Naslov
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

Autori
Bovo, Samuele ; Ribani, Anisa ; Muñoz, Maria ; Alves, E. ; Araujo, J.P. ; Bozzi, Ricardo ; Charneca, Rui ; Di Palma, F. ; Etherington, G. ; Fernandez, A. I. ; García, F. ; García‐Casco, Juan ; Karolyi, Danijel ; Gallo, Maurizio ; Gvozdanović, Kristina ; Martins, José Manuel ; Mercat, Marie-José ; Núñez, Yolanda ; Quintanilla, Raquel ; Radović, Čedomir ; Razmaite, Violeta ; Riquet, Juliette ; Savić, Radomir ; G. Schiavo, Giuseppina ; Škrlep, Martin ; Usai, G. ; Utzeri, Valerio Joe ; C. Zimmer ; Ovilo, Cristina ; Fontanesi, Luca

Kolaboracija
European Union’s Horizon 2020 research and innovation programme, grant agreement no. 634476 (project acronym TREASURE)

Izvornik
Animal genetics (0268-9146) 51 (2020); 541-556

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
copy number variant ; ELOVL6 ; genetic resource ; KIT ; MSRB3 ; next-generation sequencing ; Sus scrofa ; ZNF622

Sažetak
In this study, we identified copy number variants (CNVs) in 19 European autochthonous pigbreeds 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 abreed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depthper pool of 429. This approach maximised CNV discovery as well as the related copynumber 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 3710CNV regions (CNVRs ; 1.15% of the reference pig genome), with an average of 77 CNVRs perbreed 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 encompass-ing 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 CNVR saffecting 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.

Izvorni jezik
Engleski

Znanstvena područja
Poljoprivreda (agronomija)

POVEZANOST RADA