Fontanesi et al. BMC Genomics 2010, 11:639 http://www.biomedcentral.com/1471-2164/11/639 CNVR in bp, the number of valid probes in the CNVR (additional probes are included in CNVR considering the position between two contiguous regions without 0.175 log2 value; see Methods for the definition of CNVR), the type of CNVR (gain/loss), the frequency of CNVR in the analysed goat panel, the goat breed (C = Camosciata delle Alpi; G = Girgentana; MG = Murciano-Granadina; S = Saanaen), and the goat subject (numbers after the breed symbols indicate the different animals used in the aCGH experiment). Additional file 3: Extension of CNVRs in the different chromosomes. Proportion of the CNVRs identified in goat compared to the dimension of the bovine chromosomes. Additional file 4: List of cattle CNVRs reported in four other experiments [49-52]and overlapping with goat CNVRs. CNVRs identified in cattle have been merged from the four reported experiments [49-52]. Progressive CNVR number has been assigned using the complete list. CNVRs are indicated with nucleotide positions (begin and end) on the Btau_4.0 version. Information reported for the four different experiments includes the progressive number and in parenthesis the chromosome number and the nucleotide positions (start and end). The goat CNVRs are reported. Additional file 5: Tables reporting the P values for the overlapping between goat and cattle CNVRs and among the four CNVR datasets available in cattle. Table S1 reports the results obtained comparing the goat CNVRs with the cattle CNVRs. Table S2 reports the results obtained comparing the different cattle datasets. Additional file 6: Primers and PCR conditions used to validate goat CNVRs. The table includes the goat CNVRs number, the corresponding bovine chromosome, gene symbol, amplified gene fragment data (including Ensembl number), sequence of the PCR primers, length of the amnplified fragment and PCR conditions. Additional file 7: Semiquantitative fluorescent multiplex-PCR (SQF- PCR) results obtained for different goats. The averaged SQF-PCR ratio normalized against the reference Camosciata delle Alpi goat is reported for the goats of the aCGH panel and for additional goats (additional panel) for the validated CNVs. Additional file 8: Gene Ontology (GO) annotation of genes included in goat CNVRs. Ensembl cattle transcripts located in goat CNVRs have been annotated using GO for Biological process, Cellular component, and Molecular function. Additional file 9: PANTHER annotation of genes included in goat CNVRs. Ensembl cattle transcripts located in goat CNVRs have been annotated using PANTHER. Additional file 10: Gene ontology (GO) categories significantly overrepresented in goat CNVRs at different False Discovery Rate (FDR) levels. GO categories were Molecular function, Biological process, and Cellular component. Additional file 11: PANTHER categories significantly overrepresented in goat CNVRs. PANTHER annotation has been obtained for the whole cattle genome. Additional file 12: List of goat CNVRs with human orthologous genes. EntrezGene ID and gene name are reported for human orthologous genes. The file includes genes already mapped in goat and genes for which mutations in human cause or are associated with human genetic diseases (data have been retrieved from OMIM database, May 2010). Acknowledgements We thank Drs. Charles Lee, Omer Gökçümen (Harvard Medical School, USA), and Giuliano Galimberti (University of Bologna, Italy) for advices on statistical evaluations of goat-cattle CNVR overlaps. We thank farmers and people who helped in obtaining goat samples. We also thank the three anonymous reviewers for their useful comments to the early version of the manuscript. This work was funded by the Assessorato Agricoltura e Foreste of the Regione Siciliana - U.O.B. 108, SOAT n. 69 Aragona (AG), by the Italian MiPAAF SELMOL project and by the University of Bologna RFO funds and Page 12 of 15 was associated with the MIUR-PNR 2003 project (FIRB art.8) termed LIBI- Laboratorio Internazionale di BioInformatica. Author details 1DIPROVAL, Sezione di Allevamenti Zootecnici, University of Bologna, Via F.lli Rosselli 107, 42123 Reggio Emilia, Italy. 2Biocomputing Group, Computational Biology Network, Dept. of Biology, University of Bologna, Via San Giacomo 9/ 2, 40126 Bologna, Italy. 3Dept. S.En.Fi.Mi.Zo., Sezione di Produzioni Animali, University of Palermo, Viale delle Scienze - Parco d’Orleans, 90128 Palermo, Italy. Authors’ contributions LF conceived and designed the study, analysed data, contributed to the sampling, coordinated and organized the laboratory work, drafted the manuscript and partially funded the study. PLM conducted bioinformatic and computational analyses. FB carried out the laboratory work and prepared data for analyses. VRi and SD contributed to the sampling and data. MC collaborated in the laboratory work. RC and VRu supervised the work and were involved in the design of the study. BP provided samples, supervised, took part in designing the work and partially funded the study. All authors reviewed the manuscript and accepted the final version. Received: 9 July 2010 Accepted: 17 November 2010 Published: 17 November 2010 References 1. FAO: The State of the World’s Animal Genetic Resources for Food and Agriculture, Rome 2007. 2. Vaiman D, Schibler L, Bourgeois F, Oustry A, Amigues Y, Cribiu EP: A genetic linkage map of the male goat genome. Genetics 1996, 144:279-305. 3. Schibler L, Vaiman D, Oustry A, Giraud-Delville C, Cribiu EP: Comparative gene mapping: a fine-scale survey of chromosome rearrangements between ruminants and humans. Genome Res 1998, 8:901-915. 4. Allard MW, Miyamoto MM, Jarecki L, Kraus F, Tennant MR: DNA systematics and evolution of the artiodactyl family Bovidae. Proc Natl Acad Sci USA 1992, 89:3972-3976. 5. Gatesy J, Yelon D, DeSalle R, Vrba ES: Phylogeny of the Bovidae (Artiodactyla, Mammalia), based on mitochondrial ribosomal DNA sequences. Mol Biol Evol 1992, 9:433-446. 6. Matthee CA, Davis SK: Molecular insights into the evolution of the family Bovidae: a nuclear DNA perspective. Mol Biol Evol 2001, 18:1220-1230. 7. Schibler L, Di Meo GP, Cribiu EP, Iannuzzi L: Molecular cytogenetics and comparative mapping in goats (Capra hircus, 2n = 60). Cytogenet Genome Res 2009, 126:77-85. 8. Cribiu EP, Di Berardino D, Di Meo GP, Eggen A, Gallagher DS, Gustavsson I, Hayes H, Iannuzzi L, Popescu CP, Rubes J, Schmutz S, Stranzinger G, Vaiman A, Womack J: International System for Chromosome Nomenclature of Domestic Bovids (ISCNDB 2000). Cytogenet Cell Genet 2001, 92:283-299. 9. Schibler L, Cribiu EP, Oustry-Vaiman A, Furet JP, Vaiman D: Fine mapping suggests that the goat Polled Intersex Syndrome and the human Blepharophimosis Ptosis Epicanthus Syndrome map to a 100-kb homologous region. Genome Res 2000, 10:311-318. 10. Pailhoux E, Vigier B, Chaffaux S, Servel N, Taourit S, Furet JP, Fellous M, Grosclaude F, Cribiu EP, Cotinot C, Vaiman D: A 11.7-kb deletion triggers intersexuality and polledness in goats. Nat Genet 2001, 29:453-458. 11. Barbieri ME, Manfredi E, Elsen JM, Ricordeau G, Bouillon J, Grosclaude F, Mahé MF, Bibé B: Influence du locus de la caséine αs1 sur les performances laitières et les paramètres génétiques des chèvres de race Alpine. Genet Sel Evol 1995, 27:437-450. 12. Hayes B, Hagesaether N, Adnøy T, Pellerud G, Berg PR, Lien S: Effects on production traits of haplotypes among casein genes in Norwegian goats and evidence for a site of preferential recombination. Genetics 2006, 174:455-464. 13. Gigli I, Maizon DO, Riggio V, Sardina MT, Portolano B: Short communication: casein haplotype variability in Sicilian dairy goat breeds. J Dairy Sci 2008, 91:3687-3692. 14. Vaccari G, Panagiotidis CH, Acin C, Peletto S, Barillet F, Acutis P, Bossers A, Langeveld J, van Keulen L, Sklaviadis T, Badiola JJ, Andreéoletti O, Groschup MH, Agrimi U, Foster J, Goldmann W: State-of-the-art review of