J. R. Ellis and J. M. Burke, EST-SSRs as a resource for population genetic analyses, Heredity, vol.99, issue.2, pp.125-132, 2007.

R. K. Varshney, A. Graner, and M. E. Sorrells, Genic microsatellite markers in plants: features and applications, Trends Biotechnol, vol.23, issue.1, pp.48-55, 2005.

S. Tangphatsornruang, P. Somta, P. Uthaipaisanwong, J. Chanprasert, D. Sangsrakru et al., Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek), BMC Plant Biology, vol.9, issue.1, pp.137-149, 2009.

T. J. Vision, D. G. Brown, D. B. Shmoys, R. T. Durrett, and S. D. Tanksley, Selective mapping: A strategy for optimizing the construction of high-density linkage maps, Genetics, vol.155, issue.1, pp.407-420, 2000.

W. Howad, T. Yamamoto, E. Dirlewanger, R. Testolin, P. Cosson et al., Mapping with a few plants: Using selective mapping for microsatellite saturation of the Prunus reference map, Genetics, vol.171, issue.3, pp.1305-1309, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02678714

I. Fernandez-silva, E. I. Blanca, J. Esteras, C. Pico, B. Nuez et al., Bin mapping of genomic and EST-derived SSRs in melon, Cucumis melo L.). Theoretical and Applied Genetics, vol.118, issue.1, pp.139-150, 2008.

D. J. Sargent, G. Cipriani, S. Vilanova, D. Gil-ariza, P. Arus et al., The development of a bin mapping population and the selective mapping of 103 markers in the diploid Fragaria reference map, Genome, vol.51, issue.2, pp.120-127, 2008.

J. M. Celton, D. S. Tustin, D. Chagne, and S. E. Gardiner, Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences, Tree Genetics and Genomes, vol.5, issue.1, pp.93-107, 2009.

Y. Han, D. Chagné, K. Gasic, E. Rikkerink, J. E. Beever et al., BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple, Genomics, vol.93, issue.3, pp.282-288, 2009.

A. Ducousso, J. P. Guyon, and A. Kremer, Latitudinal and altitudinal variation of bud burst in western populations of sessile oak (Quercus petraea (Matt) Liebl), Annales Sciences Forestières, vol.53, pp.775-782, 1996.
URL : https://hal.archives-ouvertes.fr/hal-00883094

J. S. Jensen and J. K. Hansen, Geographical variation in phenology of Quercus petraea (Matt.) Liebl and Quercus robur L. oak grown in a greenhouse, Scandinavian Journal of Forest Research, vol.23, issue.2, pp.179-188, 2008.

C. Saintagne, C. Bodénès, T. Barreneche, D. Pot, C. Plomion et al., Distribution of genomic regions differentiating oak species assessed by QTL detection, Heredity, vol.92, issue.1, pp.20-30, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02678139

C. Scotti-saintagne, C. Bodénès, T. Barreneche, E. Bertocchi, C. Plomion et al., Detection of quantitative trait loci controlling bud burst and height growth in Quercus robur L. Theoretical and Applied Genetics, vol.109, pp.1648-1659, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02681266

O. Brendel, L. Thiec, D. Scotti-saintagne, C. Bodénès, C. Kremer et al., Quantitative trait loci controlling water use efficiency and related traits in Quercus robur L, Tree Genet Genomes, vol.4, issue.2, pp.263-278, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01032066

J. Parelle, M. Zapater, C. Scotti-saintagne, A. Kremer, Y. Jolivet et al., Quantitative trait loci of tolerance to waterlogging in a European oak (Quercus robur L.): physiological relevance and temporal effect patterns, Plant, Cell and Environment, vol.30, issue.4, pp.422-434, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02665582

J. Derory, C. Scotti-saintagne, E. Bertocchi, L. Dantec, L. Graignic et al., Contrasting correlations between diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks, Heredity, vol.104, pp.438-448, 2010.

J. Derory, P. Leger, V. Garcia, J. Schaeffer, M. T. Hauser et al., Transcriptome analysis of bud burst in sessile oak (Quercus petraea), New Phytol, vol.170, issue.4, pp.723-738, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02666078

M. Roussel, E. Dreyer, P. Montpied, G. Le-provost, J. M. Guehl et al., The diversity of 13C isotope discrimination in a Quercus robur full-sib family is associated with differences in intrinsic water use efficiency, transpiration efficiency, and stomatal conductance, Journal of Experimental Botany, vol.60, issue.8, pp.2419-2431, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00489874

T. Barreneche, C. Bodénès, C. Lexer, J. F. Trontin, S. Fluch et al., A genetic linkage map of Quercus robur L. (pedunculate oak) based on RAPD, SCAR, microsatellite, minisatellite, isozyme and 55 rDNA markers, Theoretical and Applied Genetics, vol.97, issue.7, pp.1090-1103, 1998.
URL : https://hal.archives-ouvertes.fr/hal-02694736

T. Barreneche, M. Casasoli, K. Russell, A. Akkak, H. Meddour et al., Comparative mapping between Quercus and Castanea using simple-sequence repeats (SSRs). Theoretical and Applied Genetics, vol.108, pp.558-566, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02679023

A. Kremer, M. Casasoli, T. T. Barreneche, C. Bodénès, P. Sisco et al., F: Fagaceae trees, Genome Mapping & Molecular Breeding. Forest Trees. Edited by: Kole CR, pp.161-187, 2007.

W. Guo, C. Cai, C. Wang, Z. Han, X. Song et al., A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium, Genetics, vol.176, issue.1, p.527, 2007.

R. Kolpakov, G. Bana, and G. Kucherov, mreps: efficient and flexible detection of tandem repeats in DNA, Nucleic Acids Res, vol.31, issue.13, pp.3672-3678, 2003.
URL : https://hal.archives-ouvertes.fr/inria-00099597

C. Iseli, C. V. Jongeneel, and P. Bucher, ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences, Proc Int Conf Intell Syst Mol Biol, pp.138-186, 1999.

S. Ueno and Y. Tsumura, Development of ten microsatellite markers for Quercus mongolica var. crispula by database mining, Conserv Genet, vol.9, issue.4, pp.1083-1085, 2008.

S. Ueno, K. Aoki, and Y. Tsumura, Generation of Expressed Sequence Tags and development of microsatellite markers for Castanopsis sieboldii var. sieboldii (Fagaceae), Annals of Forest Science, vol.66, issue.5, pp.509-509, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00883475

F. Alberto, J. Niort, J. Derory, O. Lepais, R. Vitalis et al., Population differenciation of sessile oak at the altitudinal front of migration in the French Pyrenees, Mol Ecol

A. El-mousadik and R. J. Petit, High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L) Skeels] endemic to Morocco, Molecular Ecology, vol.5, pp.547-555, 1996.

E. S. Lander, P. Green, J. Abrahamson, A. Barlow, M. J. Daly et al., MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations, Genomics, vol.1987, issue.2, pp.174-181

J. W. Van-ooijen, JoinMap® 4. Software for the calculation of genetic linkage maps in experimental populations, 2006.

D. Chagné, C. Lalanne, D. Madur, S. Kumar, J. M. Frigerio et al., A high density genetic map of maritime pine based on AFLPs, Annals of Forest Science, vol.59, pp.627-636, 2002.

X. Qi, P. Stam, and P. Lindhout, Comparison and integration of four barley genetic maps, Genome, vol.39, pp.379-394, 1996.

N. D. Young and S. D. Tanksley, Restriction fragment length polymorphism maps and the concept of graphical genotypes, Theoretical and Applied Genetics, vol.77, issue.1, pp.95-101, 1989.

S. Leclercq, E. Rivals, and P. Jarne, Detecting microsatellites within genomes: significant variation among algorithms, BMC Bioinformatics, vol.8, issue.1, pp.125-143, 2007.
URL : https://hal.archives-ouvertes.fr/lirmm-00193269

S. K. Parida, A. R. Kumar, K. Dalal, V. Singh, N. K. Mohapatra et al., Unigene derived microsatellite markers for the cereal genomes. Theoretical and applied genetics, vol.112, pp.808-817, 2006.

L. Rota, M. Kantety, R. V. Yu, J. K. Sorrells, and M. E. , Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley, BMC Genomics, vol.6, issue.1, pp.23-34, 2005.

S. P. Kumpatla and S. Mukhopadhyay, Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species, Genome, vol.48, issue.6, pp.985-998, 2005.

T. M. Yin, X. Y. Zhang, L. E. Gunter, S. X. Li, S. D. Wullschleger et al., Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome, New Phytol, vol.181, issue.2, pp.498-503, 2009.

G. A. Tuskan, S. Difazio, S. Jansson, J. Bohlmann, I. Grigoriev et al., The genome of black cottonwood, Populus trichocarpa (Torr. & Gray), Science, vol.313, issue.5793, pp.1596-1604, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02669155

N. Sharopova, Plant simple sequence repeats: distribution, variation, and effects on gene expression, Genome, vol.51, issue.2, pp.79-90, 2008.

M. Morgante, M. Hanafey, and W. Powell, Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes, Nature Genetics, vol.30, issue.2, pp.194-200, 2002.

C. Schlotterer and D. Tautz, Slippage synthesis of simple sequence DNA, Nucleic Acids Res, vol.20, issue.2, pp.211-215, 1992.

. Durand, BMC Genomics, vol.11, 2010.

D. Metzgar, J. Bytof, and C. Wills, Selection against frameshift mutations limits microsatellite expansion in coding DNA, Genome Research, vol.10, issue.1, pp.72-80, 2000.

A. Grover, V. Aishwarya, and P. C. Sharma, Biased distribution of microsatellite motifs in the rice genome, Molecular Genetics and Genomics, vol.277, issue.5, pp.469-480, 2007.

S. Fujimori, T. Washio, K. Higo, Y. Ohtomo, K. Murakami et al., A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription, FEBS Letters, vol.554, issue.1, pp.17-22, 2003.

S. G. Ralph, H. J. Chun, D. Cooper, R. Kirkpatrick, N. Kolosova et al., Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding, BMC Genomics, vol.9, issue.1, pp.57-75, 2008.

Y. Zhou, T. Bui, L. D. Auckland, and C. G. Williams, Direct fluorescent primers are superior to M13-tailed primers for Pinus taeda microsatellites, Biotechniques, vol.32, issue.1, pp.46-52, 2002.

M. Brandström and H. Ellegren, Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias, Genome Research, vol.18, issue.6, pp.881-887, 2008.

M. Morgante and A. M. Olivieri, PCR-amplified microsatellites as markers in plant genetics, The Plant Journal, vol.1993, issue.1, pp.175-182

S. Temnykh, G. Declerck, A. Lukashova, L. Lipovich, S. Cartinhour et al., Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential, Genome Research, vol.11, issue.8, pp.1441-1452, 2001.

R. V. Kantety, L. Rota, M. Matthews, D. E. Sorrells, and M. E. , Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat, Plant Molecular Biology, vol.48, issue.5, pp.501-510, 2002.

V. Kalavacharla, K. Hossain, Y. Gu, O. Riera-lizarazu, M. I. Vales et al., High-resolution radiation hydrid map of wheat chromosome 1D, Genetics, vol.173, issue.2, pp.1089-1999, 2006.

L. L. Qi, B. Echalier, S. Chao, G. R. Lazo, G. E. Butler et al., Ratnasiri A: A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat, Genetics, vol.168, issue.2, pp.701-712, 2004.

W. Deleu, C. Esteras, C. Roig, M. Gonzalez-to, I. Fernandez-silva et al., A set of EST-SNPs for map saturation and cultivar identification in melon, BMC Plant Biology, vol.9, issue.1, pp.90-99, 2009.

R. T. Miller, A. G. Christoffels, C. Gopalakrishnan, J. Burke, A. A. Ptitsyn et al., A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base, Genome Research, vol.9, issue.11, pp.1143-1155, 1999.

P. Green, /. Swat/crossmatch, and . Phrap-package, , 1999.

J. Burke, D. Davison, and W. Hide, d2_cluster: a validated method for clustering EST and full-length cDNA sequences, Genome Research, vol.9, issue.11, pp.1135-1142, 1999.

, Green P: Documentation for phrap, 1996.

A. Chou and J. Burke, CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences, Bioinformatics, vol.15, issue.5, pp.376-381, 1999.

S. Temnykh, G. Declerck, A. Lukashova, L. Lipovich, S. Cartinhour et al., Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential, Genome Research, vol.11, pp.1441-52, 2001.

J. Gouzy, S. Carrere, and T. Schiex, FrameDP: sensitive peptide detection on noisy matured sequences, Bioinformatics, vol.25, issue.5, pp.670-671, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02665259

, Primer 3.0

M. Schuelke, An economic method for the fluorescent labeling of PCR fragments, Nature Biotechnology, vol.18, issue.2, pp.233-234, 2000.

J. Williams, A. R. Kubelik, K. J. Livak, J. A. Rafalski, and S. V. Tingey, DNA polymorphisms amplified by arbitrary primers are useful as geneticmarkers, Nucleic Acids Res, vol.18, issue.22, pp.6531-6535, 1990.

D. Grattapaglia and R. Sederoff, Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers, Genetics, vol.137, issue.4, pp.1121-1137, 1994.

. Mappop,

, M: Molecular Evolutionary Genetics, 1987.

J. Goudet, FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3), Updated from Goudet, 1995.

. Durand, A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study, BMC Genomics, vol.11, p.570, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00645935