A comparative analysis of copy number variation of the sheep and goat genomes

Recent studies have shown that copy number variants (CNVs), defined as intraspecific gains or losses of 1 kb of genomic DNA (Feuk et al. (2006); Freeman et al. (2006)), are important sources of variability of mammalian genomes as reported in human (e.g. Redon et al. (2006); Shaikh et al. (2009)) and other primates (Perry et al. (2006); Lee et al. (2008)), mouse (Cutler et al. (2007); Graubert, et al. (2007)), rat (Guryev et al. (2008)), dog (Chen et al. (2009); Nicholas et al. (2009)) and pig (Fadista et al.(2008)). Genome-wide discovery and frequency evaluation of CNVs have been possible with the development of high-resolution array comparative genome hybridization (aCGH) and then with data analysis of high-density single nucleotide polymorphism (SNP) platforms (Pinkel et al. (1998); McCarroll et al. (2008)). An advantage of aCGH is that hybridization can be performed using heterologous DNA, i.e. genomic DNA of a different species but close to that used to develop the array, taking advantage from completely sequenced, assembled and annotated genomes. Cross species aCGH experiments have been successfully applied using human array to analyse CNV in chimpanzee (Perry et al. (2006)). Moreover, chicken based aCGH studies have been applied to analyse the turkey and duck genomes (Griffin et al. (2008); Skinner et al. (2009)). Sheep and goat genomes are not completely sequenced and assembled yet and no systematic studies have been carried out to analyse CNVs in these species. Here, we applied a cross species aCGH study using as reference the cattle genome to identify copy number variation in the sheep and goat genomes.