ArticleBMC genomics2020
Functional and population genetic features of copy number variations in two dairy cattle populations.
Article in BMC genomics, 2020. 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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Who cites it
24 citing papers in PubMed, 49 citations in OpenAlex.
- Causal variants in animal genomes: approaches to identification, phenotypic impact, and implications for selective breeding.BMC genomics · 2026Review
- Detecting and characterizing copy number variation in a large commercial U.S. Holstein cattle population.BMC genomics · 2025Article
- Inferring the Selective History of CNVs Using a Maximum Likelihood Model.Genome biology and evolution · 2025Article
- Whole-genome sequencing of copy number variation analysis in Ethiopian cattle reveals adaptations to diverse environments.BMC genomics · 2024Article
- Identification of consensus homozygous regions and their associations with growth and feed efficiency traits in American mink.BMC genomic data · 2024Article
- A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle.Animals : an open access journal from MDPI · 2024Article
- Clustering of countries based on dairy productivity characteristics of Holstein cattle for breeding material selection.Veterinary world · 2024Article
- The promise and pitfalls of synteny in phylogenomics.PLoS biology · 2024Article
- Copy number variant scan in more than four thousand Holstein cows bred in Lombardy, Italy.PloS one · 2024Article
- Comparative genomic diversity analysis of copy number variations (CNV) in indicine and taurine cattle thriving in Europe and Indian subcontinent.Animal biotechnology · 2023Article
- Detection of genome-wide copy number variation in Murrah buffaloes.Animal biotechnology · 2023Article
- Genome-Wide Association Study Reveals Novel Loci Associated with Body Conformation Traits in Qinchuan Cattle.Animals : an open access journal from MDPI · 2023Article
- Article
- High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data.BMC genomics · 2023Article
- Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle.Frontiers in veterinary science · 2023Article
- Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations.BMC genomics · 2022Article
- Two Different Copy Number Variations of theAnimals : an open access journal from MDPI · 2021Article
- DNA copy number variation: Main characteristics, evolutionary significance, and pathological aspects.Biomedical journal · 2021Review
- Genome-wide detection of CNVs and their association with performance traits in broilers.BMC genomics · 2021Article
- Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs.BMC genomics · 2021Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundCopy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features.
resultsWe discovered 14,272 autosomal CNVs, which were aggregated into 1755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (MAF ≥ 0.05). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes, which are related to starch digestion and body size, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF ≥ 0.05) showed slightly higher LD (r
conclusionsOur analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17, which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers.
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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 Socratic graph.