CNVs in the Pig Genome Figure 3. Example of a CNVR. CNVR 28 is shown (zoomed out on bottom left; zoomed in on bottom right) with log2ratio along with the probes (blue bars) covered in this region. Images from Nimblegen SignalMapTM and Ensembl [39]. doi:10.1371/journal.pone.0003916.g003 Discussion Here, using a custom tiling oligonucleotide array CGH approach, we reported the first CNV survey of the pig genome among twelve unrelated healthy boars which are founders of a vast pig family. It should be stressed that only four chromosomes and not the whole genome were screened here. Both gains and losses of different lengths were discovered on part of chromosomes 4, 7, 14, and 17. With the tiling nature of the array, we were able to identify 37 frequently occurring loci of copy number variation. Natural large-scale genomic size divergence between animals of the same breed was found to vary by at least 164.1 kb, showing that a substantial portion of the pig genome may vary in copy number. In comparison with CNV studies in the ‘‘finished’’ human and mouse genomes [17,22], our study found an order of magnitude less genomic size divergency. This is not surprising since the pig assembly is currently only in its draft form, covering less sequenced data. With a detection sensitivity ranging from about 2 kb (median spacing*5probes) to 248.471 kb (length of the biggest contig in the Table 2. Summary of the CNVR content (in bp) and sequence covered (including gaps) by the oligo array CGH probes. Chr CNVRs Median size Mean size Size range CNVR Content Sequence covered % CNVR 4 7 8 16 14 11 17 2 All 37 7 116 7 004 6 783 3 554 6 894 doi:10.1371/journal.pone.0003916.t002 7 279 14 639 11 792 3 554 9 316 10 182–3 600 6 1920–3 030 44 029–1 744 5 024–2 083 61 920–1 744 58 223 234 223 129 716 7 107 429 269 52983989 76062953 83175859 25535213 237758014 0.11 0.31 0.156 0.03 0.18 PLoS ONE | www.plosone.org 5 December 2008 | Volume 3 | Issue 12 | e3916