Proceeding of Veterinary and Animal Science Days 2018, 6th- 8th June, Milan, Italy HAF © 2013 Vol. V, No. 1s ISSN: 2283-3927 l Recently, many studies in livestock have focused on the identification of Copy Number Variants (CNVs) using high-density Single Nucleotide Polymorphism (SNP) arrays, but few have focused on studying chicken ecotypes coming from many locations. CNVs are polymorphisms, which may influence phenotype and are an important source of genetic variation in populations (Henrichsen et al., 2009). The aim of this study was to explore the genetic difference and structure, using a high density SNP chip in 936 individuals from seven different countries (Brazil, Italy, Egypt, Mexico, Rwanda, Sri Lanka and Uganda). The DNA was genotyped with the Affymetrix Axiom®600k Chicken Genotyping Array and processed with stringent quality controls to obtain 559,201 SNPs in 915 individuals (Stranger et al., 2007). The Log R Ratio (LRR) and the B Allele Frequency of SNPs were used to perform the CNV calling with PennCNV software based on a Hidden Markov Model analysis and the LRR was used to perform CNV detection with SVS Golden Helix software. After filtering, a total of 19,027 CNVs were detected with the SVS software, while 9,065 CNVs were identified with the Penn CNV software. The CNVs were summarized in 7,001 Copy Number Variant Regions (CNVRs) and 4,414 CNVRs, using the software BedTool. The consensus analysis across the CNVRs allowed the identification of 2,820 consensus CNVR, of which 1,721 were gain, 637 loss and 462 complex, for a total length of 53 Mb corresponding to the 5 % of the GalGal5 chicken autosomes (Table 1). Only the consensus CNV regions obtained from both detections were considered for further analysis. The intersection analysis performed between the chicken gene database (Gallus_gallus-5.0) and the 1,927 consensus CNVRs allowed the identification (within or partial overlap) of a total of Keywords SNP, CNV, Genetic variability, Chicken. CORRESPONDING AUTHOR Erica Gorla erica.gorla@unimi.it JOURNAL HOME PAGE riviste.unimi.it/index.php/haf Genomic diversity using copy number variations in worldwide chicken populations. E. Gorla1,2*, F. Bertolini2, M.G. Strillacci1, M.C. Cozzi1, S.I. Roman-Ponce3, F.J. Ruiz3, V.V. Vega3, C.M.B. Dematawewa4, D. Kugonza5, A. Elbeltagy6, C.J. Schmidt7, S.J. Lamont2, A. Bagnato1, M.F. Rothschild2 1 Department of Veterinary Medicine, Università degli Studi di Milano, Via Celoria 10, 20133 Milano, Italy. 2 Department of Animal Science, Iowa State University, Ames, Iowa, USA. 3 Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias. 4 University of Peradeniya, Faculty of Agriculture, Department of Animal Science, 20400, Sri Lanka. 5 Department of Animal Science, Makerere University, Kampala, Uganda. 6 Animal Production Research Institute, Department of Animal Biotechnology, Dokki, Cairo, Egypt. 7 University of Delaware, Animal and Food Sciences, Newark, DE, USA. http://creativecommons.org/licenses/by-nc-nd/3.0/deed.en Proceeding of Veterinary and Animal Science Days 2018, 6th- 8th June, Milan, Italy 50 HAF © 2013 Vol. V, No. 1s ISSN: 2283-3927 2,354 unique genes with an official gene ID (Quinlan et al., 2010). The CNVRs identified here represent the first comprehensive mapping in several worldwide populations, using a high- density SNP chip. References Stranger, B.E., Forrest, M.S., Dunning, M., Ingle, C.E., Beazley, C., et al., 2007. Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes. Science 315: 848–853. Henrichsen, C.N., Vinckenbosch, N., Zollner, S., Chaignat, E., Pradervand, S., Schutz, F., et al., 2009. Segmental copy number variation shapes tissue transcriptomes. Nat. Genet. 41:424–429. doi: 10.1038/ng.345. Quinlan, A.R., Hall, I.M., 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842. doi: 10.1093/bioinformatics/btq033. http://penncnv.openbioinformatics.org/en/latest. http://goldenhelix.com. Table 1: Summary statistic of CNVR identified with of PennCNV, SVS software and consensus, divided according state into Loss, Gain or Complex. CNVR Count Min Length (bp) Max Length (bp) Mean Length (bp) Total Length (bp) Coverage (%) SVS ALL 7,001 493 571,113 15,541.61 108,806,878 11.68 Gain 4,640 493 571,113 14,743.86 68,411,533 7.34 Loss 1,573 699 146,115 11,288.70 17,757,126 1.9 Complex 788 1,955 562,765 28,728.70 22,638,219 2.43 PennCNV ALL 4,414 122 2,281,744 51,853.14 228,879,785 17.8 Gain 3,281 122 750,953 47,193.85 154,843,028 12.04 Loss 731 149 181,129 11,661.74 8,524,736 0.66 Complex 402 472 2,281,744 162,965.22 65,512,021 5.09 Consensus ALL 2,820 652 562,765 19,072.43 53,784,265 5.77 Gain 1,721 652 544,758 17,181.11 29,568,693 3.17 Loss 637 1,102 146,115 12,948.43 8,248,151 0.88 Complex 462 2,696 562,765 34,561.51 15,967,421 1.71 http://creativecommons.org/licenses/by-nc-nd/3.0/deed.en