Identification of copy number variation in French dairy and beef breeds using next-generation sequencing

Autor: Didier Boichard, Lidwine Trouilh, Diane Esquerre, Cécile Grohs, Mekki Boussaha, Johanna Barbieri, Sébastien Fritz, Véronique Blanquet, Rabia Letaief, Dominique Rocha, Romain Philippe, Emmanuelle Rebours, Cédric Meersseman, Christophe Klopp
Přispěvatelé: Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), 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, Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de la Recherche Agronomique (INRA), Unité de Génétique Moléculaire Animale (UMR GMA), Institut National de la Recherche Agronomique (INRA)-Université de Limoges (UNILIM), ANR Apisgene Bovano, Unité de Génétique Moléculaire Animale (UGMA), Université de Limoges (UNILIM)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)
Jazyk: angličtina
Rok vydání: 2017
Předmět:
0301 basic medicine
bovin
génome
copy number variants
lcsh:QH426-470
DNA Copy Number Variations
In silico
[SDV]Life Sciences [q-bio]
Quantitative Trait Loci
Single-nucleotide polymorphism
Quantitative trait locus
Biology
Genome
Polymorphism
Single Nucleotide
03 medical and health sciences
Quantitative Trait
Heritable
Genetics
Animals
Genetic variability
Copy-number variation
Genotyping
Ecology
Evolution
Behavior and Systematics
lcsh:SF1-1100
2. Zero hunger
Whole Genome Sequencing
0402 animal and dairy science
High-Throughput Nucleotide Sequencing
04 agricultural and veterinary sciences
General Medicine
040201 dairy & animal science
lcsh:Genetics
Red Meat
030104 developmental biology
Animal Science and Zoology
Cattle
lcsh:Animal culture
Dairy Products
Comparative genomic hybridization
Genome-Wide Association Study
Research Article
Zdroj: Genetics Selection Evolution 1 (49), 77. (2017)
Genetics Selection Evolution
Genetics Selection Evolution, BioMed Central, 2017, 49 (1), pp.77. ⟨10.1186/s12711-017-0352-z⟩
Genetics, Selection, Evolution : GSE
Genetics Selection Evolution, 2017, 49 (1), pp.77. ⟨10.1186/s12711-017-0352-z⟩
Genetics Selection Evolution, Vol 49, Iss 1, Pp 1-15 (2017)
ISSN: 0999-193X
1297-9686
Popis: Background : We report the identification and localization of 4178 putative deletion-only, duplication-only and CNV regions, which cover 6% of the bovine autosomal genome; they were validated by two in silico approaches and/or experimentally validated using array-based comparative genomic hybridization and single nucleotide polymorphism genotyping arrays. The size of these variants ranged from 334 bp to 7.7 Mb, with an average size of ~ 54 kb. Of these 4178 variants, 3940 were deletions, 67 were duplications and 171 corresponded to both deletions and duplications, which were defined as potential CNV regions. Gene content analysis revealed that, among these variants, 1100 deletions and duplications encompassed 1803 known genes, which affect a wide spectrum of molecular functions, and 1095 overlapped with known QTL regions.[br/] Results : We report the identification and localization of 4178 putative deletion-only, duplication-only and CNV regions, which cover 6% of the bovine autosomal genome; they were validated by two in silico approaches and/or experimentally validated using array-based comparative genomic hybridization and single nucleotide polymorphism genotyping arrays. The size of these variants ranged from 334 bp to 7.7 Mb, with an average size of ~ 54 kb. Of these 4178 variants, 3940 were deletions, 67 were duplications and 171 corresponded to both deletions and duplications, which were defined as potential CNV regions. Gene content analysis revealed that, among these variants, 1100 deletions and duplications encompassed 1803 known genes, which affect a wide spectrum of molecular functions, and 1095 overlapped with known QTL regions.[br/] Conclusions : Our study is a large-scale survey of CNV in eight French dairy and beef breeds. These CNV will be useful to study the link between genetic variability and economically important traits, and to improve our knowledge on the genomic architecture of cattle.
Databáze: OpenAIRE
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