A snapshot of CNVs in the pig genome

TY - JOUR

T1 - A snapshot of CNVs in the pig genome

AU - Fadista, João

AU - Nygaard, Marianne

AU - Holm, Lars-Erik

AU - Thomsen, Bo

AU - Bendixen, Christian

PY - 2008

Y1 - 2008

N2 - Recent studies of mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report a first account of CNVs in the pig genome covering part of the chromosomes 4, 7, 14, and 17 already sequenced and assembled. A custom tiling oligonucleotide array was used with a median probe spacing of 409 bp for screening 12 unrelated Duroc boars that are founders of a large family material. After a strict CNV calling pipeline, 37 copy number variable regions (CNVRs) across all four chromosomes were identified, with five CNVRs overlapping segmental duplications, three overlapping pig unigenes and one overlapping a RefSeq pig mRNA. This CNV snapshot analysis is the first of its kind in the porcine genome and constitutes the basis for a better understanding of porcine phenotypes and genotypes with the prospect of identifying important economic traits.

AB - Recent studies of mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report a first account of CNVs in the pig genome covering part of the chromosomes 4, 7, 14, and 17 already sequenced and assembled. A custom tiling oligonucleotide array was used with a median probe spacing of 409 bp for screening 12 unrelated Duroc boars that are founders of a large family material. After a strict CNV calling pipeline, 37 copy number variable regions (CNVRs) across all four chromosomes were identified, with five CNVRs overlapping segmental duplications, three overlapping pig unigenes and one overlapping a RefSeq pig mRNA. This CNV snapshot analysis is the first of its kind in the porcine genome and constitutes the basis for a better understanding of porcine phenotypes and genotypes with the prospect of identifying important economic traits.

KW - Animals

KW - Comparative Genomic Hybridization

KW - Gene Dosage

KW - Genome

KW - Oligonucleotide Array Sequence Analysis

KW - Reproducibility of Results

KW - Reverse Transcriptase Polymerase Chain Reaction

KW - Sus scrofa

U2 - 10.1371/journal.pone.0003916

DO - 10.1371/journal.pone.0003916

M3 - Journal article

C2 - 19079605

SN - 1932-6203

VL - 3

SP - e3916

JO - P L o S One

JF - P L o S One

IS - 12

ER -