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 |
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| Authors: | S. Bovo A. Ribani M. Muñoz E. Alves J. P. Araujo R. Bozzi R. Charneca F. Di Palma G. Etherington A. I. Fernandez F. García J. García-Casco D. Karolyi M. Gallo K. Gvozdanović J. M. Martins M. J. Mercat Y. Núñez R. Quintanilla Č. Radović V. Razmaite J. Riquet R. Savić G. Schiavo M. Škrlep G. Usai V. J. Utzeri C. Zimmer C. Ovilo L. Fontanesi |
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| Affiliation: | 1. Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127 Italy;2. Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040 Spain;3. Centro de Investigação de Montanha, Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios do Lima, Ponte de Lima, 4990-706 Portugal;4. DAGRI – Animal Science Section, Università di Firenze, Via delle Cascine 5, Firenze, 50144 Italy;5. MED – Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Apartado 94, Évora, 7006-554 Portugal;6. Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ UK;7. Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, Zagreb, 10000 Croatia;8. Associazione Nazionale Allevatori Suini, Via Nizza 53, Roma, 00198 Italy;9. Faculty of Agrobiotechnical Sciences Osijek, University of Osijek, Vladimira Preloga 1, Osijek, 31000 Croatia;10. IFIP Institut Du Porc, La Motte au Vicomte, BP 35104, Le Rheu Cedex, 35651 France;11. Programa de Genética y Mejora Animal, IRTA, Torre Marimon, Caldes de Montbui, Barcelona, 08140 Spain;12. Department of Pig Breeding and Genetics, Institute for Animal Husbandry, Belgrade–Zemun, 11080 Serbia;13. Animal Science Institute, Lithuanian University of Health Sciences, R. Žebenkos 12, Baisogala, 82317 Lithuania;14. GenPhySE, INRA, Université de Toulouse, Chemin de Borde-Rouge 24, Auzeville Tolosane, Castanet Tolosan, 31326 France;15. Faculty of Agriculture, University of Belgrade, Nemanjina 6, Belgrade–Zemun, 11080 Serbia;16. Kmetijski Inštitut Slovenije, Hacquetova 17, Ljubljana, SI-1000 Slovenia;17. AGRIS SARDEGNA, Loc. Bonassai, Sassari, 07100 Italy;18. Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Haller Str. 20, Wolpertshausen, 74549 Germany |
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| 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. |
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| Keywords: | copy number variant ELOVL6 genetic resource KIT MSRB3 next-generation sequencing Sus scrofa ZNF622 |
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