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
Bovo, S.
Ribani, A.
Muñoz, M.
Alves, E.
Araujo, J. P.
Bozzi, R.
Charneca, R.
Di Palma, F.
Etherington, G.
Fernandez, A. I.
García, F.
García‐Casco, J.
Karolyi, D.
Gallo, M.
Gvozdanović, K.
Martins, J. M.
Mercat, M. J.
Núñez, Y.
Quintanilla, R.
Radović, Č.
Razmaite, V.
Riquet, J.
Savić, R.
Schiavo, G.
Škrlep, M.
Usai, G.
Utzeri, V. J.
Zimmer, C.
Ovilo, C.
Fontanesi, L.
Publication date
2020-06-08ISSN
0268-9146
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.
Document Type
Article
Document version
Accepted version
Language
English
Subject (CDU)
577 - Material bases of life. Biochemistry. Molecular biology. Biophysics
59 - Zoology
619 - Veterinary science
636 - Animal husbandry and breeding in general. Livestock rearing. Breeding of domestic animals
Pages
44
Publisher
Wiley
Is part of
Animal Genetics
Citation
Bovo, S., A. Ribani, M. Muñoz, E. Alves, J. P. Araujo, R. Bozzi, and R. Charneca et al. 2020. "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". Animal Genetics. doi:10.1111/age.12954.
Grant agreement number
EC/H2020/634476/EU/Diversity of local pig breeds and production systems for high quality traditional products and sustainable pork chains/TREASURE
EC/COST/CA15112/EU/Functional Annotation of Animal Genomes-European network/FAANG-Europe
Program
Genètica i Millora Animal
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2820]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by-nc-nd/4.0/