ArticlePloS one2015
Genome-Wide Study of Structural Variants in Bovine Holstein, Montbéliarde and Normande Dairy Breeds.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Whole-genome resequencing suggests adaptive role of copy number variation regions in Indian cattle.Tropical animal health and production · 2026Article
- Assembly of a pangenome uncovers novel non-reference unique insertion sequences in cattle highlighting their genetic diversity.Journal of animal science and biotechnology · 2026Article
- Comprehensive detection of structural variations in long and short reads dataset of French cattle.Scientific reports · 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
- Variants in Nucleotide Sequences; Gene Expression; and Hematological, Immune, and Antioxidant Biomarkers Linked to Pneumonia Risk in Holstein Calves.Veterinary sciences · 2025Article
- Genome Wide Identification of Structure Variations in Five Italian Turkey Populations.Animals : an open access journal from MDPI · 2025Article
- Defining bovine CpG epigenetic diversity by analyzing RRBS data from sperm of Montbéliarde and Holstein bulls.Frontiers in cell and developmental biology · 2025Article
- A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application.BMC genomics · 2024Article
- The Transcript Levels and the Serum Profile of Biomarkers Associated with Clinical Endometritis Susceptibility in Buffalo Cows.Veterinary sciences · 2024Article
- A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle.Animals : an open access journal from MDPI · 2024Article
- Using expression data to fine map QTL associated with fertility in dairy cattle.Genetics, selection, evolution : GSE · 2024Article
- A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle.Genetics, selection, evolution : GSE · 2024Article
- A common regulatory haplotype doubles lactoferrin concentration in milk.Genetics, selection, evolution : GSE · 2024Article
- Identification of candidate SNPs associated with embryo mortality and fertility traits in lactating Holstein cows.Frontiers in genetics · 2024Article
- Structural variations in livestock genomes and their associations with phenotypic traits: a review.Frontiers in veterinary science · 2024Review
- Article
- Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue.Genetics · 2023Article
- Integrin alpha 6 homozygous splice-site mutation causes a new form of junctional epidermolysis bullosa in Charolais cattle.Genetics, selection, evolution : GSE · 2023Article
- In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants.Genetics, selection, evolution : GSE · 2023Review
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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