.12954. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions http://www.wileyauthors.com/self- archiving. Document downloaded from: 1 Genome-wide detection of copy number variants in European autochthonous and commercial 2 pig breeds by whole genome sequencing of DNA pools identified breed-characterising copy 3 number states 4 5 Samuele Bovo1, Anisa Ribani1, Maria Muñoz2, Estefania Alves2, Jose P. Araujo3, Riccardo Bozzi4, 6 Rui Charneca5, Federica Di Palma6, Graham Etherington6, Ana I. Fernandez2, Fabián García2, Juan 7 García-Casco2, Danijel Karolyi7, Maurizio Gallo8, Kristina Gvozdanović9, José Manuel Martins5, 8 Marie-José Mercat10, Yolanda Núñez2, Raquel Quintanilla11, Čedomir Radović12, Violeta Razmaite13, 9 Juliette Riquet14, Radomir Savić15, Giuseppina Schiavo1, Martin Škrlep16, Graziano Usai17, Valerio 10 J. Utzeri1, Christoph Zimmer18, Cristina Ovilo2, Luca Fontanesi1 11 12 1 Department of Agricultural and Food Sciences, Division of Animal Sciences, University of 13 Bologna, Viale Fanin 46, 40127 Bologna, Italy. 14 2 Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, 28040, Madrid, Spain. 15 3 Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Viana do Castelo, Escola 16 Superior Agrária, Refóios do Lima, 4990-706 Ponte de Lima Portugal. -
Swine Production in Italy and Research Perspectives for the Local Breeds
Slovak J. Anim. Sci., 42, 2009 (4): 159 - 166 © 2009 CVŽV Nitra ISSN 1337-9984 SWINE PRODUCTION IN ITALY AND RESEARCH PERSPECTIVES FOR THE LOCAL BREEDS G. MAIORANO University of Molise, Campobasso, Italy ABSTRACT Autochthonous pig breeds represent a valuable genetic reserve to utilise for typical products linked to the gastronomic traditions of Italy, or for recovering some organoleptic proprieties of pork actually lost because of severe selective programmes. These ex- treme phenotypes can be used to emphasize the loci involved in the productive traits by crossing with selected pigs or as a model to understand the physiological process of fat deposition. Moreover, the importance of recovering the primitive germoplasm is suggested also by the fact that, generally, the Mediterranean pig breeds seems to be free from the halothane gene. The survival of these breeds is strictly connected to a good assessment and exploitation of their performances, considering that the latter may involve both rearing environments and interactions between feeding plan adopted and breed characteristics. Even if the free range system worsened growth performance, studies had documented that the semi- extensive (plein air) condition brings about better performances for unimproved pigs. The link with the semi extensive rearing could be suitable to increase the commercial value of products of local pigs, because of both effective characterization and consumer preferences. Considering that the information on the research on the Italian local pigs is limited, it is necessary to increase a suitable activity of research to exploit these breeds and to increase the knowledge of their rearing system. A valid example is the Iberian pig. -
Proceedings of the 6Th International Symposium on the Mediterranean Pig
ISSN 2035-4088 Proceedings of the 6th International Symposium on the Mediterranean Pig October 11 – 13, 2007 Messina - Capo d’Orlando (ME), Italy Editors L. Nanni Costa, P. Zambonelli, V. Russo TABLE OF CONTENTS Foreword ………………….………………………………………………...………..… 8 SESSION 1. IMPROVEMENT AND MANAGEMENT OF THE GENETIC RESOURCES L. Ollivier. Analyses of the European pig diversity using genetic markers ………………..… 10 A.Fernández, J. Rodrigáñez, C. Rodríguez, and L. Silió. Heterosis for litter size of Iberian sows is limited to second and later parities .… 23 A. Fernández, J.M. García-Casco, and L. Silió. Genetic trends for growth of young pigs in two breeding nuclei of Iberian breed .. 27 L. J. Royo, I. Álvarez, I. Fernández, L. Pérez-Pardal, A. Álvarez-Sevilla, J. Santos e Silva, R. Godinho, N. Ferrand, and F. Goyache Genetic characterisation of Celtic-Iberian pig breeds using microsatellites ......… 31 A. Crovetti, R. Bozzi, L. Nardi, M. Gallo, L. Buttazzoni, and O. Franci Pedigree analysis of Cinta Senese breed ……………………………………….…. 35 R. Bozzi, A. Crovetti, L. Nardi, C. Pugliese, F. Sirtori, and O. Franci Study of genes related to meat quality in Cinta Senese pig breed …………...…. 41 R. Davoli, P. Zambonelli, M. San-Cristobal, E. Scotti, L. Fontanesi, M. Colombo, S. Dall'Olio, S. Braglia, V. Russo Snps and microsatellite markers analysis for genetic diversity study in Italian pig breeds …………………………………………………………………………….... 46 D’Alessandro E., Fontanesi L., Liotta L., Scotti E., Davoli R., Chiofalo V., Russo V. Genetic analysis of the KIT and MC1R coat colour affecting genes in the Nero Siciliano pig breed and perspectives on the use of mutations at these two loci for breed traceability ……………………………………………………………..…… 54 D.