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

AbstractBackgroundCopy number variations (CNV) are known to play a major role in genetic variability and disease pathogenesis in several species including cattle. In this study, we report the identification and characterization of CNV in eight French beef and dairy breeds using whole-genome sequence data from 200 animals. Bioinformatics analyses to search for CNV were carried out using four different but complementary tools and we validated a subset of the CNV by both in silico and experimental approaches. ResultsWe 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.ConclusionsOur 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.

Mots clés

génome bovin copy number variants

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Sciences du Vivant [q-bio]

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https://hal.science/hal-01622967

Soumis le : mardi 24 octobre 2017-20:06:08

Dernière modification le : mardi 19 novembre 2024-14:58:03

Archivage à long terme le : jeudi 25 janvier 2018-14:29:19

Dates et versions

hal-01622967 , version 1 (24-10-2017)

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Paternité

Identifiants

HAL Id : hal-01622967 , version 1
DOI : 10.1186/s12711-017-0352-z
PRODINRA : 415377
PUBMED : 29065859

Citer

Rabia Letaief, Emmanuelle Rebours, Cécile Grohs, Cédric Meersseman, Sébastien Fritz, et al.. Identification of copy number variation in French dairy and beef breeds using next-generation sequencing. Genetics Selection Evolution, 2017, 49 (1), pp.77. ⟨10.1186/s12711-017-0352-z⟩. ⟨hal-01622967⟩

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