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Identification and characterization of copy number variations in cattle

Letaief, Rabia and Esquerré, Diane and Barbieri, Johanna and Grohs, Cecile and Fritz, Sebastien and Klopp, Christophe and Philippe, Romain and Blanquet, Véronique and Boichard, Didier and Rocha, Dominique and Boussaha, Mekki Identification and characterization of copy number variations in cattle. (2016) Journal of Animal Science, 94. 183. ISSN 0021-8812

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Official URL: http://dx.doi.org/10.2527/jas2016.94supplement4183a

Abstract

Copy number variations (CNVs) are an important source of genetic changes. They are defined as a gain or loss of genomic region ranging from 50 bp to several megabases. CNVs have been shown to be associated with many diseases and some phenotypic traits in several species, including cattle. We used Pindel, Delly, BreakDancer, and CNVnator to identify CNVs using whole-genome sequencing data of 200 animals from eight French dairy and beef cattle breeds. We selected only deletions and duplications predicted by at least two tools and present in at least two animals. We identified a total of 29,132 autosomal deletions and duplications which cover between 31 to 34% (784 to 865 Mb) of the autosomal genome, with an average of 6,000 events per animal. Among these deletions and duplications, 27,690 were present in at least two animals. Out of theses, 26,417 events were deletions, 674 were duplications and 599 regions were both (deletion and duplication within the same region). We defined a CNV as deletion and duplication in the same region, and we termed this region as CNV-Region (CNVR). The size of CNVRs ranged from 100 bp to 9.3 Mb with a median of 1.3 kb and a mean of 45 kb. From the identified deletions and duplications, 8,283 overlapped with 9,733 annotated genes including 290 CNVRs overlapping with 974 annotated genes, including some genes known to be implicated in some traits of economic importance. Our study provides an extensive view of the CNVRs in French dairy and beef breeds. CNVRs with an effect on some commercially interesting phenotypes could be used to improve genetic selection of these eight French breeds.

Item Type:Article
Additional Information:Thanks to American Society of Animal Science editor. The definitive version is available at https://academic.oup.com/jas The original PDF of the article can be found at Journal of Animal Science website : https://academic.oup.com/jas/article/94/suppl_4/183/4740855
ProdINRA Id:387195
Audience (journal):International peer-reviewed journal
Uncontrolled Keywords:
Institution:Other partners > AgroParisTech (FRANCE)
Université de Toulouse > Institut National Polytechnique de Toulouse - INPT (FRANCE)
French research institutions > Institut National de la Recherche Agronomique - INRA (FRANCE)
Other partners > Université de Limoges - UNILIM (FRANCE)
Other partners > ALLICE (FRANCE)
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Deposited By: INRA INRA
Deposited On:01 Mar 2019 11:44

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