I. Aguilar, I. Misztal, D. L. Johnson, A. Legarra, S. Tsuruta et al., Hot topic: A unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score1, J. Dairy Sci, vol.93, pp.743-752, 2010.

L. F. Brito, S. M. Clarke, J. C. Mcewan, S. P. Miller, N. K. Pickering et al., Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip, BMC Genet, vol.18, 2017.

L. F. Brito, M. Jafarikia, D. A. Grossi, J. W. Kijas, L. R. Porto-neto et al., Characterization of linkage disequilibrium, consistency of gametic phase and admixture in Australian and Canadian goats, BMC Genet, vol.16, p.67, 2015.

K. W. Broman and J. L. Weber, Long homozygous chromosomal segments in reference families from the Centre d'Étude du Polymorphisme Humain, Am. J. Hum. Genet, vol.65, pp.1493-1500, 1999.

M. P. Calus, H. Huang, A. Vereijken, J. Visscher, J. Napel et al., Genomic prediction based on data from three layer lines: A comparison between linear methods, Genet. Sel. Evol, vol.46, p.57, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01341237

M. P. Calus, T. H. Meuwissen, A. P. De-roos, and R. F. Veerkamp, Accuracy of genomic selection using different methods to define haplotypes, Genetics, vol.178, pp.553-561, 2008.

C. Carillier, H. Larroque, I. Palhière, V. Clément, R. Rupp et al., A first step toward genomic selection in the multi-breed French dairy goat population, J. Dairy Sci, vol.96, pp.7294-7305, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02651011

C. Carillier, H. Larroque, and C. Robert-granié, Comparison of joint versus purebred genomic evaluation in the French multibreed dairy goat population, Genet. Sel. Evol, vol.46, p.67, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01341244

O. F. Christensen and M. S. Lund, Genomic prediction when some animals are not genotyped, Genet. Sel. Evol, vol.42, issue.2, 2010.

B. C. Cuyabano, G. Su, and M. S. Lund, Genomic prediction of genetic merit using LD-based haplotypes in the Nordic Holstein population, BMC Genomics, vol.15, p.1171, 2014.

A. P. De-roos, B. J. Hayes, R. J. Spelman, and M. E. Goddard, Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle, Genetics, vol.179, pp.1503-1512, 2008.

A. Doublet, P. Croiseau, S. Fritz, A. Michenet, C. Hozé et al., The impact of genomic selection on genetic diversity and genetic gain in three French dairy cattle breeds, Genet. Sel. Evol, vol.51, p.52, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02300856

C. Edel, E. Pimentel, L. Plieschke, R. Emmerling, and K. Götz, Effects of selective genotyping and selective imputation in single-step, GBLUP. Interbull Bull, vol.51, pp.22-25, 2017.

F. L. Feitosa, A. S. Pereira, S. T. Amorim, E. Peripolli, R. M. De-oliviera et al., Comparison between haplotype-based and individual snp-based genomic predictions for beef fatty, 2020.

, J. Anim. Breed. Genet, vol.137, pp.468-476

M. H. Ferdosi, J. Henshall, and B. Tier, Study of the optimum haplotype length to build genomic relationship matrices, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01479279

. Sel, , vol.48, p.75

F. Grosclaude, M. Mahé, G. Brignon, L. D. Stasio, and R. Jeunet, A Mendelian polymorphism underlying quantitative variations of goat ? S1 -casein, Genet. Sel. Evol, vol.19, pp.399-412, 1987.
URL : https://hal.archives-ouvertes.fr/hal-02727018

M. Hess, T. Druet, A. Hess, and D. Garrick, Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population, Genet. Sel. Evol, vol.49, p.54, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01555253

J. M. Hickey, B. P. Kinghorn, B. Tier, S. A. Clark, J. H. Van-der-werf et al., Genomic evaluations using similarity between haplotypes, J. Anim. Breed. Genet, vol.130, pp.1299-1320, 2005.

D. Jónás, V. Ducrocq, M. Fouilloux, and P. Croiseau, Alternative haplotype construction methods for genomic evaluation, J. Dairy Sci, vol.99, pp.4537-4546, 2016.

Z. Karimi, M. Sargolzaei, J. A. Robinson, and F. S. Schenkel, Assessing haplotype-based models for genomic evaluation in Holstein cattle. Can, J. Anim. Sci, vol.98, pp.750-759, 2018.

H. Larroque, J. Astruc, A. Barbat, F. Barillet, D. Boichard et al., National genetic evaluations in dairy sheep and goats in France. Page 62, Proc. Annual Meeting of the European Federation of Animal Science (EAAP), 2011.
URL : https://hal.archives-ouvertes.fr/hal-01193670

A. Legarra, I. Aguilar, and I. Misztal, A relationship matrix including full pedigree and genomic information, J. Dairy Sci, vol.92, pp.4656-4663, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02668784

B. O. Makanjuola, F. Miglior, E. A. Abdalla, C. Maltecca, F. S. Schenkel et al., Effect of genomic selection on rate of inbreeding and coancestry and effective population size of Holstein and Jersey cattle populations, J. Dairy Sci, vol.103, pp.5183-5199, 2020.

P. Martin, I. Palhière, C. Maroteau, P. Bardou, K. Canale-tabet et al., A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content, Sci. Rep, vol.7, p.1872, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02622800

P. Martin, I. Palhière, C. Maroteau, V. Clément, I. David et al., type and mammary health traits in French dairy goats identifies a pleiotropic region on chromosome 19 in the Saanen breed, GENOMIC PREDICTION IN DAIRY GOATS Journal of Dairy Science, vol.103, issue.12, pp.5214-5226, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02627638

T. H. Meuwissen, J. Odegard, I. Andersen-ranberg, and E. Grindflek, On the distance of genetic relationships and the accuracy of genomic prediction in pig breeding, Genet. Sel. Evol, vol.46, p.49, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01341267

I. Misztal, A. Legarra, and I. Aguilar, Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information, J. Dairy Sci, vol.92, pp.4648-4655, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02668727

I. Misztal, S. Tsuruta, D. A. Lourenco, Y. Masuda, I. Aguilar et al., Manual for BLUPF90 Family of Programs, 2016.

M. L. Piccoli, L. F. Brito, J. Braccini, H. R. Oliveira, F. F. Cardoso et al., Comparison of genomic prediction methods for evaluation of adaptation and productive efficiency traits in Braford and Hereford cattle, Livest. Sci, vol.231, p.103864, 2020.

S. Purcell, B. Neale, K. Todd-brown, L. Thomas, M. A. Ferreira et al., PLINK: A tool set for whole-genome association and population-based linkage analyses, Am. J. Hum. Genet, vol.81, pp.559-575, 2007.

A. Ricard, S. Danvy, and A. Legarra, Computation of deregressed proofs for genomic selection when own phenotypes exist with an application in French show-jumping horses, J. Anim. Sci, vol.91, pp.1076-1085, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01000368

A. R. Rogers and C. Huff, Linkage disequilibrium between loci with unknown phase, Genetics, vol.182, pp.839-844, 2009.

R. Rupp, S. Mucha, H. Larroque, J. Mcewan, and J. E. , Genomic application in sheep and goat breeding, Anim. Front, vol.6, pp.39-44, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02637118

M. Sargolzaei, J. P. Chesnais, and F. S. Schenkel, A new approach for efficient genotype imputation using information from relatives, BMC Genomics, vol.15, p.478, 2014.

H. Signer-hasler, A. Burren, M. Neuditschko, M. Frischknecht, D. Garrick et al., Population structure and genomic inbreeding in nine Swiss dairy cattle populations, Genet. Sel. Evol, vol.49, p.83, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01631051

M. Teissier, H. Larroque, and C. Robert-granié, Weighted single-step genomic BLUP improves accuracy of genomic breeding values for protein content in French dairy goats: a quantitative trait influenced by a major gene, Genet. Sel. Evol, vol.50, p.31, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02405243

M. Teissier, H. Larroque, and C. Robert-granie, Accuracy of genomic evaluation with weighted single-step genomic best linear unbiased prediction for milk production traits, udder type traits, and somatic cell scores in French dairy goats, J. Dairy Sci, vol.102, pp.2018-15650, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02625689

G. Tosser-klopp, P. Bardou, O. Bouchez, C. Cabau, R. Crooijmans et al., Design and characterization of a 52K SNP chip for goats, PLoS One, vol.9, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01602260

Y. Uemoto, S. Sato, T. Kikuchi, S. Egawa, K. Kohira et al., Genomic evaluation using SNP-and haplotype-based genomic relationship matrices in a closed line of Duroc pigs, Anim. Sci. J, vol.88, pp.1465-1474, 2017.

P. M. Vanraden, Efficient methods to compute genomic predictions, J. Dairy Sci, vol.91, pp.4414-4423, 2008.

P. M. Vanraden and G. R. Wiggans, Derivation, calculation, and use of national animal model information, J. Dairy Sci, vol.74, issue.91, pp.78453-78454, 1991.

H. Wang, I. Misztal, I. Aguilar, A. Legarra, and W. M. Muir, Genome-wide association mapping including phenotypes from relatives without genotypes, Genet. Res. (Camb.), vol.94, pp.73-83, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02652510

X. Zhang, D. Lourenco, I. Aguilar, A. Legarra, and I. Misztal, Weighting strategies for single-step genomic BLUP: An iterative approach for accurate calculation of GEBV and GWAS, Front. Genet, vol.7, p.151, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01602498

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S. Flavio and . Schenkel,

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. Teissier, GENOMIC PREDICTION IN DAIRY GOATS
URL : https://hal.archives-ouvertes.fr/hal-02625689