M. B. Hufford, X. Xu, J. Van-heerwaarden, T. Pyhajarvi, and J. Chia, Comparative population genomics of maize domestication and improvement, Nat Genet, vol.44, pp.808-811, 2012.

J. Van-heerwaarden, M. B. Hufford, and J. Ross-ibarra, Historical genomics of North American maize, Proc Natl Acad Sci, vol.109, pp.12420-12425, 2012.

N. Kuleshov, World's diversity of phenotypes of maize, J Am Soc Agron, vol.25, pp.688-700, 1933.

E. S. Buckler, J. B. Holland, P. J. Bradbury, C. B. Acharya, and P. J. Brown, The genetic architecture of maize flowering time, Science, vol.325, pp.714-718, 2009.

J. Bolanos and G. O. Edmeades, The importance of the anthesis-silking interval in breeding for drought tolerance in tropical maize, Field Crops Research, vol.48, pp.65-80, 1996.

B. Brachi, N. Faure, M. Horton, E. Flahauw, and A. Vazquez, Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature, PLoS Genet, vol.6, p.1000940, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00468455

Y. R. Lin, K. F. Schertz, and A. H. Paterson, Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population, Genetics, vol.141, pp.391-411, 1995.

M. Yano, Y. Harushima, Y. Nagamura, N. Kurata, and Y. Minobe, Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map, Theor Appl Genet, vol.95, pp.1025-1032, 1997.

A. Turner, J. Beales, S. Faure, R. P. Dunford, and L. Da, The pseudoresponse regulator Ppd-H1 provides adaptation to photoperiod in barley, Science's STKE, vol.310, p.1031, 2005.

F. Chardon, B. Virlon, L. Moreau, M. Falque, and J. Joets, Genetic architecture of flowering time in maize as inferred from Quantitative Trait Loci meta-analysis and synteny conservation with the rice genome, Genetics, vol.168, pp.2169-2185, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02678548

L. Corbesier and G. Coupland, The quest for florigen: a review of recent progress, J Exp Bot, vol.57, pp.3395-3403, 2006.

J. Zeevaart, Florigen coming of age after 70 years, Plant Cell, vol.18, pp.1783-1789, 2006.

J. Zeevaart, Physiology of flower formation, Annu Rev Plant Physiol, vol.27, pp.321-348, 1976.

C. M. Lazakis, V. Coneva, and J. Colasanti, ZCN8 encodes a potential orthologue of Arabidopsis FT florigen that integrates both endogenous and photoperiod flowering signals in maize, J Exp Bot, vol.62, pp.4833-4842, 2011.

M. J. Banfield and R. L. Brady, The structure of Antirrhinum centroradialis protein (CEN) suggests a role as a kinase regulator, J Mol Biol, vol.297, pp.1159-1170, 2000.

A. Mouradov, F. Cremer, and G. Coupland, Control of Flowering Time, Plant Cell, vol.14, pp.111-130, 2002.

O. N. Danilevskaya, X. Meng, Z. Hou, E. V. Ananiev, and C. R. Simmons, A genomic and expression compendium of the expanded PEBP gene family from maize, Plant Physiol, vol.146, pp.250-264, 2008.

M. G. Muszynski, T. Dam, B. Li, D. M. Shirbroun, and Z. Hou, Delayed flowering1 encodes a basic leucine zipper protein that mediates floral inductive signals at the shoot apex in maize, Plant Physiol, vol.142, pp.1523-1536, 2006.

D. Van-inghelandt, A. E. Melchinger, J. P. Martinant, and B. Stich, Genome-wide association mapping of flowering time and northern corn leaf blight (Setosphaeria turcica) resistance in a vast commercial maize germplasm set, BMC Plant Biol, vol.12, p.56, 2012.

F. Chardon, D. Hourcade, V. Combes, and A. Charcosset, Mapping of a spontaneous mutation for early flowering time in maize highlights contrasting allelic series at two-linked QTL on chromosome 8, Theor Appl Genet, vol.112, pp.1-11, 2005.

S. Ducrocq, D. Madur, J. Veyrieras, L. Camus-kulandaivelu, and M. Kloiber-maitz, Key impact of Vgt1 on flowering time adaptation in maize: Evidence from association mapping and ecogeographical information, Genetics, vol.178, pp.2433-2437, 2008.

J. Veyrieras, B. Goffinet, and A. Charcosset, MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments, BMC Bioinformatics, vol.8, p.49, 2007.

S. Salvi, S. Castelletti, and R. Tuberosa, An updated consensus map for flowering time QTLs in maize, Maydica, vol.54, p.501, 2009.

S. Salvi, G. Sponza, M. Morgante, D. Tomes, and X. Niu, Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize, Proc Natl Acad Sci, vol.104, pp.11376-11381, 2007.

D. Gianola, R. L. Fernando, and A. Stella, Genomic-assisted prediction of genetic value with semiparametric procedures, Genetics, vol.173, p.1761, 2006.

D. Gianola and J. B. Van-kaam, Reproducing kernel Hilbert spaces regression methods for genomic assisted prediction of quantitative traits, Genetics, vol.178, p.2289, 2008.

O. Gonzalez-recio, D. Gianola, N. Long, K. A. Weigel, and G. Rosa, Nonparametric methods for incorporating genomic information into genetic evaluations: An application to mortality in broilers, Genetics, vol.178, p.2305, 2008.

J. Steinhoff, W. Liu, J. Reif, G. Porta, and N. Ranc, Detection of QTL for flowering time in multiple families of elite maize, Theor Appl Genet, pp.1-13, 2012.

S. A. Flint-garcia, A. Thuillet, J. Yu, G. Pressoir, and S. M. Romero, Maize association population: a high-resolution platform for quantitative trait locus dissection, The Plant Journal, vol.44, pp.1054-1064, 2005.

L. Camus-kulandaivelu, J. B. Veyrieras, D. Madur, V. Combes, and M. Fourmann, Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene, Genetics, vol.172, pp.2449-2463, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02664567

M. W. Ganal, G. Durstewitz, A. Polley, A. Bzrard, and E. S. Buckler, A large maize (Zea mays L.) SNP genotyping array: Development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome, PLoS ONE, vol.6, p.28334, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02652466

S. Ducrocq, C. Giauffret, D. Madur, V. Combes, and F. Dumas, Fine mapping and haplotype structure analysis of a major flowering time Quantitative Trait Locus on maize chromosome 10, Genetics, vol.183, pp.1555-1563, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02667927

S. A. Flint-garcia, J. M. Thornsberry, and E. S. Buckler, Structure of linkage disequilibrium in plants, Annu Rev Plant Biol, vol.54, pp.357-374, 2003.

B. Mangin, A. Siberchicot, S. Nicolas, A. Doligez, and P. This, Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness, Heredity, vol.108, pp.285-291, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01267769

Y. Vigouroux, J. S. Jaqueth, Y. Matsuoka, O. S. Smith, and W. D. Beavis, Rate and pattern of mutation at microsatellite loci in maize, Mol Biol Evol, vol.19, pp.1251-1260, 2002.

M. A. Gore, J. Chia, R. J. Elshire, Q. Sun, and E. S. Ersoz, A firstgeneration haplotype map of maize, Science, vol.326, pp.1115-1117, 2009.

H. M. Kang, N. A. Zaitlen, C. M. Wade, A. Kirby, and D. Heckerman, Efficient control of population structure in model organism association mapping, Genetics, vol.178, pp.1709-1723, 2008.

B. A. Loiselle, V. L. Sork, J. Nason, and C. Graham, Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae), Am J Bot, pp.1420-1425, 1995.

S. Maenhout, D. Baets, B. Haesaert, and G. , CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data, Bioinformatics, vol.25, pp.2753-2754, 2009.

J. K. Pritchard, M. Stephens, and P. Donnelly, Inference of population structure using multilocus genotype data, Genetics, vol.155, pp.945-959, 2000.

D. Falush, M. Stephens, and J. K. Pritchard, Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies, Genetics, vol.164, pp.1567-1587, 2003.

D. H. Alexander, J. Novembre, and K. Lange, Fast model-based estimation of ancestry in unrelated individuals, Genome Res, vol.19, pp.1655-1664, 2009.

M. Nei, Analysis of gene diversity in subdivided populations, Proc Natl Acad Sci, vol.70, pp.3321-3323, 1973.

M. Nei, Molecular evolutionary genetics, 1987.

B. S. Weir and C. C. Cockerham, Estimating F-statistics for the analysis of population structure, Evolution, vol.38, pp.1358-1370, 1984.

J. Goudet, Hierfstat, a package for r to compute and test hierarchical Fstatistics, Mol Ecol Notes, vol.5, pp.184-186, 2005.

M. Foll and O. Gaggiotti, A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: A bayesian perspective, Genetics, vol.180, pp.977-993, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00377961

D. J. Balding, Likelihood-based inference for genetic correlation coefficients, Theor Popul Biol, vol.63, pp.221-230, 2003.

S. Jeffrey, Theory of Probability, 1961.

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

D. M. Bates and D. G. Watts, Nonlinear regression analysis and its applications, 1988.

J. A. Sved, Linkage disequilibrium and homozygosity of chromosome segments in finite populations, Theor Popul Biol, vol.2, pp.125-141, 1971.

W. Hill and B. Weir, Variances and covariances of squared linkage disequilibria in finite populations, Theor Popul Biol, vol.33, pp.54-78, 1988.

M. Jakobsson, S. Scholz, P. Scheet, J. Gibbs, and J. Vanliere, Genotype, haplotype and copy-number variation in worldwide human populations, Nature, vol.451, p.998, 2008.

P. Scheet and M. Stephens, A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase, Am J Hum Genet, vol.78, pp.629-644, 2006.

J. Ritchie and D. Nesmith, Temperature and crop development. Modeling plant and soil systems, 1991.

J. Yu, G. Pressoir, W. H. Briggs, V. Bi, I. Yamasaki et al., A unified mixed-model method for association mapping that accounts for multiple levels of relatedness, Nat Genet, vol.38, pp.203-208, 2006.

J. S. Rogers, Measures of genetic similarity and genetic distance, Univ Texas Publ, vol.7213, pp.145-153, 1972.

V. Segura, B. J. Vilhjalmsson, A. Platt, A. Korte, and U. Seren, An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations, Nat Genet, vol.44, pp.825-830, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01267792

A. Gilmour, B. Gogel, B. Cullis, and R. Thompson, ASReml user guide release 2.0. VSN International Ltd, p.320, 2006.

M. Kenward and J. Roger, The precision of fixed effects estimates from restricted maximum likelihood, Biometrics, vol.53, pp.983-997, 1997.

P. Duggal, E. M. Gillanders, T. N. Holmes, and J. E. Bailey-wilson, Establishing an adjusted p-value threshold to control the family-wide type 1 error in genome wide association studies, BMC Genomics, vol.9, p.516, 2008.

K. Strimmer, fdrtool: a versatile R package for estimating local and tail area-based false discovery rates, Bioinformatics, vol.24, pp.1461-1462, 2008.

K. Strimmer, A unified approach to false discovery rate estimation, BMC Bioinformatics, vol.9, p.303, 2008.

G. Haseneyer, S. Stracke, H. Piepho, S. Sauer, and H. Geiger, DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits, BMC Plant Biol, vol.10, p.5, 2010.

T. K. Wolfgruber, A. Sharma, K. L. Schneider, P. S. Albert, and D. Koo, Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic loci shaped primarily by retrotransposons, PLoS Genet, vol.5, p.1000743, 2009.

Y. Vigouroux, J. C. Glaubitz, Y. Matsuoka, M. M. Goodman, and G. Sanchez, Population structure and genetic diversity of New World maize races assessed by DNA microsatellites, Am J Bot, vol.95, pp.1240-1253, 2008.

V. Wahl, J. Ponnu, A. Schlereth, S. Arrivault, and T. Langenecker, Regulation of flowering by Trehalose-6-Phosphate signaling in Arabidopsis thaliana, Science, vol.339, pp.704-707, 2013.

E. Frascaroli, T. Schrag, and A. Melchinger, Genetic diversity analysis of elite European maize (Zea mays L.) inbred lines using AFLP, SSR, and SNP markers reveals ascertainment bias for a subset of SNPs, Theor Appl Genet, pp.1-9, 2012.

R. J. Elshire, J. C. Glaubitz, Q. Sun, J. A. Poland, and K. Kawamoto, A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species, PLoS ONE, vol.6, p.19379, 2011.

J. Chia, C. Song, P. J. Bradbury, D. Costich, and N. De-leon, Maize HapMap2 identifies extant variation from a genome in flux, Nat Genet, vol.44, pp.803-807, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02650682

M. Hamblin, M. Warburton, and E. Buckler, Empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness, PLoS ONE, vol.2, 2007.

Y. Lu, J. Yan, C. T. Guimaraes, S. Taba, and Z. Hao, Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms, Theor Appl Genet, vol.120, pp.93-115, 2009.

M. Truntzler, N. Ranc, M. Sawkins, S. Nicolas, and D. Manicacci, Diversity and linkage disequilibrium features in a composite public/private dent maize panel: consequences for association genetics as evaluated from a case study using flowering time, Theor Appl Genet, pp.1-17, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02643782

D. Van-inghelandt, A. E. Melchinger, C. Lebreton, and B. Stich, Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers, Theor Appl Genet, vol.120, pp.1289-1299, 2010.

J. Yang, B. Benyamin, B. P. Mcevoy, S. Gordon, and A. K. Henders, Common SNPs explain a large proportion of the heritability for human height, Nat Genet, vol.42, pp.565-569, 2010.

G. T. Marth, E. Czabarka, J. Murvai, and S. T. Sherry, The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations, Genetics, vol.166, pp.351-372, 2004.

M. D. Mcmullen, S. Kresovich, H. S. Villeda, P. Bradbury, and H. Li, Genetic properties of the maize nested association mapping population, Science, vol.325, pp.737-740, 2009.

R. G. Thompson, J. P. Hart, H. J. Brumbach, and R. Lusteck, Phytolith evidence for twentieth-century BP maize in northern Iroquoia, Northeast Anthropology, vol.68, pp.25-40, 2004.

B. D. Smith, Origins of agriculture in Eastern North America, Science, vol.246, pp.1566-1571, 1989.

E. Anderson and W. L. Brown, The history of the common maize varieties of the United States corn belt, Agricultural History, vol.26, pp.2-8, 1952.

J. Doebley, J. Wendel, J. Smith, C. Stuber, and M. Goodman, The origin of cornbelt maize: The isozyme evidence, Econ Bot, vol.42, pp.120-131, 1988.

P. Dubreuil, M. Warburton, M. Chastanet, D. Hoisington, and A. Charcosset, More on the introduction of temperate maize into Europe: Large-scale bulk SSR genotyping and new historical elements, Maydica, vol.51, p.281, 2006.

C. Rebourg, M. Chastanet, B. Gouesnard, C. Welcker, and P. Dubreuil, Maize introduction into Europe: the history reviewed in the light of molecular data, Theor Appl Genet, vol.106, pp.895-903, 2003.
URL : https://hal.archives-ouvertes.fr/hal-02678281

J. Yan, T. Shah, M. L. Warburton, E. S. Buckler, and M. D. Mcmullen, Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers, PLoS ONE, vol.4, p.8451, 2009.

D. L. Remington, J. M. Thornsberry, Y. Matsuoka, L. M. Wilson, and S. R. Whitt, Structure of linkage disequilibrium and phenotypic associations in the maize genome, Proc Natl Acad Sci, vol.98, pp.11479-11484, 2001.

A. Ching, K. S. Caldwell, M. Jung, M. Dolan, and O. S. Smith, SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines, BMC Genet, vol.3, p.19, 2002.

M. Jung, A. Ching, D. Bhattramakki, M. Dolan, and S. Tingey, Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm, Theor Appl Genet, vol.109, pp.681-689, 2004.

D. Van-inghelandt, J. Reif, B. Dhillon, P. Flament, and A. Melchinger, Extent and genome-wide distribution of linkage disequilibrium in commercial maize germplasm, Theor Appl Genet, vol.123, pp.11-20, 2011.

M. Carneiro, J. A. Blanco-aguiar, R. Villafuerte, N. Ferrand, and M. W. Nachman, Speciation in the European rabbit (Oryctolagus cuniculus): islands of differentiation on the X chromosome and autosomes, Evolution, vol.64, pp.3443-3460, 2010.

M. Carneiro, N. Ferrand, and M. W. Nachman, Recombination and speciation: loci near centromeres are more differentiated than loci near telomeres between subspecies of the European rabbit, Oryctolagus cuniculus). Genetics, vol.181, pp.593-606, 2009.

D. Weetman, C. S. Wilding, K. Steen, J. Pinto, and M. J. Donnelly, Gene flowdependent genomic divergence between Anopheles gambiae M and S forms, Mol Biol Evol, vol.29, pp.279-291, 2012.

L. Fan, J. Bao, Y. Wang, J. Yao, and Y. Gui, Post-Domestication Selection in the Maize Starch Pathway, PLoS ONE, vol.4, p.7612, 2009.

L. Fan, L. Quan, X. Leng, X. Guo, and W. Hu, Molecular evidence for post-domestication selection in the Waxy gene of Chinese waxy maize, Mol Breed, vol.22, pp.329-338, 2008.

S. R. Whitt, L. M. Wilson, M. I. Tenaillon, B. S. Gaut, and E. S. Buckler, Genetic diversity and selection in the maize starch pathway, Proc Natl Acad Sci, vol.99, pp.12959-12962, 2002.

L. M. Wilson, S. R. Whitt, A. M. Ibanez, T. R. Rocheford, and M. M. Goodman, Dissection of maize kernel composition and starch production by candidate gene association, Plant Cell, vol.16, pp.2719-2733, 2004.

H. Wang, T. Nussbaum-wagler, B. Li, Q. Zhao, and Y. Vigouroux, The origin of the naked grains of maize, Nature, vol.436, pp.714-719, 2005.

M. I. Tenaillon, U. 'ren, J. Tenaillon, O. Gaut, and B. S. , Selection versus demography: A multilocus investigation of the domestication process in maize, Mol Biol Evol, vol.21, pp.1214-1225, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02677791

J. Corbi, M. Debieu, A. Rousselet, P. Montalent, L. Guilloux et al., Contrasted patterns of selection since maize domestication on duplicated genes encoding a starch pathway enzyme, Theor Appl Genet, vol.122, pp.705-722, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02645710

A. Charcosset and A. Gallais, Estimation of the contribution of Quantitative Trait Loci (QTL) to the variance of a quantitative trait by means of genetic markers, Theor Appl Genet, vol.93, pp.1193-1201, 1996.
URL : https://hal.archives-ouvertes.fr/hal-02684444

E. S. Ersoz, J. Yu, and E. S. Buckler, Applications of linkage disequilibrium and association mapping in crop plants, Genomics-assisted crop improvement, pp.97-119, 2007.

K. Arumuganathan and E. Earle, Nuclear DNA content of some important plant species, Plant Molecular Biology Reporter, vol.9, pp.208-218, 1991.

H. Tsuji, S. Tamaki, R. Komiya, and K. Shimamoto, Florigen and the photoperiodic control of flowering in rice, Rice, vol.1, pp.25-35, 2008.

J. Yu, X. Li, C. Zhu, C. T. Yeh, and W. Wu, Genic and non-genic contributions to natural variation of quantitative traits in maize, Genome Res, 2012.

M. I. Tenaillon and A. Charcosset, A European perspective on maize history, C R Biol, vol.334, pp.221-228, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02647592

M. Noor, K. L. Grams, L. A. Bertucci, and J. Reiland, Chromosomal inversions and the reproductive isolation of species, Proc Natl Acad Sci, vol.98, p.12084, 2001.

L. H. Rieseberg, Chromosomal rearrangements and speciation, Trends Ecol Evol, vol.16, pp.351-358, 2001.

A. Navarro and N. H. Barton, Chromosomal speciation and molecular divergence accelerated evolution in rearranged chromosomes, Science, vol.300, pp.321-324, 2003.

A. D. Stump, M. C. Fitzpatrick, N. F. Lobo, S. Traore, and N. Sagnon, Centromere-proximal differentiation and speciation in Anopheles gambiae, Proc Natl Acad Sci, vol.102, p.15930, 2005.

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

K. Kizilkaya, R. Fernando, and D. Garrick, Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes, J Anim Sci, vol.88, p.544, 2009.

R. Tibshirani, Regression shrinkage and selection via the lasso, Journal of the Royal Statistical Society Series B (Methodological, pp.267-288, 1996.

D. Habier, R. Fernando, and J. Dekkers, The impact of genetic relationship information on genome-assisted breeding values, Genetics, vol.177, p.2389, 2007.

D. B. Lobell, M. Banziger, C. Magorokosho, and B. Vivek, Nonlinear heat effects on African maize as evidenced by historical yield trials, Nature Clim Change, vol.1, pp.42-45, 2011.