A first comparative map of copy number variations in the sheep genome

We carried out a cross species cattle-sheep array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the sheep genome analysing animals of Italian dairy breeds (Sarda, Bagnolese, Laticauda, Massese and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs) covering about 10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and median equal to 77.6 kb and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in the cattle and goat genomes indicated that overlaps between sheep and goat and sheep and cattle CNVRs are highly significant (P<0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Many sheep CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs. In this study we made use of the high conservation and homology between the cattle and sheep genomes determined by their phylogenetic closeness to identify CNVs in sheep applying the same approach we carried out to identify CNVs in the goat genome. We used a custom tiling array including ~385,000 oligonucleotide probes designed on the Btau_4.0 version of the Bos taurus genome assembly and analysed genomic DNA samples of 11 sheep belonging to 6 different Italian dairy sheep breeds (2 Sarda, 2 Bagnolese, 2 Comisana, 2 Massese, 2 Laticauda and 1 Valle del Belice) compared to the reference DNA of another Sarda sheep.