Fontanesi et al. BMC Genomics 2010, 11:639 http://www.biomedcentral.com/1471-2164/11/639 R E S E A R C H A R T I C L E Open Access An initial comparative map of copy number variations in the goat (Capra hircus) genome Luca Fontanesi1*, Pier Luigi Martelli2, Francesca Beretti1,3, Valentina Riggio3, Stefania Dall’Olio1, Michela Colombo1, Rita Casadio2, Vincenzo Russo1, Baldassare Portolano3 Abstract Background: The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi, Girgentana, and Murciano-Granadina) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. Results: We identified a total of 161 CNVs (an average of 17.9 CNVs per goat), with the largest number in the Saanen breed and the lowest in the Camosciata delle Alpi goat. By aggregating overlapping CNVs identified in different animals we determined CNV regions (CNVRs): on the whole, we identified 127 CNVRs covering about 11.47 Mb of the virtual goat genome referred to the bovine genome (0.435% of the latter genome). These 127 CNVRs included 86 loss and 41 gain and ranged from about 24 kb to about 1.07 Mb with a mean and median equal to 90,292 bp and 49,530 bp, respectively. To evaluate whether the identified goat CNVRs overlap with those reported in the cattle genome, we compared our results with those obtained in four independent cattle experiments. Overlapping between goat and cattle CNVRs was highly significant (P < 0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Genes with environmental functions were over-represented in goat CNVRs as reported in other mammals. Conclusions: We describe a first map of goat CNVRs. This provides information on a comparative basis with the cattle genome by identifying putative recurrent interspecies CNVs between these two ruminant species. Several goat CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs and their effects on behavior, production, and disease resistance traits in goats. Background The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all conti- nents with an estimated world population of about 800 million of animals and about 560 breeds, which consti- tute approximately 12% of the total number of recorded domesticated mammalian livestock breeds of the world [1]. The diffusion of this species is mainly due to its capacity to supply milk, meat, and fibers for human * Correspondence: luca.fontanesi@unibo.it 1DIPROVAL, Sezione di Allevamenti Zootecnici, University of Bologna, Via F.lli Rosselli 107, 42123 Reggio Emilia, Italy Full list of author information is available at the end of the article consumption and use in a large number of different environments, including those poor of vegetation. In general, goat breeding represents an essential support for marginal economies in most developed and develop- ing countries. Despite the importance of this species, studies on the goat genome are still in their infancy compared to those in other farm animal species. A first and a second gen- eration genetic maps of the goat genome have been obtained by Vaiman et al. [2] and Schibler et al. [3] by mapping a few hundred microsatellite markers in half- sib paternal goat families, with about 90% genome cov- erage. The relatively short evolutionary time separating © 2010 Fontanesi et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.