ArticleBMC genomics2016
Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits.
Article in BMC genomics, 2016. 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, 50 citations in OpenAlex.
- Genome-wide characterization of copy number variants and their functional relevance in indigenous draught cattle of South Asia.PloS one · 2026Article
- 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
- Genome-wide copy number variation regions in indigenous (Bos indicus) cattle breeds of Tamil Nadu, India.Animal bioscience · 2025Article
- A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle.Animals : an open access journal from MDPI · 2024Article
- Detection and characterization of copy number variation in three differentially-selected Nellore cattle populations.Frontiers in genetics · 2024Article
- Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits.Frontiers in veterinary science · 2023Review
- Identification and Characterization of Copy Number Variations Regions in West African Taurine Cattle.Animals : an open access journal from MDPI · 2022Article
- The copy number variation of3 Biotech · 2022Article
- Molecular subtyping of ependymoma and prognostic impact of Ki-67.Brain tumor pathology · 2022Article
- Two Different Copy Number Variations of theAnimals : an open access journal from MDPI · 2021Article
- Genomic Structural Diversity in Local Goats: Analysis of Copy-Number Variations.Animals : an open access journal from MDPI · 2020Article
- High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data.Scientific reports · 2020Article
- Copy Number Variation of theAnimals : an open access journal from MDPI · 2020Article
- The Association of the Copy Number Variation of theAnimals : an open access journal from MDPI · 2020Article
- Genomic copy number variation of the CHKB gene alters gene expression and affects growth traits of Chinese domestic yak (Bos grunniens) breeds.Molecular genetics and genomics : MGG · 2019Article
- Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip.BMC genomics · 2019Article
- First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data.BMC genomics · 2018Article
- Characterization of copy number variants in a large multibreed population of beef and dairy cattle using high-density single nucleotide polymorphism genotype data.Journal of animal science · 2018Article
- Integrating CNVs into meta-QTL identified GBP4 as positional candidate for adult cattle stature.Functional & integrative genomics · 2018Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCopy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance.
resultsGenome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed 14, 13, 6 and 14 regions in high (>20 %), low (<20 %) and divergent (NEL > HOL, NEL < HOL) frequencies, respectively.
conclusionsObtained results significantly enriched the bovine CNV map and enabled the identification of variants that are potentially associated with traits under selection in Nelore cattle, particularly in genome regions harboring QTLs affecting production traits.
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