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.
ELOVL6
KIT
MSRB3
Sus scrofa
ZNF622
copy number variant
genetic resource
next-generation sequencing
Journal
Animal genetics
ISSN: 1365-2052
Titre abrégé: Anim Genet
Pays: England
ID NLM: 8605704
Informations de publication
Date de publication:
Aug 2020
Aug 2020
Historique:
accepted:
30
04
2020
pubmed:
9
6
2020
medline:
21
11
2020
entrez:
9
6
2020
Statut:
ppublish
Résumé
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.
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
541-556Subventions
Organisme : European Cooperation in Science and Technology
ID : CA15112
Organisme : Slovenian Agency of Research
ID : P4-0133
Organisme : H2020 Societal Challenges
ID : 634476
Organisme : Università di Bologna
ID : RFO 2016-2019 programme
Organisme : Ministero dell'Istruzione, dell'Università e della Ricerca
ID : PigPhenomics
Informations de copyright
© 2020 Stichting International Foundation for Animal Genetics.
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