Copy number variation in the bovine genome

TY - JOUR

T1 - Copy number variation in the bovine genome

AU - Fadista, João

AU - Thomsen, Bo

AU - Holm, Lars-Erik

AU - Bendixen, Christian

PY - 2010

Y1 - 2010

N2 - BackgroundCopy 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.ResultsWe 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.ConclusionsTogether, this analysis provides a useful resource for assessment of the impact of CNVs regarding variation in bovine health and production traits

AB - BackgroundCopy 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.ResultsWe 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.ConclusionsTogether, this analysis provides a useful resource for assessment of the impact of CNVs regarding variation in bovine health and production traits

U2 - 10.1186/1471-2164-11-284

DO - 10.1186/1471-2164-11-284

M3 - Journal article

C2 - 20459598

SN - 1471-2164

VL - 11

JO - B M C Genomics

JF - B M C Genomics

IS - article 284

ER -