T. Meuwissen, B. Hayes, and M. Goddard, Prediction of total genetic value using genome-wide dense marker maps, Genetics, vol.157, pp.1819-1848, 2001.

Y. Li, C. Willer, S. Sanna, and G. Abecasis, Genotype Imputation, Annual Review of Genomics and Human Genetics, vol.10, issue.1, pp.387-406, 2009.
DOI : 10.1146/annurev.genom.9.081307.164242

B. Hayes, P. Bowman, H. Daetwyler, J. Kijas, and J. Van-der-werf, Accuracy of genotype imputation in sheep breeds, Animal Genetics, vol.18, issue.1, pp.72-80, 2012.
DOI : 10.1111/j.1365-2052.2011.02208.x

K. Weigel, C. De-los, A. Vazquez, G. Rosa, D. Gianola et al., Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle, Journal of Dairy Science, vol.93, issue.11, pp.5423-5458, 2010.
DOI : 10.3168/jds.2010-3149

D. Habier, R. Fernando, and J. Dekkers, Genomic Selection Using Low-Density Marker Panels, Genetics, vol.182, issue.1, pp.343-53, 2009.
DOI : 10.1534/genetics.108.100289

J. Hickey, J. Crossa, R. Babu, D. Campos, and G. , Factors Affecting the Accuracy of Genotype Imputation in Populations from Several Maize Breeding Programs, Crop Science, vol.52, issue.2, pp.654-63, 2012.
DOI : 10.2135/cropsci2011.07.0358

A. Loberg and J. Dürr, Interbull survey on the use of genomic information, Interbull Bull, vol.39, pp.3-14, 2009.

J. Fulton, Genomic selection for poultry breeding, Animal Frontiers, vol.2, issue.1, pp.30-36, 2012.
DOI : 10.2527/af.2011-0028

N. Ibán?z-escriche, R. Fernando, A. Toosi, and J. Dekkers, Genomic selection of purebreds for crossbred performance, Genetics Selection Evolution, vol.41, issue.1, p.12, 2009.
DOI : 10.1186/1297-9686-41-12

O. Christensen, P. Madsen, B. Nielsen, and G. Su, Genomic evaluation of both purebred and crossbred performances, Genetics Selection Evolution, vol.46, issue.1, p.23, 2014.
DOI : 10.1038/nrg2865

URL : https://hal.archives-ouvertes.fr/hal-01341227

J. Dekkers, Marker-assisted selection for commercial crossbred performance, Journal of Animal Science, vol.85, issue.9, pp.2104-2118, 2007.
DOI : 10.2527/jas.2006-683

S. Browning, Missing data imputation and haplotype phase inference for genome-wide association studies, Human Genetics, vol.316, issue.5, pp.439-50, 2008.
DOI : 10.1007/s00439-008-0568-7

B. Browning and S. Browning, A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals, The American Journal of Human Genetics, vol.84, issue.2, pp.210-233, 2009.
DOI : 10.1016/j.ajhg.2009.01.005

H. Iwata and J. Jannink, Marker Genotype Imputation in a Low-Marker-Density Panel with a High-Marker-Density Reference Panel: Accuracy Evaluation in Barley Breeding Lines, Crop Science, vol.50, issue.4, pp.1269-78, 2010.
DOI : 10.2135/cropsci2009.08.0434

Z. Zhang and T. Druet, Marker imputation with low-density marker panels in Dutch Holstein cattle, Journal of Dairy Science, vol.93, issue.11, pp.5487-94, 2010.
DOI : 10.3168/jds.2010-3501

J. Hickey, B. Kinghorn, B. Tier, J. Van-der-werf, and M. Cleveland, A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation, Genetics Selection Evolution, vol.44, issue.1, p.9, 2012.
DOI : 10.1186/1297-9686-42-2

J. Duarte, R. Bates, C. Ernst, N. Raney, R. Cantet et al., Genotype imputation accuracy in a F2 pig population using high density and low density SNP panels, BMC Genetics, vol.14, issue.1, p.38, 2013.
DOI : 10.1016/j.ajhg.2009.01.013

Y. Badke, R. Bates, C. Ernst, J. Fix, and J. Steibel, Accuracy of Estimation of Genomic Breeding Values in Pigs Using Low-Density Genotypes and Imputation, G3: Genes|Genomes|Genetics, vol.4, issue.4, pp.623-654, 2014.
DOI : 10.1534/g3.114.010504

R. Ventura, D. Lu, F. Schenkel, Z. Wang, C. Li et al., Impact of reference population on accuracy of imputation from 6K to 50K single nucleotide polymorphism chips in purebred and crossbreed beef cattle, Journal of Animal Science, vol.92, issue.4, pp.1433-1477, 2014.
DOI : 10.2527/jas.2013-6638

C. Hozé, M. Fouilloux, E. Venot, F. Guillaume, R. Dassonneville et al., High-density marker imputation accuracy in sixteen French cattle breeds, Genetics Selection Evolution, vol.45, issue.1, p.33, 2013.
DOI : 10.3168/jds.2011-4299

A. Ramos, R. Crooijmans, N. Affara, A. Amaral, A. Archibald et al., Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology, PLoS ONE, vol.10, issue.5715, p.6524, 2009.
DOI : 10.1371/journal.pone.0006524.s002

G. Company and L. Ggp-for-porcine, GeneSeek Genomic Profiler for Porcine Low Density), Genomics, 2012.

M. Groenen, A. Archibald, H. Uenishi, C. Tuggle, Y. Takeuchi et al., Analyses of pig genomes provide insight into porcine demography and evolution, Nature, vol.475, issue.7424, pp.393-401, 2012.
DOI : 10.1038/nature11622

URL : https://hal.archives-ouvertes.fr/cea-00880676

J. Haldane, The combination of linkage values and the calculation of distances between the loci of linked factors, J Genet, vol.8, pp.299-309, 1919.

L. Huang, Y. Li, A. Singleton, J. Hardy, G. Abecasis et al., Genotype-Imputation Accuracy across Worldwide Human Populations, The American Journal of Human Genetics, vol.84, issue.2
DOI : 10.1016/j.ajhg.2009.01.013

M. Calus, A. Bouwman, J. Hickey, R. Veerkamp, and H. Mulder, Evaluation of measures of correctness of genotype imputation in the context of genomic prediction: a review of livestock applications, animal, vol.44, issue.11, pp.1743-53, 2014.
DOI : 10.1186/1471-2164-13-538

P. Vanraden, Efficient Methods to Compute Genomic Predictions, Journal of Dairy Science, vol.91, issue.11, pp.4414-4437, 2008.
DOI : 10.3168/jds.2007-0980

H. Daetwyler, M. Calus, R. Pong-wong, G. De-los-campos, and J. Hickey, Genomic Prediction in Animals and Plants: Simulation of Data, Validation, Reporting, and Benchmarking, Genetics, vol.193, issue.2, pp.347-65, 2013.
DOI : 10.1534/genetics.112.147983

A. Legarra, G. Baloche, F. Barillet, J. Astruc, C. Soulas et al., Within- and across-breed genomic predictions and genomic relationships for Western Pyrenees dairy sheep breeds Latxa, Manech, and Basco-B??arnaise, Journal of Dairy Science, vol.97, issue.5, pp.3200-3212, 2014.
DOI : 10.3168/jds.2013-7745

G. Mcvean, A Genealogical Interpretation of Principal Components Analysis, PLoS Genetics, vol.27, issue.10, p.1000686, 2009.
DOI : 10.1371/journal.pgen.1000686.g006

L. Wang, P. Sørensen, L. Janss, T. Ostersen, and D. Edwards, Genome-wide and local pattern of linkage disequilibrium and persistence of phase for 3 Danish pig breeds, BMC Genetics, vol.14, issue.1, p.115, 2013.
DOI : 10.1111/j.1365-2052.2011.02301.x

R. Brøndum, B. Guldbrandtsen, G. Sahana, M. Lund, and G. Su, Strategies for imputation to whole genome sequence using a single or multi-breed reference population in cattle, BMC Genomics, vol.15, issue.1, p.728, 2014.
DOI : 10.1186/1471-2164-15-728

B. Howie, J. Marchini, and M. Stephens, Genotype Imputation with Thousands of Genomes, G3: Genes|Genomes|Genetics, vol.1, issue.6, pp.457-70, 2011.
DOI : 10.1534/g3.111.001198

J. Marchini and B. Howie, Genotype imputation for genome-wide association studies, Nature Reviews Genetics, vol.42, issue.7, pp.499-511, 2010.
DOI : 10.1038/nrg2796

M. Pszczola, T. Strabel, H. Mulder, and M. Calus, Reliability of direct genomic values for animals with different relationships within and to the reference population, Journal of Dairy Science, vol.95, issue.1, pp.389-400, 2012.
DOI : 10.3168/jds.2011-4338

J. King, Pig breeds of the world:Their distributions and adaptation, Genetic resources of pig, pp.52-53, 1991.

J. Hickey and A. Kranis, Extending long-range phasing and haplotype library imputation methods to impute genotypes on sex chromosomes, Genetics Selection Evolution, vol.45, issue.1, p.10, 2013.
DOI : 10.1186/1297-9686-44-25

Y. Huang, J. Hickey, M. Cleveland, and C. Maltecca, Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost, Genetics Selection Evolution, vol.44, issue.1, p.25, 2012.
DOI : 10.1186/1297-9686-43-12

R. Wellmann, S. Preuss, E. Tholen, J. Heinkel, K. Wimmers et al., Genomic selection using low density marker panels with application to a sire line in pigs, Genetics Selection Evolution, vol.45, issue.1, p.28, 2013.
DOI : 10.1017/S0016672308009981