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Copy number variation in the bovine genome.

Fadista J, Thomsen B, Holm LE, Bendixen C - BMC Genomics (2010)

Bottom Line: 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.About 10% of the human orthologous of these genes are associated with human disease susceptibility and, hence, may have important phenotypic consequences.Together, this analysis provides a useful resource for assessment of the impact of CNVs regarding variation in bovine health and production traits.

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Affiliation: Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark.

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.

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Size range distribution of the CNVRs detected.
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Figure 4: Size range distribution of the CNVRs detected.

Mentions: Out of the total number of CNVRs detected, 49.7% (151) partially overlap gaps in the assembly (BT4), which indicates that the CNVRs have a high probability of being linked with gaps within the reference cattle genome assembly (permutation test, p-value < 0.001). This stresses the need for unraveling of these genomic regions of high structural complexity. The CNVRs detected vary in size from 1.7 kb to 2 Mb with a median size of 16.7 kb, and encompass approximately 23 Mb or 0.68% of the bovine genome (Table 1 and Figure 4). The biggest region showing copy loss is 2.03 Mb on chromosome 13 in animal 16, while the biggest region showing copy number gain was detected in animals 6 and 7 showing a 417 kb amplification without overlapping any gene nor SD (Additional file 1, Table S1).


Copy number variation in the bovine genome.

Fadista J, Thomsen B, Holm LE, Bendixen C - BMC Genomics (2010)

Size range distribution of the CNVRs detected.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2902221&req=5

Figure 4: Size range distribution of the CNVRs detected.
Mentions: Out of the total number of CNVRs detected, 49.7% (151) partially overlap gaps in the assembly (BT4), which indicates that the CNVRs have a high probability of being linked with gaps within the reference cattle genome assembly (permutation test, p-value < 0.001). This stresses the need for unraveling of these genomic regions of high structural complexity. The CNVRs detected vary in size from 1.7 kb to 2 Mb with a median size of 16.7 kb, and encompass approximately 23 Mb or 0.68% of the bovine genome (Table 1 and Figure 4). The biggest region showing copy loss is 2.03 Mb on chromosome 13 in animal 16, while the biggest region showing copy number gain was detected in animals 6 and 7 showing a 417 kb amplification without overlapping any gene nor SD (Additional file 1, Table S1).

Bottom Line: 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.About 10% of the human orthologous of these genes are associated with human disease susceptibility and, hence, may have important phenotypic consequences.Together, this analysis provides a useful resource for assessment of the impact of CNVs regarding variation in bovine health and production traits.

View Article: PubMed Central - HTML - PubMed

Affiliation: Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark.

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.

Show MeSH