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1. Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

Author

Christoph Zimmer, Marie-José Mercat, Rui Charneca, Cristina Óvilo, Goran Kušec, Anisa Ribani, Estefania Alves, J.M. Martins, Juliette Riquet, Raquel Quintanilla, G. Usai, Samuele Bovo, Valerio Joe Utzeri, Maurizio Gallo, Ana Isabel Fernández, Yolanda Núñez, Danijel Karolyi, Violeta Razmaite, María Muñoz, Giuseppina Schiavo, Fabián García, Riccardo Bozzi, Luca Fontanesi, Čedomir Radović, Radomir Savić, Marjeta Čandek-Potokar, José Pedro Araújo, University of Bologna, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Polytechnic Institute of Porto, Université de Florence, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Mediterranean Institute for Agriculture, Environment and Development (MED), University of Évora [Portugal], Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Bologna RFO 2016-2019 programs, European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Schiavo G., Bovo S., Munoz M., Ribani A., Alves E., Araujo J.P., Bozzi R., Candek-Potokar M., Charneca R., Fernandez A.I., Gallo M., Garcia F., Karolyi D., Kusec G., Martins J.M., Mercat M.-J., Nunez Y., Quintanilla R., Radovic C., Razmaite V., Riquet J., Savic R., Usai G., Utzeri V.J., Zimmer C., Ovilo C., Fontanesi L., University of Bologna/Università di Bologna, Università degli Studi di Firenze = University of Florence (UniFI), Agricultural Institute of Slovenia, University of Zagreb, J.J. Strossmayer University of Osijek, Institut du Porc (IFIP), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Inst Anim Husb, Lithuanian Univ Hlth Sci, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Belgrade [Belgrade], AGRIS sardegna, Bäuerliche Erzeugergemeinschaft Schwäbisch Hall (BESH), Università di Bologna, European Commission, Schiavo, G., Bovo, S., Ribani, A., Araújo, J.P., Bozzi, R., Čandek-Potokar, M., Charneca, R., Fernandez, A.I., Kušec, G., Campos Martín, José Miguel, Mercat, M.J., Núñez, Y., Quintanilla, R., Radović, Č., Razmaite, V., Riquet, J., Savić, R., Usai, G., Utzeri, V.J., Fontanesi, L., Géosciences Montpellier, Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Université des Antilles (UA)-Centre National de la Recherche Scientifique (CNRS), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Centro de Ciências e Tecnologias Nucleares (C2TN), Instituto Politécnico de Viana do Castelo, UNIVERSITY OF FIRENZE (UNIVERSITY OF FIRENZE), and Spanish National Research Council [Madrid] (CSIC)

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Sus scrofa, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Runs of Homozygosity, population genomic, Population genomics, single nucleotide polymorphism, Genotype, Inbreeding, autozygosity, population genomics, selection signature, 2. Zero hunger, education.field_of_study, Genome, [SDV.BA]Life Sciences [q-bio]/Animal biology, Homozygote, Single Nucleotide, 04 agricultural and veterinary sciences, General Medicine, Europe, Genetic structure, Population, Autozygosity, Single-nucleotide polymorphism, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genetics, Animals, Population Density, Polymorphism, education, 0402 animal and dairy science, Selection signature, biology.organism_classification, 040201 dairy & animal science, Single nucleotide polymorphism, 030104 developmental biology, Evolutionary biology, Animal Science and Zoology, Sarda
Abstract

16 Pág. Departamento de ​Mejora Genética Animal, ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources., This work has been funded by University of Bologna RFO 2016-2019 programs and by the European Union’s Horizon 2020 research and innovation programme (TREASURE project – grant agreement no. 634476). The content of this work reflects only the authors’ view and the European Union Agency is not responsible for any use that may be made of the information it contains.

Published
2022
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2. Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Author

Giuseppina Schiavo, Valeria Taurisano, Raquel Quintanilla, Anisa Ribani, Juan García-Casco, Rui Charneca, Valerio Joe Utzeri, Marie-José Mercat, Estefania Alves, Fabián García, Graham J Etherington, Samuele Bovo, Juliette Riquet, Danijel Karolyi, Christoph Zimmer, Ivona Djurkin Kušec, Federica Di Palma, Ana Isabel Fernández, G. Usai, Violeta Razmaite, María Muñoz, Yolanda Núñez, José Pedro Araújo, Martin Škrlep, Radomir Savić, J.M. Martins, Maurizio Gallo, Luca Fontanesi, Čedomir Radović, Mohamad Ballan, Cristina Óvilo, Riccardo Bozzi, University of Bologna, Instituto Nacional de Investigación Agropecuaria (INIA), Centro de Investigação de Montanha [Bragança, Portugal] (CIMO), Instituto Politécnico de Bragança, Department of Agriculture, Food, Environment and Forestry (DAGRI), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Universidade de Évora, University of East Anglia [Norwich] (UEA), Josip Juraj Strossmayer University of Osijek, Earlham Institute [Norwich], University of Zagreb, Associazione Nazionale Allevatori Suini, Institut du Porc (IFIP), Institute of Agrifood Research and Technology (IRTA), Institute for Animal Husbandry, Lithuanian University of Health Sciences [Kaunas, Lithuania], Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Belgrade [Belgrade], Kmetijski Inštitut Slovenije (KIS), AGRIS sardegna, Bäuerliche Erzeugergemeinschaft Schwäbisch Hall (BESH), European Cooperation in Science and Technology (COST)Ministry of Foreign Affairs of ItalyUniversity of Bologna RFO 2016-2019 programmesItalian MIUR 2017 PigPhenomics projectEuropean Commission634476European Open Science Cloud (EOSC) Secretariat, project 'Application of animal genomics and data mining to predict and monitor novel coronavirus potential infections (VirAnimalOne)'EGI call for COVID-19 research projects (AnGen1H project)Por Fesr Emilia-Romagna 2014-2020 (actions 1.1.4 and 1.2.2-Bando per sostenere progetti di ricerca ed innovazione per lo sviluppo di soluzioni finalizzate al contrasto dell'epidemia da COVID-19-Project LIVESTOCK-STOP-COVI), European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Producció Animal, Genètica i Millora Animal, University of Bologna/Università di Bologna, Università degli Studi di Firenze = University of Florence (UniFI), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università di Bologna, European Commission, Bovo, Samuele, Schiavo, Giuseppina, Ribani, Anisa, Utzeri, Valerio J, Taurisano, Valeria, Araujo, Jose P, Bozzi, Riccardo, Charneca, Rui, Di Palma, Federica, Djurkin Kušec, Ivona, Etherington, Graham, Fernandez, Ana I, Suárez García, Fabián, García-Casco, Juan, Karolyi, D 0000-003-0409-9071], Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Škrlep, Martin, Usai, Graziano, Ovilo, Cristina, Bovo S., Schiavo G., Ribani A., Utzeri V.J., Taurisano V., Ballan M., Munoz M., Alves E., Araujo J.P., Bozzi R., Charneca R., Di Palma F., Djurkin Kusec I., Etherington G., Fernandez A.I., Garcia F., Garcia-Casco J., Karolyi D., Gallo M., Martins J.M., Mercat M.-J., Nunez Y., Quintanilla R., Radovic C., Razmaite V., Riquet J., Savic R., Skrlep M., Usai G., Zimmer C., Ovilo C., and Fontanesi L.

Subjects
0301 basic medicine, Candidate gene, Population genetics, Swine, MESH: Coronavirus Infections, Sus scrofa, MESH: Angiotensin-Converting Enzyme 2, MESH: One Health, Breeding, MESH: INDEL Mutation, 0302 clinical medicine, Gene Frequency, INDEL Mutation, Receptors, Receptors, Viru, MESH: Animals, MESH: Serine Endopeptidases, MESH: Genetic Variation, MESH: High-Throughput Nucleotide Sequencing, MESH: Swine, 2. Zero hunger, Genetics, education.field_of_study, Multidisciplinary, MESH: Polymorphism, Single Nucleotide, Serine Endopeptidases, High-Throughput Nucleotide Sequencing, Single Nucleotide, Genomics, Virus, Serine Endopeptidase, One Health, 030220 oncology & carcinogenesis, Microsomal aminopeptidase, Medicine, Infectious diseases, Receptors, Virus, Angiotensin-Converting Enzyme 2, Coronavirus Infections, MESH: Whole Genome Sequencing, Human, Agricultural genetics, pig, local breed, whole genome sequencing, coronavirus, Science, Dipeptidyl Peptidase 4, Population, MESH: Genetics, Population, Context (language use), MESH: Breeding, CD13 Antigens, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Animals, Genetics, Population, Humans, Whole Genome Sequencing, Genetic Variation, Genetic variation, MESH: Gene Frequency, Polymorphism, education, Data mining, Gene, CD13 Antigen, Animal breeding, Whole genome sequencing, MESH: Humans, Animal, Coronavirus Infection, Host (biology), Virus receptor, MESH: CD13 Antigens, MESH: Dipeptidyl Peptidase 4, MESH: Receptors, Virus, MESH: Sus scrofa, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Dipeptidyl peptidase IV, Next-generation sequencing, Genetic markers, Serine proteinase
Abstract

14 Pág. Departamento de ​Mejora Genética Animal, Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a "One Health" perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a "One Health" perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources., This work has received funding from the University of Bologna RFO 2016-2019 programmes, the Italian MIUR 2017 PigPhenomics project, from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 634476 for the project with acronym TREASURE, from the European Open Science Cloud (EOSC) Secretariat, project “Application of animal genomics and data mining to predict and monitor novel coronavirus potential infections (VirAnimalOne)”, the EGI call for COVID-19 research projects (AnGen1H project) and from the Por Fesr Emilia-Romagna 2014-2020 (actions 1.1.4 and 1.2.2—Bando per sostenere progetti di ricerca ed innovazione per lo sviluppo di soluzioni finalizzate al contrasto dell’epidemia da COVID-19—Project LIVESTOCK-STOP-COVI). The content of this article reflects only the authors' view and the European Union Agency is not responsible for any use that may be made of the information it contains.

Published
2021
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3. 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

Author

Valerio Joe Utzeri, Ana Isabel Fernández, G. Usai, Marjeta Čandek-Potokar, María Muñoz, José Pedro Araújo, Maurizio Gallo, Riccardo Bozzi, Čedomir Radović, Fabián García, Giuseppina Schiavo, Federica Di Palma, Cristina Óvilo, Marie J. Mercat, Juan García-Casco, Christoph Zimmer, Anisa Ribani, Juliette Riquet, Danijel Karolyi, Vladimir Margeta, Samuele Bovo, Luca Fontanesi, Giulia Moscatelli, Radomir Savić, Violeta Razmaite, Estefania Alves, Rui Charneca, J.M. Martins, Raquel Quintanilla, Yolanda Núñez, Graham J Etherington, University of Bologna/Università di Bologna, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Instituto Politécnico de Viana do Castelo = Polytechnic Institute of Viana do Castelo (IPVC), Università degli Studi di Firenze = University of Florence (UniFI), Kmetijski Institut Slovenije, Partenaires INRAE, Universidade de Évora, Earlham Institute [Norwich], University of Zagreb, Associazione Nazionale Allevatori Suini, Josip Juraj Strossmayer University of Osijek, Institut du Porc (IFIP), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Institute for Animal Husbandry, Lithuanian University of Health Sciences [Kaunas, Lithuania], Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Belgrade [Belgrade], AGRIS sardegna, Bäuerliche Erzeugergemeinschaft Schwäbisch Hall (BESH), Europe-FAANG COST Action, University of Bologna RFO 2016–2019 programme, European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Producció Animal, Genètica i Millora Animal, University of Bologna, Instituto Politécnico de Viana do Castelo, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institute of Agrifood Research and Technology (IRTA), Bovo S., Ribani A., Munoz M., Alves E., Araujo J.P., Bozzi R., Candek-Potokar M., Charneca R., Di Palma F., Etherington G., Fernandez A.I., Garcia F., Garcia-Casco J., Karolyi D., Gallo M., Margeta V., Martins J.M., Mercat M.J., Moscatelli G., Nunez Y., Quintanilla R., Radovic C., Razmaite V., Riquet J., Savic R., Schiavo G., Usai G., Utzeri V.J., Zimmer C., Ovilo C., and Fontanesi L.

Subjects
Male, Genotyping Techniques, Swine, Acclimatization, [SDV]Life Sciences [q-bio], Breeding, Fixation index, Domestication, Chromosome regions, local pig breeds, WGS, genome variability, ComputingMilieux_MISCELLANEOUS, lcsh:SF1-1100, 2. Zero hunger, 0303 health sciences, Genome, biology, Genomics, 04 agricultural and veterinary sciences, General Medicine, Adaptation, Physiological, Alentejana, Algorithm, Europe, Phenotype, Pigs, Female, Algorithms, SNPs, Research Article, lcsh:QH426-470, Genotype, Whole-genome sequencing, pig, autochthonous breeds, selection, adaptation, Polymorphism, Single Nucleotide, Crossbreed, 03 medical and health sciences, Genetics, Animals, Selection, Genetic, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Whole genome sequencing, Genetic diversity, Models, Genetic, Whole Genome Sequencing, Animal, Directional selection, 0402 animal and dairy science, biology.organism_classification, 040201 dairy & animal science, Bísaro pig, Alentejano pig, European local breeds, lcsh:Genetics, Evolutionary biology, Genomic, Animal Science and Zoology, lcsh:Animal culture, Genotyping Technique
Abstract

Background Natural and artificial 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 different 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 commercial 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. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. Results We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. Conclusions Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.

Published
2020
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4. 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

Author

Čedomir Radović, Valerio Joe Utzeri, Rui Charneca, Juan García-Casco, Christoph Zimmer, Raquel Quintanilla, Samuele Bovo, Danijel Karolyi, E. Alves, Angeles Fernandez, Luca Fontanesi, João P. Araújo, J.M. Martins, Martin Škrlep, F. Di Palma, Radomir Savić, Marie-José Mercat, Ricardo Bozzi, María Muñoz, Violeta Razmaite, Graham J Etherington, Kristina Gvozdanović, Giuseppina Schiavo, Anisa Ribani, Yolanda Núñez, Maurizio Gallo, G. Usai, Cristina Óvilo, Felisa Laíz García, Juliette Riquet, Bovo S., Ribani A., Munoz M., Alves E., Araujo J.P., Bozzi R., Charneca R., Di Palma F., Etherington G., Fernandez A.I., Garcia F., Garcia-Casco J., Karolyi D., Gallo M., Gvozdanovic K., Martins J.M., Mercat M.J., Nunez Y., Quintanilla R., Radovic C., Razmaite V., Riquet J., Savic R., Schiavo G., Skrlep M., Usai G., Utzeri V.J., Zimmer C., Ovilo C., Fontanesi L., University of Bologna/Università di Bologna, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Instituto Nacional de Investigación Agropecuaria (INIA), Instituto Politécnico de Viana do Castelo = Polytechnic Institute of Viana do Castelo (IPVC), UNIVERSITY OF FIRENZE (UNIVERSITY OF FIRENZE), Università degli Studi di Firenze = University of Florence (UniFI), Universidade de Évora, Earlham Institute [Norwich], University of Zagreb, Assoc Nazl Allevatori Suini, University of Osijek, Institut du Porc (IFIP), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Lithuanian University of health Sciences, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Belgrade [Belgrade], Agricultural Institute of Slovenia, Agenzia della Regione Sardegna per la Ricerca Scientifica (AGRIS), Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Institute of animal husbandry, Slovenian Agency of Research / P4-0133, European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), University of Bologna, Instituto Politécnico de Viana do Castelo, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institute of Agrifood Research and Technology (IRTA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Producció Animal, and Genètica i Millora Animal

Subjects
0301 basic medicine, Male, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], DNA Copy Number Variations, Sus scrofa, Breeding, Genome, DNA sequencing, 03 medical and health sciences, Species Specificity, copy number variant, ELOVL6, genetic resource, KIT, MSRB3, next-generation sequencing, ZNF622, Genetics, Animals, Copy-number variation, Gene, 2. Zero hunger, Whole genome sequencing, Genetic diversity, biology, Genetic ressource, Whole Genome Sequencing, Animal, 0402 animal and dairy science, Turopolje pig, 04 agricultural and veterinary sciences, General Medicine, DNA, biology.organism_classification, 040201 dairy & animal science, Breed, 030104 developmental biology, Phenotype, Italy, Evolutionary biology, Animal Science and Zoology, Female
Abstract

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed‐specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed‐specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems. info:eu-repo/semantics/acceptedVersion

Published
2020
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5. Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip

Author

Marie-José Mercat, Christoph Zimmer, Anisa Ribani, I. Djurkin-Kušec, Danijel Karolyi, Luca Fontanesi, Radomir Savić, Giuseppina Schiavo, Jordi Estellé, Martin Škrlep, Čedomir Radović, María Muñoz, Marjeta Čandek-Potokar, Samuele Bovo, Valerio Joe Utzeri, Ana Isabel Fernández, Juliette Riquet, Maurizio Gallo, José Pedro Araújo, Vladimir Margeta, Cristina Óvilo, Riccardo Bozzi, Fabián García, Juan García-Casco, J.M. Martins, Rui Charneca, Raquel Quintanilla, Oreste Franci, Violeta Razmaite, Yolanda Núñez, J. Tibau, Producció Animal, Genètica i Millora Animal, Departamento de Mejora Genética Animal, Instituto Nacional de Investigaciones Agronomicas, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Department of Agricultural and Food Sciences, University of Bologna, Kmetijski Institut Slovenije, Partenaires INRAE, Universidade de Évora, Institute of Agrifood Research and Technology (IRTA), University of Osijek, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Bäuerliche Erzeugergemeinschaft Schwäbisch Hall (BESH), Lithuanian University of health Sciences, Centro de Investigação de Montanha [Bragança, Portugal] (CIMO), Instituto Politécnico de Bragança, Faculty of Agriculture, Université nationale du Rwanda, Department of Animal Science, Faculty of Agriculture, University of Ghana, Associazione Nazionale Allevatori Suini, European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Munoz M., Bozzi R., Garcia-Casco J., Nunez Y., Ribani A., Franci O., Garcia F., Skrlep M., Schiavo G., Bovo S., Utzeri V.J., Charneca R., Martins J.M., Quintanilla R., Tibau J., Margeta V., Djurkin-Kusec I., Mercat M.J., Riquet J., Estelle J., Zimmer C., Razmaite V., Araujo J.P., Radovic C., Savic R., Karolyi D., Gallo M., Candek-Potokar M., Fernandez A.I., Fontanesi L., Ovilo C., Óvilo, C., Università degli Studi di Firenze = University of Florence (UniFI), University of Bologna/Università di Bologna, Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), and Université de Toulouse (UT)-Université de Toulouse (UT)

Subjects
0301 basic medicine, Linkage disequilibrium, pig, breed, genomic diversity, SNP chip, SNP chips, Molecular biology, Swine, Population genetics, [SDV]Life Sciences [q-bio], Sus scrofa, lcsh:Medicine, Breeding, selection signatures, Linkage Disequilibrium, Effective population size, local pig breeds, lcsh:Science, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, education.field_of_study, Principal Component Analysis, Multidisciplinary, Genome, biology, 04 agricultural and veterinary sciences, Genomics, Breed, SNP genotyping, Alentejana, genomic diversity, selection signatures, local pig breeds, SNPs, Phenotype, Animals, Domestic, Pigs, SNPs, Genotype, Population, SNP, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Genetic variation, Animals, Genetic resource, [INFO]Computer Science [cs], education, Animal breeding, Population Density, genomics, local breeds, diversity, Genetic diversity, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genomic diversity, lcsh:R, 0402 animal and dairy science, Genetic Variation, Phenotypic trait, Selection signature, biology.organism_classification, 040201 dairy & animal science, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Genetics, Population, Evolutionary biology, Local breeds, lcsh:Q
Abstract

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 Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective 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 effective 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. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.

Published
2019
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