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
Authors
Bovo, SamueleRibani, Anisa
Munoz, Maria
Alves, Estefania
Araujo, Jose P.
Bozzi, Riccardo

Charneca, Rui

Di Palma, Federica
Etherington, Graham
Fernandez, Ana I.
Garcia, Fabian
Garcia-Casco, Juan
Karolyi, Danijel
Gallo, Maurizio
Gvozdanović, Katarina
Martins, Jose Manuel
Mercat, Marie J.
Nunez, Yolanda
Quintailla, Raquel
Radović, Čedomir

Razmaite, Violeta
Riquet, Juliette
Savić, Radomir
Schiavo, Giuseppina
Škrlep, Martin
Usai, Graziano
Utzeri, Valerio J.
Zimmer, Christoph
Ovilo, Cristina
Fontanesi, Luca
Article (Published version)
Metadata
Show full item recordAbstract
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 429. 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 multi...ple 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
Keywords:
copy number variant / ELOVL6 / genetic resource / KIT / MSRB3 / next-generation sequencing / Sus scrofa / ZNF622Source:
Animal Genetics, 2020Publisher:
- International Foundation for Animal Genetics