ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2016
Diversity and population-genetic properties of copy number variations and multicopy genes in cattle.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed, 99 citations in OpenAlex.
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- Ancient Mongolian aurochs and cattle genomes reveal population shifts associated with the expansion of herding.iScience · 2026Article
- Identification of the Genetic Characteristics of Copy Number Variation Regions in Diverse Goat Populations.Genes · 2026Article
- Insights into Copy Number Variation Architecture in Black Bengal Goat Genome.International journal of molecular sciences · 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
- Exploring cattle structural variation in the era of long reads, pangenome graphs, and near-complete assemblies.Journal of animal science and biotechnology · 2025Review
- Detection and functional assessment of structural variants using whole-genome re-sequencing data in Nellore cattle.Scientific reports · 2025Article
- Identification of IGFBP2 gene polymorphism and association of genotypes with performance traits in Large White Yorkshire pigs.Tropical animal health and production · 2025Article
- Genome-wide copy number variation regions in indigenous (Bos indicus) cattle breeds of Tamil Nadu, India.Animal bioscience · 2025Article
- Study on the Carcass Traits, Meat Quality, and Nutritional Attributes of Six Kinds of Jiangxi Local Breeds Cattle.Animals : an open access journal from MDPI · 2024Article
- Mapping and functional characterization of structural variation in 1060 pig genomes.Genome biology · 2024Article
- Detection and characterization of copy number variation in three differentially-selected Nellore cattle populations.Frontiers in genetics · 2024Article
- Article
- Evolutionary origin of genomic structural variations in domestic yaks.Nature communications · 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
- Optical mapping compendium of structural variants across global cattle breeds.Scientific data · 2022Article
- Copy Number Variants in Two Northernmost Cattle Breeds Are Related to Their Adaptive Phenotypes.Genes · 2022Article
- Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity.Genome research · 2022Article
- Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds.Animals : an open access journal from MDPI · 2022Article
- Genome-Wide Selection Signatures and Human-Mediated Introgression Events inFrontiers in genetics · 2022Article
Corrections and comments
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Authors and funding
14 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1 Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future.
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