ArticleGenome research2012
Copy number variation of individual cattle genomes using next-generation sequencing.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 175 papers.
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Who cites it
175 citing papers in PubMed, 330 citations in OpenAlex.
- Association ofAnimals : an open access journal from MDPI · 2026Article
- Whole-genome resequencing suggests adaptive role of copy number variation regions in Indian cattle.Tropical animal health and production · 2026Article
- Article
- Genome-wide characterization of copy number variants and their functional relevance in indigenous draught cattle of South Asia.PloS one · 2026Article
- Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle.Journal of advanced research · 2026Article
- Detection and evaluation of copy number variation using both linked-read and short-read sequencing in New Zealand dairy cattle.Frontiers in genetics · 2026Article
- Genome-wide detection of copy number variations in indigenous Red Sindhi cattle using ddRAD sequencing.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Mapping copy number variable regions correlated with reproduction and production traits in Karan Fries cattle mammalian genomics.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Exploring cattle structural variation in the era of long reads, pangenome graphs, and near-complete assemblies.Journal of animal science and biotechnology · 2025Review
- Transcriptome and Metabolome Profiles Reveal the Underlying Mechanism of Fat Deposition Changes in Three-Way Crossbred Yak for High-Quality Beef Production.Animals : an open access journal from MDPI · 2025Article
- Global Pangenome Analysis Highlights the Critical Role of Structural Variants in Cattle Improvement and Identifies a Unique Event as a Novel Enhancer in IGFBP7+ Cells.Molecular biology and evolution · 2025Article
- Detection and functional assessment of structural variants using whole-genome re-sequencing data in Nellore cattle.Scientific reports · 2025Article
- Population-level gene copy number variations reveal distinct genetic properties of different Malus species.BMC genomics · 2025Article
- Skeletal muscle lncRNA profile associated with fatty acids in Nellore beef 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
- The CNV map construction and ROH analysis of Pinan cattle.BMC genomics · 2025Article
- AMPed up immunity: 418 whole genomes reveal intraspecific diversity of koala antimicrobial peptides.Immunogenetics · 2025Article
- Impact of β-defensin 103 (DEFB103) copy number variation on bull sperm parameters and post-insemination uterine gene expression.PloS one · 2025Article
- Whole-genome sequencing of copy number variation analysis in Ethiopian cattle reveals adaptations to diverse environments.BMC genomics · 2024Article
- A comprehensive map of copy number variations in dromedary camels based on whole genome sequence data.Scientific reports · 2024Article
115 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 7 institutions in 4 countries.
Funding
Abstract
Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising ~55.6-Mbp sequence--476 of which (~38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (~52%, χ(2) test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.