@article{c0d2ab3a0be0419dad924c3e7a8adf87,
title = "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",
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.",
author = "S. Bovo and A. Ribani and M. Mu{\~n}oz and E. Alves and Araujo, {J. P.} and R. Bozzi and R. Charneca and {Di Palma}, F. and G. Etherington and Fernandez, {A. I.} and F. Garc{\'i}a and J. Garc{\'i}a-Casco and D. Karolyi and M. Gallo and K. Gvozdanovi{\'c} and Martins, {J. M.} and Mercat, {M. J.} and Y. N{\'u}{\~n}ez and R. Quintanilla and Radovi{\'c} and V. Razmaite and J. Riquet and R. Savi{\'c} and G. Schiavo and M. {\v S}krlep and G. Usai and Utzeri, {V. J.} and C. Zimmer and C. Ovilo and L. Fontanesi",
note = "Funding Information: S.B. received a fellowship from the Europe‐FAANG COST Action. This work received funding from the University of Bologna RFO 2016–2019 programme, the Italian MIUR 2017 project, the Slovenian Agency of Research (grant P4‐0133) and the European Union{\textquoteright}s Horizon 2020 research and innovation programme under grant agreement no. 634476 for the project with acronym TREASURE. The content of this article reflects only the authors{\textquoteright} view and the European Union Agency is not responsible for any use that may be made of the information it contains. PigPhenomics Funding Information: S.B. received a fellowship from the Europe-FAANG COST Action. This work received funding from the University of Bologna RFO 2016?2019 programme, the Italian MIUR 2017 PigPhenomics project, the Slovenian Agency of Research (grant P4-0133) and the European Union?s Horizon 2020 research and innovation programme under grant agreement no. 634476 for the project with acronym TREASURE. 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. Publisher Copyright: {\textcopyright} 2020 Stichting International Foundation for Animal Genetics",
year = "2020",
month = aug,
day = "1",
doi = "10.1111/age.12954",
language = "English (US)",
volume = "51",
pages = "541--556",
journal = "Animal Genetics",
issn = "0268-9146",
publisher = "Wiley-Blackwell",
number = "4",
}