A. Breeding, G. Centre, W. University, and P. , The Netherlands. 2 Genetics and Genomics group The Pirbright Institute, 4 L'institut du thorax

. France, 19717, USA. 6 Avian Disease and Oncology Laboratory, 4279 E Mount Hope Road, East Lansing, MI 48823-5338, USA. 7 The Roslin Institute and R(D)SVS

C. Rubin, M. Zody, J. Eriksson, J. Meadows, E. Sherwood et al., Wholegenome resequencing reveals loci under selection during chicken domestication, Nature, vol.25, pp.464-587, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01193349

F. Zhang, W. Gu, M. Hurles, and R. Lupski, Copy Number Variation in Human Health, Disease, and Evolution, Annual Review of Genomics and Human Genetics, vol.10, issue.1, pp.451-481, 2009.
DOI : 10.1146/annurev.genom.9.081307.164217

J. Freeman, G. Perry, L. Feuk, R. Redon, S. Mccarroll et al., Copy number variation: New insights in genome diversity, Genome Research, vol.16, issue.8, pp.949-961, 2006.
DOI : 10.1101/gr.3677206

D. Hinds, A. Kloek, J. M. Chen, X. Frazer, and K. , Common deletions and SNPs are in linkage disequilibrium in the human genome, Nature Genetics, vol.13, issue.1, pp.82-85, 2006.
DOI : 10.1038/ng1695

Y. Hasin, T. Olender, M. Khen, C. Gonzga-jauegui, P. Kim et al., High-Resolution Copy-Number Variation Map Reflects Human Olfactory Receptor Diversity and Evolution, PLoS Genetics, vol.83, issue.11
DOI : 10.1371/journal.pgen.1000249.s014

J. Bailey, J. Kidd, and E. Eichler, Human copy number polymorphic genes, Cytogenetic and Genome Research, vol.123, issue.1-4, pp.234-243, 2008.
DOI : 10.1159/000184713

L. Feuk, A. Carson, and S. Scherer, Structural variation in the human genome, Nature Reviews Genetics, vol.37, issue.2, pp.85-97, 2006.
DOI : 10.1038/nrg1767

L. Feuk, C. Marshall, R. Wintle, and S. Scherer, Structural variants: changing the landscape of chromosomes and design of disease studies, Human Molecular Genetics, vol.15, issue.90001, pp.57-66, 2006.
DOI : 10.1093/hmg/ddl057

D. Conrad and M. Hurles, The population genetics of structural variation, Nature Genetics, vol.1, issue.7s, pp.30-36, 2007.
DOI : 10.1038/ng2042

D. Conrad, D. Pinto, R. Redon, L. Feuk, O. Gokcumen et al., Origins and functional impact of copy number variation in the human genome, Nature, vol.36, issue.7289, pp.704-712, 2010.
DOI : 10.1038/nature08516

G. Liu, Y. Hou, B. Zhu, M. Cardone, L. Jiang et al., Analysis of copy number variations among diverse cattle breeds, Genome Research, vol.20, issue.5, pp.693-703, 2010.
DOI : 10.1101/gr.105403.110

M. Elferink, A. Vallee, A. Jungerius, R. Crooijmans, and M. Groenen, Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken, BMC Genomics, vol.9, issue.1, pp.391-399, 2008.
DOI : 10.1186/1471-2164-9-391

D. Wright, H. Boije, J. Meadows, B. Bed-'hom, D. Gourichon et al., Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens, PLoS Genetics, vol.88, issue.6, p.1000512, 2009.
DOI : 10.1371/journal.pgen.1000512.s005
URL : https://hal.archives-ouvertes.fr/hal-01193583

U. Gunnarsson, S. Kerje, B. Bed-'hom, A. Sahlqvist, O. Ekwall et al., The Dark brown plumage color in chickens is caused by an 8.3-kb deletion upstream of SOX10, Pigment Cell & Melanoma Research, vol.5, issue.2, pp.268-274, 2011.
DOI : 10.1111/j.1755-148X.2011.00825.x
URL : https://hal.archives-ouvertes.fr/hal-01000175

J. Na-m,-r-u-b-i-nc, J. , M. Chen, C. Hallböök, F. Ashwell et al., h a n s s o nA M ,S t r ö m s t e d tL Ac o m p l e x genomic rearrangement involving the endothelium 3 locus causes dermal hyperpigmenta t i o ni nt h ec h i c k e n, PLoS Genetics, vol.7, p.1002412, 2011.

X. Wang, S. Nahashon, T. Feaster, A. Bohannon-stewart, and N. Adefope, An initial map of chromosomal segmental copy number variations in the chicken, BMC Genomics, vol.11, issue.1, p.351, 2010.
DOI : 10.1186/1471-2164-11-351

Y. Wang, X. Gu, C. Feng, C. Song, X. Hu et al., A genome-wide survey of copy number variation regions in various chicken breeds by array comparative genomic hybridization method, Animal Genetics, vol.83, issue.3, pp.282-289, 2012.
DOI : 10.1111/j.1365-2052.2011.02308.x

R. Redon, S. Ishikawa, K. Fitch, L. Feuk, G. Perry et al., S o m e r v i l l eM J ,T c h i n d aJ ,V a l s e s i aA, ME: Global variation in copy number in the human genome, pp.444-454, 2006.

Y. Hou, G. Liu, D. Bickhart, L. Matukumalli, C. Li et al., Genomic characteristics of cattle copy number variations, BMC Genomics, vol.3, issue.1, p.127, 2011.
DOI : 10.1371/journal.pgen.0030003

D. Griffin, L. Robertson, H. Tempest, A. Vignal, V. Fillon et al., Whole genome comparative studies between chicken en turkey and their implications for avian genome evolution, BMC Genomics, vol.9, p.357, 2008.

B. Skinner, L. Robertson, H. Tempest, E. Langley, D. Ioannou et al., Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis, BMC Genomics, vol.10, issue.1, p.168, 2009.
DOI : 10.1186/1471-2164-10-357

M. Völker, N. Backström, B. Skinner, E. Langley, S. Bunzey et al., Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution, Genome Research, vol.20, issue.4, pp.503-511, 2010.
DOI : 10.1101/gr.103663.109

D. Huang, B. Sherman, and R. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nature Protocols, vol.99, issue.1, pp.44-57, 2009.
DOI : 10.1038/nprot.2008.211

M. Greenwold and R. Sawyer, Genomic organization and molecular phylogenies of the beta (??) keratin multigene family in the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata): implications for feather evolution, BMC Evolutionary Biology, vol.10, issue.1, p.148, 2010.
DOI : 10.1186/1471-2148-10-148

F. Pazderka, B. Longenecker, G. Law, H. Stone, and R. Ruth, Histocompatibility of chicken populations selected for resistance to Marek's disease, Immunogenetics, vol.134, issue.1, pp.93-100, 1975.
DOI : 10.1007/BF01572279

N. Waters, Breeding for Resistance and Susceptibility to Avian Lymphomatosis, Poultry Science, vol.24, issue.3, pp.259-269, 1945.
DOI : 10.3382/ps.0240259

H. Stone, Use of highly inbred chickens in research, 1975.

L. Bacon, H. Hunt, and H. Cheng, A Review of the Development of Chicken Lines to Resolve Genes Determining Resistance to Diseases, Poultry Science, vol.79, issue.8, pp.1082-1093, 2000.
DOI : 10.1093/ps/79.8.1082

N. Bumstead, L. Messer, and N. Greenwood, loci as a measure of inbreeding in domestic fowls, British Poultry Science, vol.65, issue.4, pp.717-725, 1987.
DOI : 10.1086/279872

T. Fitzgerald, L. Larcombe, L. Scouarnec, S. Clayton, S. Rajan et al., aCGH.Spline--an R package for aCGH dye bias normalization, Bioinformatics, vol.27, issue.9, pp.1195-1200, 2011.
DOI : 10.1093/bioinformatics/btr107

T. Graubert, P. Cahan, D. Edwin, R. Selzer, T. Richmond et al., A High-Resolution Map of Segmental DNA Copy Number Variation in the Mouse Genome, PLoS Genetics, vol.444, issue.1, pp.3-10, 2007.
DOI : 10.1371/journal.pgen.0030003.st004

S. Baigent, L. Petherbridge, K. Howes, L. Smith, R. Currie et al., Absolute quantitation of Marek's disease virus genome copy number in chicken feather and lymphocyte samples using real-time PCR, Journal of Virological Methods, vol.123, issue.1, pp.53-64, 2005.
DOI : 10.1016/j.jviromet.2004.08.019

R. Weksberg, S. Hughes, L. Moldovan, A. Bassett, E. Chow et al., A method for accurate detection of genomic microdeletions using real-time quantitative PCR, BMC Genomics, vol.6, issue.1, p.180, 2005.
DOI : 10.1186/1471-2164-6-180