Genome-wide study of structural variants in bovine Holstein, Montbéliarde and Normande dairy breeds
| Autor: | Alain Pinton, Frédéric Escudié, Maria Bernard, Anis Djari, Alain Roulet, Mekki Boussaha, Franck Samson, Diane Esquerre, Cécile Grohs, Johanna Barbieri, Sébastien Fritz, Rabia Letaief, Christophe Klopp, Gerald Salin, Didier Boichard, Dominique Rocha |
|---|---|
| Přispěvatelé: | Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), Unité Mathématique, Informatique et Génome (MIG), ANR-Apisgene Cartoseq, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale |
| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
bovin
Genotype variants structuraux [SDV]Life Sciences [q-bio] Quantitative Trait Loci Genomic Structural Variation lcsh:Medicine Single-nucleotide polymorphism Genome-wide association study Quantitative trait locus Biology Genome Structural variation Animals Copy-number variation lcsh:Science 2. Zero hunger Genetics Multidisciplinary génome lcsh:R Dairying Bovine genome lcsh:Q Cattle Animals Inbred Strains Genome-Wide Association Study Research Article |
| Zdroj: | PLoS ONE PLoS ONE, Public Library of Science, 2015, 10 (8), pp.1-21. ⟨10.1371/journal.pone.0135931⟩ Plos One 8 (10), 1-21. (2015) PLoS ONE, Vol 10, Iss 8, p e0135931 (2015) |
| ISSN: | 1932-6203 |
| Popis: | High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest. |
| Databáze: | OpenAIRE |
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