Fontanesi et al. BMC Genomics 2010, 11:639 http://www.biomedcentral.com/1471-2164/11/639 Page 5 of 15 Figure 2 Comparative map of CNVRs identified in goats reported on the bovine chromosomes. Considering this additional CNVR, on the whole we identified 127 CNVRs for a total of 11.47 Mb (Figure 2 and Additional file 2). These 127 CNVRs included 86 losses and 41 gains, whereas none reported both events. Of these CNVRs, 14 were found in multiple animals of different breeds (no. = 7) or in multiple animals of the same and different breeds (no. = 6) or in multiple ani- mals of the same breed only (no. = 1). All other events (no. = 113) were found only in one animal. The regions that were affected by these gain or loss events in goats ranged from 24,605 bp (BTA22, CNVR no. 101) to 1,075,778 bp (BTA17, CNVR no. 90) with mean and median equal to 90,292 bp and 49,530 bp, respectively (Additional file 2). Using a similar aCGH experiment Liu et al. [51] reported that cattle CNVRs are on average a little bit larger than those we reported in goats (mean and median equal to 159,031 bp and 89,053 bp, respec- tively). This is in contrast to Fadista et al. [52] who, using more dense arrays in another aCGH experiment reported a median size of CNVRs equal to 16.7 kb. Mean and median differences between goat and cattle experiments might be due to i) the cross species experi- ment performed in goat that might not be able to cor- rectly identify the borders of the CNVRs, ii) the oligonucleotide density in the aCGH experiments, iii) true differences between species/breeds. It is interesting to note that the number of loss events was about two fold the number of gain events in both cattle and goat. This finding might be derived by both biological and technical reasons. Non-allelic homologous recombina- tion, which seems to be one of the most important mechanisms responsible for CNV formation, has been shown to generate more deletions than duplications [79]. On the other hand, aCGH detection methods seem to favor the identification of deletions as reported by several other studies [28,47,51,52]. Additional file 3 reports the extension of CNVRs dis- tributed for the different bovine chromosomes used in the comparative analysis with the goat genome. In only three chromosomes (BTA11, BTA20, and BTA21) we did not identify any CNVRs. BTA5 included the largest number of CNVRs (no. = 11), whereas BTA17, BTA10, and BTA18 included the largest extension of regions affected by CNVs (1.6%, 1.3% and 1.0% of their length, respectively) (Figure 2). In cattle a similar aCGH experi- ment (that however included a larger number of animals [51]) showed the greatest enrichment for CNVRs on BTA5, BTA15, BTA18, BTA27, BTA29, and BTAX. Comparative mapping and chromosome banding simila- rities between cattle and goat indicate highly conserved synteny between these two ruminant species even if a few rearrangements have been evidenced mainly on CHI14 containing a small BTA9q11-q13 segment, and some other gene order rearrangements for chromo- somes CHI2 compared to BTA2, CHI19 compared to BTA19, and CHIX compared to BTAX [7,8]. CNVRs were evidenced in these interested chromosome regions. However, it is not possible to evidence if CNVs are pre- cisely positioned in rearranged regions because of the low resolution of the rearrangements so far described between goat and cattle chromosomes due to the few mapped genes.