Copy number variation in the porcine genome

Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, are currently being associated with phenotypes of clinical relevance, mostly in humans and mice. Notwithstanding, little is known about the extent of CNV that contributes to genetic variation in farm animals, including pig. This Nimblegen experiment reports a genome-wide high resolution map of copy number variation in the porcine genome. After remapping the initial CNV sequences to the latest genome assembly (Sus scrofa v.9), 84 CNV regions (CNVRs) were identified among the genomes of 21 related porcine samples from Duroc breed. We used a set of NimbleGen CGH arrays that tile across the assayable portion of the pig genome with approximately 2.1 million probes, at a 502 bp average probe spacing (Sus scrofa pre assembly version 6). These CNVRs covered 2 Mb of the genome, and ranged in size from 4 to 352 kb (median size of 12 kb). Together, this analysis provides a useful resource to assist with the assessment of CNVs in the contexts of porcine variation, health and productive efficiency. 21 samples were analyzed in a dye swap loop design. In order to cover the latest, at the time of the experiment, porcine genome assembly (Sus scrofa v.6) with high density, custom Nimblegen HD2 CGH arrays were planned to cover all the chromosomes available with 2.1M probes, which yielded 502 bp of average probe spacing.