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.

TitleGenome-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.
Publication TypeJournal Article
Year of Publication2020
AuthorsBovo, S, Ribani, A, Muñoz, M, Alves, E, Araujo, JP, Bozzi, R, Charneca, R, Di Palma, F, Etherington, G, Fernández, AI, García, F, García-Casco, J, Karolyi, D, Gallo, M, Gvozdanović, K, Martins, JM, Mercat, MJ, Núñez, Y, Quintanilla, R, Radović, Č, Razmaite, V, Riquet, J, Savić, R, Schiavo, G, Škrlep, M, Usai, G, Utzeri, VJ, Zimmer, C, Óvilo, C, Fontanesi, L
JournalAnim Genet
Volume51
Issue4
Pagination541-556
Date Published2020 Aug
ISSN1365-2052
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.

DOI10.1111/age.12954
Alternate JournalAnim. Genet.
PubMed ID32510676
Grant ListCA15112 / / European Cooperation in Science and Technology /
P4-0133 / / Slovenian Agency of Research /
634476 / / H2020 Societal Challenges /
RFO 2016-2019 programme / / Università di Bologna /
PigPhenomics / / Ministero dell'Istruzione, dell'Università e della Ricerca /