E. S. Buckler, J. B. Holland, P. J. Bradbury, C. B. Acharya, P. J. Brown et al., The Genetic Architecture of Maize Flowering Time, Science, vol.40, issue.5, pp.325-714, 2009.
DOI : 10.1038/ng0508-489

P. Bühlmann, Statistical significance in high-dimensional linear models, Bernoulli, vol.19, issue.4, pp.1212-1242, 2013.
DOI : 10.3150/12-BEJSP11

J. Burstin, P. Salloignon, M. Martinello, J. B. Magnin-robert, M. Siol et al., Genetic diversity and trait genomic prediction in a pea diversity panel, BMC Genomics, vol.16, issue.1, p.105, 2015.
DOI : 10.1007/BF00015981

D. Habier, R. Fernando, and J. Dekkers, The impact of genetic relationship information on genome-assisted breeding values, Genetics, vol.177, issue.4, pp.2389-2397, 2007.
DOI : 10.1534/genetics.107.081190

J. Haldane, The combination of linkage values and the calculation of distances between the loci of linked factors, J Genet, vol.8, issue.29, pp.299-309, 1919.

B. Hayes, P. Bowman, A. Chamberlain, and M. Goddard, Invited review: Genomic selection in dairy cattle: Progress and challenges, Journal of Dairy Science, vol.92, issue.2, pp.433-443, 2009.
DOI : 10.3168/jds.2008-1646

W. Hill and B. Weir, Variances and covariances of squared linkage disequilibria in finite populations. Theoretical population biology, pp.54-78, 1998.

A. E. Hoerl and R. W. Kennard, Ridge Regression: Biased Estimation for Nonorthogonal Problems, Technometrics, vol.24, issue.1, pp.55-67, 1970.
DOI : 10.2307/1909769

J. L. Jannink, A. J. Lorenz, and H. Iwata, Genomic selection in plant breeding: from theory to practice, Briefings in Functional Genomics, vol.125, issue.5, pp.166-177, 2010.
DOI : 10.1111/j.1439-0388.2007.00717.x

S. Kumar, D. Chagné, M. C. Bink, R. K. Volz, C. Whitworth et al., Genomic selection for fruit quality traits in apple (Malus× domestica Borkh.). PloS One, p.36674, 2012.
DOI : 10.1371/journal.pone.0036674

URL : https://doi.org/10.1371/journal.pone.0036674

E. S. Lander and D. Botstein, Mapping mendelian factors underlying quantitative traits using RFLP linkage maps, Genetics, vol.121, issue.1, pp.185-199, 1989.

J. Li and L. Ji, Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix, Heredity, vol.19, issue.3, pp.221-227, 2005.
DOI : 10.1002/1098-2272(200012)19:4<323::AID-GEPI4>3.0.CO;2-5

M. Lynch and B. Walsh, Genetics and analysis of quantitative traits, 1998.

T. H. Meuwissen, B. Hayes, and M. E. Goddard, Prediction of total genetic value using genome-wide dense marker maps, Genetics, vol.157, issue.4, pp.1819-1829, 2001.

C. E. Rabier, P. Barre, T. Asp, G. Charmet, and B. Mangin, On the Accuracy of Genomic Selection, PLOS ONE, vol.112, issue.6, 2016.
DOI : 10.1371/journal.pone.0156086.s004

URL : https://hal.archives-ouvertes.fr/hal-01595179

R. Rincent, D. Laloë, N. S. Altmann, T. Brunel, D. Revilla et al., Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea mays L.), Genetics, vol.192, issue.2, pp.192-715, 2012.
DOI : 10.1534/genetics.112.141473

URL : https://hal.archives-ouvertes.fr/hal-01019845

J. Shao and X. Deng, Estimation in high-dimensional linear models with deterministic design matrices. The Annals of Statistics, pp.812-831, 2012.
DOI : 10.1214/12-aos982

URL : http://doi.org/10.1214/12-aos982

J. Spindel, H. Begum, D. Akdemir, P. Virk, B. Collard et al., Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines, PLOS Genetics, vol.45, issue.2, p.1004982, 2015.
DOI : 10.1371/journal.pgen.1004982.s011

F. Technow, R Package hypred: Simulation of Genomic Data in Applied Genetics, 2014.

R. Tibshirani, Regression shrinkage and selection via the lasso, Journal of the Royal Statistical Society. Series B (Methodological, pp.267-288, 1996.
DOI : 10.1111/j.1467-9868.2011.00771.x

A. N. Tikhonov, On the solution of ill-posed problems and the method of regularization, Dokl. Akad. Nauk.. SSSR, vol.151, pp.501-504, 1963.

P. M. Visscher, J. Yang, M. E. Goddard, and . Yang, A Commentary on ???Common SNPs Explain a Large Proportion of the Heritability for Human Height??? by Yang et al. (2010), Twin Research and Human Genetics, vol.460, issue.06, pp.517-524, 2010.
DOI : 10.1038/ng.608

J. C. Whittaker, R. Thompson, and M. C. Denham, Marker-assisted selection using ridge regression, Genetical Research, vol.75, issue.2, pp.249-252, 2000.
DOI : 10.1017/S0016672399004462

T. Würschum, J. C. Reif, T. Kraft, G. Janssen, and Y. Zhao, Genomic selection in sugar beet breeding populations, BMC Genetics, vol.14, issue.1, p.85, 2013.
DOI : 10.1111/j.1439-0388.2007.00701.x

M. Yuan and Y. Lin, Model selection and estimation in regression with grouped variables, Journal of the Royal Statistical Society: Series B (Statistical Methodology), vol.58, issue.1, pp.49-67, 2006.
DOI : 10.1198/016214502753479356

URL : http://www2.isye.gatech.edu/~myuan/papers/glasso.final.pdf

H. Zou, The Adaptive Lasso and Its Oracle Properties, Journal of the American Statistical Association, vol.101, issue.476, pp.1418-1429, 2006.
DOI : 10.1198/016214506000000735

URL : http://cbio.ensmp.fr/~jvert/svn/bibli/local/Zou2006adaptive.pdf

J. Fan and J. Lv, Sure independence screening for ultrahigh dimensional feature space, Journal of the Royal Statistical Society: Series B (Statistical Methodology), vol.36, issue.5, pp.849-911, 2008.
DOI : 10.1255/jnirs.271

URL : http://europepmc.org/articles/pmc2709408?pdf=render

C. E. Rabier, P. Barre, T. Asp, G. Charmet, and B. Mangin, On the Accuracy of Genomic Selection, PLOS ONE, vol.112, issue.6, 2016.
DOI : 10.1371/journal.pone.0156086.s004

URL : https://hal.archives-ouvertes.fr/hal-01595179

J. Shao and X. Deng, Estimation in high-dimensional linear models with deterministic design matrices. The Annals of Statistics, pp.812-831, 2012.
DOI : 10.1214/12-aos982

URL : http://doi.org/10.1214/12-aos982