E. M. Southern, Detection of specific sequences among DNA fragments separated by gel electrophoresis, Journal of Molecular Biology, vol.98, issue.3, pp.503-517, 1975.

R. K. Saiki, S. Scharf, F. Faloona, K. B. Mullis, G. T. Horn et al., Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia, Science, vol.230, issue.4732, pp.1350-1354, 1985.

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

K. Semagn, R. Babu, S. Hearne, and M. Olsen, Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement, Molecular Breeding, vol.33, issue.1, pp.1-14, 2013.

M. W. Ganal, A. Polley, E. M. Graner, J. Plieske, R. Wieseke et al., Large SNP arrays for genotyping in crop plants, Journal of Biosciences, vol.37, issue.5, pp.821-828, 2012.

J. He, X. Zhao, A. Laroche, Z. X. Lu, H. Liu et al., Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding, Frontiers in Plant Science, vol.5, 2014.

A. A. Deokar, L. Ramsay, A. G. Sharpe, M. Diapari, A. Sindhu et al., Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly, BMC Genomics, vol.15, issue.1, p.708, 2014.

Q. Su, X. Zhang, W. Zhang, N. Zhang, L. Song et al., QTL Detection for Kernel Size and Weight in Bread Wheat (Triticum aestivum L.) Using a High-Density SNP and SSR-Based Linkage Map, Frontiers in Plant Science, vol.9, 2018.

G. Cipriani, A. Spadotto, I. Jurman, G. Di-gaspero, M. Crespan et al., The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin, Theoretical and Applied Genetics, vol.121, issue.8, pp.1569-1585, 2010.

M. Morgante and A. M. Olivieri, PCR-amplified microsatellites as markers in plant genetics, The Plant Journal, vol.3, issue.1, pp.175-182, 1993.

?. St?pie?, V. Mohler, J. Bocianowski, and G. Koczyk, Assessing genetic diversity of Polish wheat (Triticum aestivum) varieties using microsatellite markers, Genetic Resources and Crop Evolution, vol.54, issue.7, pp.1499-1506, 2007.

H. J. Jacob, K. Lindpaintner, S. E. Lincoln, K. Kusumi, R. K. Bunker et al., Genetic mapping of a gene causing hypertension in the stroke-prone spontaneously hypertensive rat, Cell, vol.67, issue.1, pp.213-224, 1991.

A. Edwards, H. A. Hammond, L. Jin, C. T. Caskey, and R. Chakraborty, Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups, Genomics, vol.12, issue.2, pp.241-253, 1992.

S. K. Parida, V. Dalal, A. K. Singh, N. K. Singh, and T. Mohapatra, Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups, BMC Genomics, vol.10, issue.1, p.140, 2009.

W. Powell, G. C. Machray, and J. Provan, Polymorphism revealed by simple sequence repeats, Trends in Plant Science, vol.1, issue.7, pp.215-222, 1996.

G. F. Richard, C. Hennequin, A. Thierry, and B. Dujon, Trinucleotide repeats and other microsatellites in yeasts, Research in Microbiology, vol.150, issue.9-10, pp.589-602, 1999.

G. F. Richard and F. Pâques, Mini? and microsatellite expansions: the recombination connection, EMBO reports, vol.1, issue.2, pp.122-126, 2000.

E. L. Van-dijk, H. Auger, Y. Jaszczyszyn, and C. Thermes, Ten years of next-generation sequencing technology, Trends in Genetics, vol.30, issue.9, pp.418-426, 2014.

D. M. Bornman, M. E. Hester, J. M. Schuetter, M. D. Kasoji, A. Minard-smith et al., Short-read, high-throughput sequencing technology for STR genotyping, BioTechniques, 2012.

S. L. Fordyce, M. C. Ávila-arcos, E. Rockenbauer, C. Børsting, R. Frank-hansen et al., High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform, BioTechniques, vol.51, pp.127-133, 2011.

B. J. Darby, S. F. Erickson, S. D. Hervey, and S. N. Ellis?felege, Digital fragment analysis of short tandem repeats by high?throughput amplicon sequencing, Ecology and Evolution, vol.6, issue.13, pp.4502-4512, 2016.

O. Lepais, E. Chancerel, C. Boury, F. Salin, A. Manicki et al., Fast sequence-based microsatellite genotyping development workflow, PeerJ, vol.8, p.e9085, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02936408

M. N. Albarghouthi, B. A. Buchholz, E. A. Doherty, F. M. Bogdan, H. Zhou et al., Impact of polymer hydrophobicity on the properties and performance of DNA sequencing matrices for capillary electrophoresis, Electrophoresis, vol.22, pp.737-747, 2001.

O. Tu, T. Knott, M. Marsh, K. Bechtol, D. Harris et al., The influence of fluorescent dye structure on the electrophoretic mobility of end-labeled DNA, Nucleic Acids Research, vol.26, issue.11, pp.2797-2802, 1998.

A. Estoup, P. Jarne, and J. M. Cornuet, Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis, Molecular Ecology, vol.11, issue.9, pp.1591-1604, 2002.

T. Kõressaar, M. Lepamets, L. Kaplinski, K. Raime, R. Andreson et al., Primer3_masker: integrating masking of template sequence with primer design software, Bioinformatics, vol.34, issue.11, pp.1937-1938, 2018.

V. Laucou, T. Lacombe, F. Dechesne, R. Siret, J. P. Bruno et al., High throughput analysis of grape genetic diversity as a tool for germplasm collection management, Theoretical and Applied Genetics, vol.122, issue.6, pp.1233-1245, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01506050

B. Kump and B. Javornik, Evaluation of genetic variability among common buckwheat (Fagopyrum esculentum Moench) populations by RAPD markers, Plant Science, vol.114, issue.2, pp.149-158, 1996.

D. M. Gohl, D. M. Gohl, A. Maclean, A. Hauge, A. Becker et al., An optimized protocol for high-throughput amplicon-based microbiome profiling, Protocol Exchange, 2016.

S. Vartia, J. L. Villanueva-cañas, J. Finarelli, E. D. Farrell, P. C. Collins et al., A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding, Royal Society Open Science, vol.3, issue.1, p.150565, 2016.

K. M. Sefc, F. Regner, E. Turetschek, J. Glössl, and H. Steinkellner, Identification of microsatellite sequences in Vitis riparia and their applicability for genotyping of different Vitis species, Genome, vol.42, issue.3, pp.367-373, 1999.

D. Merdinoglu, G. Butterlin, L. Bevilacqua, V. Chiquet, A. F. Adam-blondon et al., Development and characterization of a large set of microsatellite markers in grapevine (Vitis vinifera L.) suitable for multiplex PCR, Molecular Breeding, vol.15, issue.4, pp.349-366, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02682085

J. E. Bowers, G. S. Dangl, R. Vignani, and C. P. Meredith, Isolation and characterization of new polymorphic simple sequence repeat loci in grape (Vitis vinifera L.), Genome, vol.39, issue.4, pp.628-633, 1996.

E. Aronesty, Comparison of Sequencing Utility Programs, The Open Bioinformatics Journal, vol.7, issue.1, pp.1-8, 2013.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, vol.17, issue.1, p.10, 2011.

S. Beier, T. Thiel, T. Münch, U. Scholz, and M. Mascher, MISA-web: a web server for microsatellite prediction, Bioinformatics, vol.33, issue.16, pp.2583-2585, 2017.

P. Rice, I. Longden, and A. Bleasby, EMBOSS: The European Molecular Biology Open Software Suite, Trends in Genetics, vol.16, issue.6, pp.276-277, 2000.

K. Z. Kedzierska, L. Gerber, D. Cagnazzi, M. Krützen, A. Ratan et al., SONiCS: PCR stutter noise correction in genome-scale microsatellites, Bioinformatics, vol.34, issue.23, pp.4115-4117, 2018.

M. Gymrek, D. Golan, S. Rosset, and Y. Erlich, lobSTR: A short tandem repeat profiler for personal genomes, Genome Research, vol.22, issue.6, pp.1154-1162, 2012.

G. Highnam, C. Franck, A. Martin, C. Stephens, A. Puthige et al., Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles, Nucleic Acids Research, vol.41, issue.1, pp.e32-e32, 2012.

M. D. Cao, E. Tasker, K. Willadsen, M. Imelfort, S. Vishwanathan et al., Inferring short tandem repeat variation from paired-end short reads, Nucleic Acids Research, vol.42, issue.3, pp.e16-e16, 2013.

A. Fungtammasan, G. Ananda, S. E. Hile, M. S. Su, C. Sun et al., Accurate typing of short tandem repeats from genome-wide sequencing data and its applications, Genome Research, vol.25, issue.5, pp.736-749, 2015.

C. Cantarella and N. D?agostino, PSR: polymorphic SSR retrieval, BMC Research Notes, vol.8, issue.1, 2015.

E. S. Buckler, D. C. Ilut, X. Wang, T. Kretzschmar, M. A. Gore et al., rAmpSeq: Using repetitive sequences for robust genotyping, BioRxiv, 2016.

H. Tang and E. Nzabarushimana, STRScan: targeted profiling of short tandem repeats in whole-genome sequencing data, BMC Bioinformatics, vol.18, issue.S11, 2017.

S. Riaz, K. E. Garrison, G. S. Dangl, J. Boursiquot, and C. P. Meredith, Genetic Divergence and Chimerism within Ancient Asexually Propagated Winegrape Cultivars, Journal of the American Society for Horticultural Science, vol.127, issue.4, pp.508-514, 2002.

M. Crespan, Evidence on the evolution of polymorphism of microsatellite markers in varieties of Vitis vinifera L., Theoretical and Applied Genetics, vol.108, issue.2, pp.231-237, 2003.

J. Ibanez, M. T. De-andres, and J. Borrego, Allelic variation observed at one microsatellite locus between the two synonym grape cultivars Black Currant and Mavri Corinthiaki, vol.39, pp.173-174, 2000.

S. Hocquigny, F. Pelsy, V. Dumas, S. Kindt, M. C. Heloir et al., Diversification within grapevine cultivars goes through chimeric states, Genome, vol.47, issue.3, pp.579-589, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02682749

N. Stajner, D. Rusjan, Z. Korosec-koruza, and B. Javornik, Genetic Characterization of Old Slovenian Grapevine Varieties of Vitis vinifera L. by Microsatellite Genotyping, American Journal of Enology and Viticulture, vol.62, issue.2, pp.250-255, 2011.

K. Koncilja, Intravarietal Variability analysis of Grapevine Variety 'Merlot' (Vitis vinifera L.) with Microsatelites Markers, 2010.

M. D. Vélez and J. Ibáñez, Assessment of the uniformity and stability of grapevine cultivars using a set of microsatellite markers, Euphytica, vol.186, issue.2, pp.419-432, 2012.

M. M. Thompson and H. P. Olmo, CYTOHISTOLOGICAL STUDIES OF CYTOCHIMERIC AND TETRAPLOID GRAPES, American Journal of Botany, vol.50, issue.9, pp.901-906, 1963.

S. Deschamps, V. Llaca, and G. D. May, Genotyping-by-Sequencing in Plants, Biology, vol.1, issue.3, pp.460-483, 2012.

F. Mertes, A. Elsharawy, S. Sauer, J. M. Van-helvoort, P. J. Van-der-zaag et al., Targeted enrichment of genomic DNA regions for next-generation sequencing, Briefings in Functional Genomics, vol.10, issue.6, pp.374-386, 2011.

L. Zhou and J. A. Holliday, Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture, BMC Genomics, vol.13, issue.1, p.703, 2012.

C. B. Hill, D. Wong, J. Tibbits, K. Forrest, M. Hayden et al., Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley, Scientific Data, vol.6, issue.1, 2019.

V. B. Lachagari, R. Gupta, S. P. Lekkala, L. Mahadevan, B. Kuriakose et al., Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu), Frontiers in Plant Science, vol.10, 2019.

P. ?arhanová, S. Pfanzelt, R. Brandt, A. Himmelbach, and F. R. Blattner, SSR-seq: Genotyping of microsatellites using next-generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring, Ecology and Evolution, vol.8, issue.22, pp.10817-10833, 2018.

M. Curto, S. Winter, A. Seiter, L. Schmid, K. Scheicher et al., Application of a SSR-GBS marker system on investigation of European Hedgehog species and their hybrid zone dynamics, Ecology and Evolution, vol.9, issue.5, pp.2814-2832, 2019.

E. D. Farrell, J. E. Carlsson, and J. E. Carlsson, Next Gen Pop Gen: implementing a high-throughput approach to population genetics in boarfish ( Capros aper ), Royal Society Open Science, vol.3, issue.12, p.160651, 2016.

, Figure 2?figure supplement 1. Representative images used in the experiment, sampled from http://commons.wikimedia.org/wiki/Main_Page under the Creative Commons Attribution 4.0 International Public License https://creativecommons.org/licenses/by/4.0/., © 2020 by the authors. Licensee MDPI