Copy number variation in the bovine genome

João Fadista, Bo Thomsen, Lars-Erik Holm, Christian Bendixen

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    Abstract

    Background

    Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, have been shown to be associated with phenotypes of clinical relevance and to be causative of disease. Notwithstanding, little is known about the extent to which CNV contributes to genetic variation in cattle.

    Results

    We designed and used a set of NimbleGen CGH arrays that tile across the assayable portion of the cattle genome with approximately 6.3 million probes, at a median probe spacing of 301 bp. This study reports the highest resolution map of copy number variation in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. The CNVRs identified covered 0.68% (22 Mb) of the genome, and ranged in size from 1.7 to 2,031 kb (median size 16.7 kb). About 20% of the CNVs co-localized with segmental duplications, while 30% encompass genes, of which the majority is involved in environmental response. About 10% of the human orthologous of these genes are associated with human disease susceptibility and, hence, may have important phenotypic consequences.

    Conclusions

    Together, this analysis provides a useful resource for assessment of the impact of CNVs regarding variation in bovine health and production traits

    Original languageEnglish
    JournalB M C Genomics
    Volume11
    Issuearticle 284
    Number of pages12
    ISSN1471-2164
    DOIs
    Publication statusPublished - 2010

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