ArticleGenetics, selection, evolution : GSE2017
Identification of copy number variation in French dairy and beef breeds using next-generation sequencing.
Article in Genetics, selection, evolution : GSE, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
- Relationship between theAnimal biotechnology · 2025Article
- Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes.Genetics, selection, evolution : GSE · 2025Article
- Detection and functional assessment of structural variants using whole-genome re-sequencing data in Nellore cattle.Scientific reports · 2025Article
- Identification of Genomic Structural Variations in Xinjiang Brown Cattle by Deep Sequencing and Their Association with Body Conformation Traits.International journal of molecular sciences · 2025Article
- A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle.Genetics, selection, evolution : GSE · 2024Article
- Read-depth based approach on whole genome resequencing data reveals important insights into the copy number variation (CNV) map of major global buffalo breeds.BMC genomics · 2023Article
- Integrin alpha 6 homozygous splice-site mutation causes a new form of junctional epidermolysis bullosa in Charolais cattle.Genetics, selection, evolution : GSE · 2023Article
- Mutation of the MYH3 gene causes recessive cleft palate in Limousine cattle.Genetics, selection, evolution : GSE · 2022Article
- Genome-wide detection of copy number variation in American mink using whole-genome sequencing.BMC genomics · 2022Article
- Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds.Scientific reports · 2022Article
- Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing.Frontiers in genetics · 2022Article
- Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions.Genetics, selection, evolution : GSE · 2021Article
- Discovering Copy Number Variation in Dual-Purpose XinJiang Brown Cattle.Frontiers in genetics · 2021Article
- Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing.BMC genomics · 2020Article
- Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms.BMC bioinformatics · 2020Article
- Comparative analyses of copy number variations between Bos taurus and Bos indicus.BMC genomics · 2020Article
- A genome-wide analysis of copy number variation in Murciano-Granadina goats.Genetics, selection, evolution : GSE · 2020Article
- High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data.Scientific reports · 2020Article
- CNV analysis of Meishan pig by next-generation sequencing and effects ofJournal of animal science and biotechnology · 2020Article
- Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays.Frontiers in genetics · 2020Article
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Authors and funding
14 authors.
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Abstract
backgroundCopy 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.
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