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BMC Genomics

, 14:124

Non-human and non-rodent vertebrate genomics


BackgroundCopy number variations CNVs represent a significant source of genomic structural variation. Their length ranges from approximately one hundred to millions of base pair. Genome-wide screenings have clarified that CNVs are a ubiquitous phenomenon affecting essentially the whole genome. Although Bos taurus is one of the most important domestic animal species worldwide and one of the most studied ruminant models for metabolism, reproduction, and disease, relatively few studies have investigated CNVs in cattle and little is known about how CNVs contribute to normal phenotypic variation and to disease susceptibility in this species, compared to humans and other model organisms.

ResultsHere we characterize and compare CNV profiles in 2654 animals from five dairy and beef Bos taurus breeds, using the Illumina BovineSNP50 genotyping array 54001 SNP probes. In this study we applied the two most commonly used algorithms for CNV discovery QuantiSNP and PennCNV and identified 4830 unique candidate CNVs belonging to 326 regions. These regions overlap with 5789 known genes, 76.7% of which are significantly co-localized with segmental duplications SD.

ConclusionsThis large scale screening significantly contributes to the enrichment of the Bos taurus CNV map, demonstrates the ubiquity, great diversity and complexity of this type of genomic variation and sets the basis for testing the influence of CNVs on Bos taurus complex functional and production traits.

KeywordsCopy number variants Structural variations Cattle Bos taurus AbbreviationsBAFB-allele frequency

BFBayes factor

BTABos taurus autosome

CGHComparative genomic hybridization

CNVCopy number variation

CNVRCopy number variation region

GO termGene Ontology term

LRRLog R ratio


qRT-PCRQuantitative real-time polymerase chain reaction

rRNARibosomial RNA

SDSegmental duplication

snoRNASmall nucleolar RNA

SNPSingle nucleotide polymorphism

snRNASmall nuclear RNA

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-124 contains supplementary material, which is available to authorized users.

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Autor: Francesco Cicconardi - Giovanni Chillemi - Anna Tramontano - Cinzia Marchitelli - Alessio Valentini - Paolo Ajmone-Marsan -


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