M. W. Ganal, T. Altmann, and M. S. Röder, SNP identification in crop plants, Curr Opin Plant Biol, vol.12, pp.211-217, 2009.

M. W. Ganal, A. Polley, E. M. Graner, J. Plieske, R. Wieseke et al., Large SNP arrays for genotyping in crop plants, J Biosci, vol.37, pp.821-828, 2012.

E. Paux, P. Sourdille, I. Mackay, and C. Feuillet, Sequence-based marker development in wheat: advances and applications to breeding, Biotechnol Adv, vol.30, pp.1071-1088, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00964394

J. Cao, K. Schneeberger, S. Ossowski, T. Gunther, S. Bender et al., Whole-genome sequencing of multiple Arabidopsis thaliana populations, Nat Genet, vol.43, pp.956-963, 2011.

N. Kim, Y. M. Jeong, S. Jeong, G. B. Kim, S. Baek et al., Identification of candidate domestication regions in the radish genome based on high-depth resequencing analysis of 17 genotypes, Theor Appl Genet, vol.129, p.27377547, 2016.

Q. B. Kwong, C. K. Teh, A. L. Ong, H. Y. Heng, H. L. Lee et al., Development and validation of a high-density SNP genotyping array for african oil palm, Mol Plant, vol.9, pp.1132-1141, 2016.

H. Lam, X. Xu, X. Liu, W. Chen, G. Yang et al., Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection, Nat Genet, vol.42, pp.1053-1059, 2010.

X. Xu, X. Liu, S. Ge, J. D. Jensen, F. Hu et al., Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes, Nat Biotechnol, vol.30, pp.105-111, 2012.

M. O. Winfield, A. M. Allen, A. J. Burridge, G. L. Barker, H. R. Benbow et al., High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool, Plant Biotechnol J, vol.14, pp.1195-1206, 2015.

K. Jordan, S. Wang, Y. Lun, L. Gardiner, R. Maclachlan et al., A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes, Genome Biol, vol.16, p.25886949, 2015.

S. Wang, D. Wong, K. Forrest, A. Allen, S. Chao et al., Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array, Plant Biotechnol J, vol.12, pp.787-796, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02285461

J. A. Poland, P. J. Brown, M. E. Sorrells, and J. Jannink, Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach, PLoS One, vol.7, 2012.

F. Kobayashi, T. Tanaka, H. Kanamori, J. Wu, Y. Katayose et al., Characterization of a mini core collection of Japanese wheat varieties using single-nucleotide polymorphisms generated by genotypingby-sequencing, Breeding Sci, vol.66, pp.213-225, 2016.

K. Lai, M. T. Lorenc, H. C. Lee, P. J. Berkman, P. E. Bayer et al., Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat, Plant Biotechnol J, vol.13, pp.97-104, 2015.

J. D. Montenegro, A. A. Golicz, P. E. Bayer, B. Hurgobin, H. Lee et al., The pangenome of hexaploid bread wheat, Plant J, vol.90, pp.1007-1013, 2017.

E. Akhunov, C. Nicolet, and J. Dvorak, Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay, Theor Appl Genet, vol.119, p.19449174, 2009.

A. M. Allen, G. L. Barker, S. T. Berry, J. A. Coghill, R. Gwilliam et al., Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat

, Plant Biotechnol J, vol.9, pp.1086-1099, 2011.

N. Cubizolles, E. Rey, F. Choulet, H. Rimbert, C. Laugier et al., Exploiting the repetitive fraction of the wheat genome for high-throughput single-nucleotide polymorphism discovery and genotyping, Plant Genome, vol.9, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02635405

K. J. Edwards, A. L. Reid, J. A. Coghill, S. T. Berry, and G. L. Barker, Multiplex single nucleotide polymorphism (SNP)-based genotyping in allohexaploid wheat using padlock probes, Plant Biotechnol J, vol.7, p.19379286, 2009.

E. Paux, S. Faure, F. Choulet, D. Roger, V. Gauthier et al., Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat, Plant Biotechnol J, vol.8, pp.196-210, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00964403

C. R. Cavanagh, S. Chao, S. Wang, B. E. Huang, S. Stephen et al., Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars, Proc Natl Acad Sci U S A, vol.110, pp.8057-8062, 2013.

A. M. Allen, M. O. Winfield, A. J. Burridge, R. C. Downie, H. R. Benbow et al., Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum), Plant Biotechnol J, vol.15, pp.390-401, 2016.

F. Choulet, A. Alberti, S. Theil, N. Glover, V. Barbe et al., Structural and functional partitioning of bread wheat chromosome 3B, Science, vol.345, p.1249721, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02638189

N. Glover, J. Daron, L. Pingault, K. Vandepoele, E. Paux et al., Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B, Genome Biol, vol.16, p.26353816, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01244498

, The International Wheat Genome Sequencing Consortium. A chromosome-based draft sequence of the hexaploid bread wheat genome, Science, vol.345, p.1251788, 2014.

F. Choulet, T. Wicker, C. Rustenholz, E. Paux, J. Salse et al., Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces, Plant Cell, vol.22, pp.1686-1701, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00964451

T. Wicker, D. E. Matthews, and B. Keller, TREP: a database for Triticeae repetitive elements, Trends Plant Sci, vol.7, pp.561-562, 2002.

E. Paux, D. Roger, E. Badaeva, G. Gay, M. Bernard et al., Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BACend sequencing on chromosome 3B, Plant J, vol.48, pp.463-474, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00964354

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009.

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009.

X. Perrier, A. Flori, F. Bonnot, P. Hamon, M. Seguin et al., Data analysis methods, Genetic diversity of cultivated tropical plants, pp.43-76, 2003.
URL : https://hal.archives-ouvertes.fr/halshs-00752878

Y. Wu, P. R. Bhat, T. J. Close, and S. Lonardi, Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph, PLoS Genet, vol.4, p.1000212, 2008.

R. M. Clark, S. Tavare, and J. Doebley, Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus, Mol Biol Evol, vol.22, pp.2304-2312, 2005.

P. D. Rabinowicz, R. Citek, M. A. Budiman, A. Nunberg, J. A. Bedell et al., Differential methylation of genes and repeats in land plants, Genome Res, vol.15, pp.1431-1440, 2005.

F. Balfourier, V. Roussel, P. Strelchenko, F. Exbrayat-vinson, P. Sourdille et al., A worldwide bread wheat core collection arrayed in a 384-well plate, Theor Appl Genet, vol.114, p.17318494, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00964182

N. V. Bassil, T. M. Davis, H. Zhang, S. Ficklin, M. Mittmann et al., Development and preliminary evaluation of a 90 K Axiom ® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa, BMC Genomics, vol.16, pp.1-30, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02639308

J. P. Didion, H. Yang, K. Sheppard, C. Fu, L. Mcmillan et al., Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias, BMC Genomics, vol.13, pp.1-18, 2012.

M. E. Sorrells, J. P. Gustafson, D. Somers, S. Chao, D. Benscher et al., Reconstruction of the synthetic W7984 x Opata M85 wheat reference population, Genome, vol.54, pp.875-882, 2011.

A. Horvath, A. Didier, J. Koenig, F. Exbrayat, G. Charmet et al., Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.), Theor Appl Genet, vol.119, pp.1523-1537, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00964187

F. Cui, N. Zhang, X. L. Fan, W. Zhang, C. H. Zhao et al., Utilization of a Wheat660K SNP arrayderived high-density genetic map for high-resolution mapping of a major QTL for kernel number, Sci Rep, vol.7, p.28630475, 2017.

A. M. Allen, G. L. Barker, P. Wilkinson, A. Burridge, M. Winfield et al., Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.), Plant Biotechnol J, vol.11, pp.279-295, 2013.

J. Wang, M. C. Luo, Z. Chen, F. M. You, Y. Wei et al., Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat, New Phytol, vol.198, pp.925-937, 2013.

R. Salomon-torres, V. M. Gonzalez-vizcarra, G. E. Medina-basulto, M. F. Montano-gomez, P. Mahadevan et al., Genome-wide identification of copy number variations in Holstein cattle from Baja California, Mexico, using high-density SNP genotyping arrays, Genet Mol Res, vol.14, pp.11848-11859, 2015.

M. C. Huang, T. P. Chuang, C. H. Chen, J. Y. Wu, Y. T. Chen et al., An integrated analysis tool for analyzing hybridization intensities and genotypes using new-generation population-optimized human arrays, BMC Genomics, vol.17, p.27029637, 2016.

X. Zhang, R. Du, S. Li, F. Zhang, J. L. Wang et al., Evaluation of copy number variation detection for a SNP array platform, BMC Bioinformatics, vol.15, p.24555668, 2014.

M. Fanciulli, E. Petretto, and T. J. Aitman, Gene copy number variation and common human disease, Clinical Genetics, vol.77, pp.201-213, 2010.

J. Weischenfeldt, O. Symmons, F. Spitz, and J. O. Korbel, Phenotypic impact of genomic structural variation: insights from and for human disease, Nat Rev Genet, vol.14, pp.125-138, 2013.

A. Diaz, M. Zikhali, A. S. Turner, P. Isaac, and L. Da, Copy number variation affecting the Photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat

, PLoS One, vol.7, 2012.

Y. Li, J. Xiao, J. Wu, J. Duan, Y. Liu et al., A tandem segmental duplication (TSD) in green revolution gene Rht-D1b region underlies plant height variation, New Phytol, vol.196, p.22849513, 2012.

L. G. Maron, C. T. Guimaraes, M. Kirst, P. S. Albert, J. A. Birchler et al., Aluminum tolerance in maize is associated with higher MATE1 gene copy number, Proc Natl Acad Sci U S A, vol.110, pp.5241-5246, 2013.

R. K. Saxena, D. Edwards, and R. K. Varshney, Structural variations in plant genomes, Brief Funct Genomics, vol.13, pp.296-307, 2014.

T. Sutton, U. Baumann, J. Hayes, N. C. Collins, B. J. Shi et al., Boron-toxicity tolerance in barley arising from efflux transporter amplification, Science, vol.318, pp.1446-1449, 2007.

L. Pingault, F. Choulet, A. Alberti, N. Glover, P. Wincker et al., Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome, Genome Biol, vol.16, p.25853487, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02635440

K. Lin, S. Smit, G. Bonnema, G. Sanchez-perez, and D. De-ridder, Making the difference: integrating structural variation detection tools, Brief Bioinform, vol.16, pp.852-864, 2015.

A. Ferreira, M. F. Da-silva, C. Da, L. Silva, and C. D. Cruz, Estimating the effects of population size and type on the accuracy of genetic maps, Gen Mol Biol, vol.29, pp.187-192, 2006.

R. Mercier, C. Mezard, E. Jenczewski, N. Macaisne, and M. Grelon, The molecular biology of meiosis in plants, Annu Rev Plant Biol, vol.66, pp.297-327, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01204185

C. Saintenac, M. Falque, O. C. Martin, E. Paux, C. Feuillet et al., Detailed recombination studies along chromosome 3B provide new insights on crossover distribution in wheat (Triticum aestivum L.), Genetics, vol.181, pp.393-403, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00964380

C. Saintenac, S. Faure, A. Remay, F. Choulet, C. Ravel et al., Variation in crossover rates across a 3-Mb contig of bread wheat (Triticum aestivum) reveals the presence of a meiotic recombination hotspot, Chromosoma, vol.120, p.21161258, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00964315

K. A. Gardner, L. M. Wittern, and I. J. Mackay, A highly recombined, high-density, eight-founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments, Plant Biotechnol J, vol.14, pp.1406-1417, 2016.

J. Chapman, M. Mascher, A. Buluc, K. Barry, E. Georganas et al., A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome, Genome Biol, vol.16, p.25637298, 2015.

F. Gao, W. Wen, J. Liu, A. Rasheed, G. Yin et al., Genome-wide linkage mapping of QTL for yield components, plant height and yield-related physiological traits in the chinese wheat cross Zhou 8425B/ Chinese Spring, Front Plant Sci, vol.6, p.1099, 2015.

W. Wen, Z. He, F. Gao, J. Liu, H. Jin et al., A high-density consensus map of common wheat integrating four mapping populations scanned by the 90K SNP array, Front Plant Sci, vol.8, p.1389, 2017.