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
| العنوان: | 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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| المؤلفون: | 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 |
| المساهمون: | 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, Genètica i Millora Animal |
| المصدر: | Animal Genetics Animal Genetics, 2020, 51 (4), pp.541-556. ⟨10.1111/age.12954⟩ Animal Genetics, Wiley-Blackwell, 2020, 51 (4), pp.541-556. ⟨10.1111/age.12954⟩ IRTA Pubpro. Open Digital Archive Institut de Recerca i Tecnologia Agroalimentàries (IRTA) Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) Agência para a Sociedade do Conhecimento (UMIC)-FCT-Sociedade da Informação instacron:RCAAP |
| سنة النشر: | 2020 |
| مصطلحات موضوعية: | 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 |
| الوصف: | 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 |
| وصف الملف: | ELETTRONICO; application/pdf |
| اللغة: | English |
| تدمد: | 0268-9146 1365-2052 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::65525ae9bbf8243a74f15a9aac48e6b3 http://hdl.handle.net/11585/805594 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....65525ae9bbf8243a74f15a9aac48e6b3 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 02689146 13652052 |
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