Fontanesi et al. BMC Genomics 2010, 11:639 http://www.biomedcentral.com/1471-2164/11/639 binds to mineralocorticoid response elements in order to transactivate target genes. Mutations in this gene in humans cause autosomal dominant pseudohypoaldoster- onism type I, a disorder characterized by renal resistance to aldosterone as well as salt wasting, dehydration, hyper- kalemia, metabolic acidosis and failure to thrive in the newborn [84]. Defects in this gene are also associated with early onset hypertension [85], whereas overexpres- sion of this gene in forebrain decreases anxiety-like beha- vior [86]. It is tempting to speculate that additional copies of the NR3C2 gene (if functional) could contribute to specific adaptation traits to harsh and dry environ- ments and to the very mild behavior of the Girgentana goats compared to other breeds. Considering all 127 goat CNVRs, 78 of them (61.4%) partially or completely spanned cattle Ensembl anno- tated genes (Btau_4.0 version), including 249 Ensembl peptides, corresponding to 199 unique Ensembl cattle genes, representing 261, 126, and 864 gene ontology (GO) categories for molecular function, cellular compo- nents and biological processes, and 870 different PANTHER terms (Additional file 8 and Additional file 9). For example, considering GO annotation for biologi- cal processes, several GO categories are significantly (P < 0.001) over-represented in goat CNVRs (Table 4; Additional file 10). A few of these GO terms (response to stimulus; defense response) have been also already reported to be over-represented in CNVRs of the mouse and human genomes [39,87]. In general, goat CNVRs resulted particularly enriched in “environmental” func- tions (Table 4; Additional file 10 and Additional file 11) as already reported in other species [39,46,50-52,87]. This indication might be important in understanding the evolutionary and selection processes that determined the occurrence and diffusion of this variability in the goat genome. It could be possible that positive selection on duplications (based on functional effects) has occurred for these particular gene categories or that these enrichments might instead have been arisen from nonuniform negative selection on gene copy changes. This could be due to the fact that duplication or dele- tion of nonenvironmental genes might be more fre- quently deleterious than copy number changes of environmental genes [88]. The complex domestication process and artificial selection for breeding purposes (including bottleneck and expansion) that largely con- tributed to establish goat breed differences [89] might further complicate the evaluation of these two different hypotheses. Considering the 199 unique Ensembl cattle genes included in the CNVRs identified in goats, for 119 we retrieved a human orthologous gene. Mutations in only 8 of these genes cause Mendelian disorders or are asso- ciated with genetic diseases in human (Additional file Page 8 of 15 12). None of these 199 cattle genes is involved in any reported genetic disease in goat, sheep or cattle. Among the goat genes already mapped [7] only one (TTN) is included in a CNVR (Additional file 12). Few QTL studies have been reported in goats so far [15-20] and all used breeds/populations not included in our CNV study, except one in which a few Saanen crosses were analysed [15]. In addition, the identified QTL have very large confidence intervals including most of the CNVRs we observed in several chromosomes (data not shown). Therefore a comparison among CNVRs we identified in goats, their gene content and QTL regions is not very informative. However, it is interesting to note that Bolormaa et al. [20] reported putative QTL for faecal worm egg and eosinophil counts on CHI23, in the region including the major histocom- patibility complex (MHC), in which we reported two CNVRs, one affecting a MHC class I antigen gene (CNVR no. 108, gain of copies) and the other one including MHC class II alpha and beta chain genes (CNVR no. 107, loss of copies) (Additional file 8 and Additional file 9). In sheep, several reports have identi- fied polymorphisms in the class I and class II regions of the MHC being associated with resistance to nematodes [90]. It will be interesting to evaluate if these CNVs we identified in goats are associated with resistance to nematode infection and other diseases. Conclusions We provide a first comparative map of CNVRs in the goat genome using a cross-species aCGH experiment based on the cattle genome. Considering the limited number of analysed animals and breeds and the fact that the cross-species hybridization could have limited the detection power of this study, the reported goat CNVRs largely underestimate the true number of this kind of variation in the goat genome. Additional studies including other breeds should be carried out in order to better evaluate the extension and distribution of CNVs in the genome of this farm animal species. However, it appeared that possible evolutionary conserved mechan- isms might be the causative factors of putative recurrent interspecies CNVs between cattle and goat. Using this cross-species design it seems possible to analyse several other genomes of the Bovidae family in order to obtain comparative CNV maps in other species close to the cattle and provide additional evidence on the co-occur- rence of CNVs in particular chromosome regions. Sev- eral 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.