Theoretical and Applied Genetics

, Volume 117, Issue 4, pp 499–511 | Cite as

A reference integrated map for cultivated grapevine (Vitis vinifera L.) from three crosses, based on 283 SSR and 501 SNP-based markers

  • Silvia VezzulliEmail author
  • Michela Troggio
  • Giuseppina Coppola
  • Angelica Jermakow
  • Dustin Cartwright
  • Andrey Zharkikh
  • Marco Stefanini
  • M. Stella Grando
  • Roberto Viola
  • Anne-Françoise Adam-Blondon
  • Mark Thomas
  • Patrice This
  • Riccardo Velasco
Original Paper


We have developed an integrated map from five elite cultivars of Vitis vinifera L.; Syrah, Pinot Noir, Grenache, Cabernet Sauvignon and Riesling which are parents of three segregating populations. A new source of markers, SNPs, identified in ESTs and unique BAC-end sequences was added to the available IGGP reference set of SSRs. The complete integrated map comprises 1,134 markers (350 AFLP®, 332 BESs, 169 ESTs, 283 SSRs) spanning 1,443 cM over 19 linkage groups and shows a mean distance between neighbouring loci of 1.27 cM. Marker order was mainly conserved between the integrated map and the highly dense Syrah × Pinot Noir consensus map except for few inversions. Moreover, the marker order has been validated through the assembled genome sequence of Pinot Noir. We have also assessed the transferability of SNP-based markers among five V. vinifera varieties, enabling marker validation across different genotypes. This integrated map can serve as a fundamental tool for molecular breeding in V. vinifera and related species and provide a basis for studies of genome organization and evolution in grapevines.


Quantitative Trait Locus Simple Sequence Repeat Marker Single Nucleotide Polymorphism Marker Marker Order Whole Genome Amplification 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors are grateful to Marco Facci, Jessica Zambanini, Diego Micheletti and Alexandre Fournier-Level for their technical support, and to Alessandro Cestaro, Paolo Fontana and Lorenzo Dematté for their bioinformatics assistance. They also wish to thank Agnès Doligez for helpful discussions. This work was supported in part by the Fondazione Cassa di Risparmio di Trento e Rovereto, the Autonomous Province of Trento, CSIRO Plant Industry and the Commonwealth Cooperative Research Centre Program, and specifically the Cooperative Research Centre for Viticulture (CRCV) and the Grape and Wine Research and Development Cooperation (GWRDC).

Supplementary material

122_2008_794_MOESM1_ESM.ppt (265 kb)
Supplementary Figure S1 (PPT 265 kb)
122_2008_794_MOESM2_ESM.ppt (1.3 mb)
Supplementary Figure S2 (PPT 1366 kb)
122_2008_794_MOESM3_ESM.xls (196 kb)
Table S1 (supplementary information). The 501 SNP-based markers mapped in the integrated map. (XLS 196 kb)
122_2008_794_MOESM4_ESM.xls (28 kb)
Table S2 (supplementary information). Distribution of marker type in the linkage groups and physical genome contigs. (XLS 28 kb)


  1. Adam-Blondon A-F, Roux C, Claux D, Butterlin G, Merdinoglu D, This P (2004) Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics. Theor Appl Genet 109:1017–1027PubMedCrossRefGoogle Scholar
  2. Akkurt M, Welter L, Maul E, Töpfer R, Zyprian E (2007) Development of SCAR markers linked to powdery mildew (Uncinula necator) resistance in grapevine (Vitis vinifera L. and Vitis sp.). Mol Breed 19:103–111CrossRefGoogle Scholar
  3. Arroyo-Garcia R, Martinez-Zapater JM (2004) Development and characterization of new microsatellite markers for grape. Vitis 4:175–178Google Scholar
  4. Batley J, Barker G, O’Sullivan H, Edwards KJ, Edwards D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 132:84–91PubMedCrossRefGoogle Scholar
  5. Bowers JE, Dangl GS, Meredith CP (1999) Development and characterization of additional microsatellite DNA markers for grape. Am J Enol Vitic 50:243–246Google Scholar
  6. Bowers JE, Dangl GS, Vignani R, Meredith CP (1996) Isolation and characterization of new polymorphic simple sequence repeat loci in grape (Vitis vinifera L.). Genome 39:628–633PubMedCrossRefGoogle Scholar
  7. Brown GR, Kadel EE, Bassoni DL, Kiehne KL, Temesgen B, van Buijtenen JP, Sewell MM, Marshall KA, Neale DB (2001) Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics. Genetics 159:799–809PubMedGoogle Scholar
  8. Cartwright DA, Troggio M, Velasco R, Gutin A (2007) Genetic mapping in the presence of genotyping errors. Genetics 176:2521–2527PubMedCrossRefGoogle Scholar
  9. Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Rothan C (2004) A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J Exp Bot 55:1671–1685PubMedCrossRefGoogle Scholar
  10. Dalbò MA, Ye GN, Weeden NF, Steinkellner H, Sefc KM, Reisch BI (2000) Gene controlling sex in grapevines placed on a molecular marker-based genetic map. Genome 43:333–340PubMedCrossRefGoogle Scholar
  11. Decroocq V, Favé MG, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106:912–922PubMedGoogle Scholar
  12. Di Gaspero G, Peterlunger E, Testolin R, Edwards KJ, Cipriani C (2000) Conservation of microsatellite loci within the genus Vitis. Theor Appl Genet 101:301–308CrossRefGoogle Scholar
  13. Di Gaspero G, Cipriani G, Adam-Blondon A-F, Testolin R (2007) Linkage maps of grapevine displaying the chromosomal locations of 420 microsatellite markers and 82 markers for R-gene candidates. Theor Appl Genet 114:1249–1263PubMedCrossRefGoogle Scholar
  14. Doligez A, Bouquet A, Danglot Y, Lahogue F, Riaz S, Meredith CP, Edwards KJ, This P (2002) Genetic mapping of grapevine (Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight. Theor Appl Genet 105:780–795PubMedCrossRefGoogle Scholar
  15. Doligez A, Adam-Blondon A-F, Cipriani G, Di Gaspero G, Laucou V, Merdinoglu D, Meredith CP, Riaz S, Roux C, This P (2006) An integrated SSR map of grapevine based on five different populations. Theor Appl Genet 113:369–382PubMedCrossRefGoogle Scholar
  16. Doucleff M, Jin Y, Gao F, Riaz S, Krivanek AF (2004) A genetic linkage map of grape, utilizing Vitis rupestris and Vitis arizonica. Theor Appl Genet 109:1178–1187PubMedCrossRefGoogle Scholar
  17. Fanizza G, Lamaj F, Costantini L, Chaabane R, Grando MS (2005) QTL analysis for fruit yield components in table grapes (Vitis vinifera). Theor Appl Genet 111:658–664PubMedCrossRefGoogle Scholar
  18. Fischer B, Salakhutdinov I, Akkurt M, Eibach R, Edwards KJ, Töpfer R, Zyprian EM (2004) Quantitative trait locus analysis of fungal disease resistance factor on a molecular map of grapevine. Theor Appl Genet 108:501–515PubMedCrossRefGoogle Scholar
  19. Gaafar RM, Hohmann U, Jung C (2005) Bacterial artificial chromosome-derived molecular markers for early bolting in sugar beet. Theor Appl Genet 110:1027–1037PubMedCrossRefGoogle Scholar
  20. Garg K, Green P, Nickerson DA (1999) Identification of candidate coding region single nucleotide polymorphisms in 165 human genes using assembled expressed sequence tags. Genome Res 9:1087–1092PubMedCrossRefGoogle Scholar
  21. Gianfranceschi L, McDermott JM, Seglias N, Koller B, Kellerhals M, Gessler C (1994) Towards a marker assisted breeding for resistance against apple scab. Euphytica 77:93–96CrossRefGoogle Scholar
  22. Grando MS, Bellin D, Edwards KJ, Pozzi C, Stefanini M, Velasco R (2003) Molecular linkage maps of Vitis vinifera L. and Vitis riparia Mchx. Theor Appl Genet 106:1213–1224PubMedGoogle Scholar
  23. Gupta PK, Roy JK, Prasad M (2001) Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr Sci 80:524–535Google Scholar
  24. Hori K, Kobayashi T, Shimizu A, Sato K, Takeda K, Kawasaki S (2003) Efficient construction of high-density linkage map and its application to QTL analysis in barley. Theor Appl Genet 107:806–813PubMedCrossRefGoogle Scholar
  25. Huang N, Angeles ER, Domingo J, Magpantay G, Singh S, Zhang G, Kumaravadivel N, Bennett J, Khush GS (1996) Pyramiding of bacterial blight resistance genes in rice: marker-assisted selection using RFLP and PCR. Theor Appl Genet 95:313–320CrossRefGoogle Scholar
  26. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pè ME, Valle G, Morgante M, Caboche M, Adam-Blondon A-F, Weissenbach J, Quétier F, Wincker P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467PubMedCrossRefGoogle Scholar
  27. Lijavetzky D, Cabezas J, Ibanez A, Rodriguez V, Martinez-Zapater J (2007) High-throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology. BMC Genomics 8:424PubMedCrossRefGoogle Scholar
  28. Lodhi MA, Daly MJ, Ye GN, Weeden NF, Reisch BI (1995) A molecular marker based linkage map of Vitis. Genome 38:786–794PubMedCrossRefGoogle Scholar
  29. Lodhi MA, Reisch BI (1995) Nuclear DNA content of Vitis species, cultivars and other genera of the Vitaceae. Theor Appl Genet 90:11–16CrossRefGoogle Scholar
  30. Lowe KM, Walker MA (2006) Genetic linkage map of the interspecific grape rootstock cross Ramsey (Vitis champinii) × Riparia Gloire (Vitis riparia). Theor Appl Genet 112:1582–1592PubMedCrossRefGoogle Scholar
  31. Mazur BJ, Tingey SV (1995) Genetic mapping and introgression of genes of agronomic importance. Curr Opin Biotechnol 6:175–182CrossRefGoogle Scholar
  32. Merdinoglu D, Butterlin G, Bevilacqua L, Chiquet V, Adam-Blondon A-F, Decrooocq S (2005) Development and characterization of a large set of microsatellite markers in grapevine (Vitis vinifera L.) suitable for multiplex PCR. Mol Breed 15:349–366CrossRefGoogle Scholar
  33. Morgante M, Salamini F (2003) From plant genomics to breeding practice. Curr Opin Biotechnol 14:214–219PubMedCrossRefGoogle Scholar
  34. Mun JH, Kim DJ, Choi HK, Gish J, Debellé F, Mudge J, Denny R, Endré G, Oliver Saurat, Dudez AM, Kiss GB, Roe B, Young ND, Cook DR (2006) Distribution of microsatellites in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps. Genetics 172:2541–2555PubMedCrossRefGoogle Scholar
  35. Owens CL (2003) SNP detection and genotyping in Vitis. Acta Hort 603:139–140Google Scholar
  36. Pindo M, Vezzulli S, Coppola G, Cartwright DA, Zharkikh A, Velasco R, Troggio M (2008) SNP-high-throughput screening in grapevine using the SNPlexTM genotyping system. BMC Plant Biol 8:12PubMedCrossRefGoogle Scholar
  37. Qi X, Stam P, Lindhout P (1996) Comparison and integration of four barley genetic maps. Genome 39:379–394PubMedCrossRefGoogle Scholar
  38. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100PubMedCrossRefGoogle Scholar
  39. Riaz S, Dangl GS, Edwards KJ, Meredith CJ (2004) A microsatellite marker based framework linkage map of Vitis vinifera L. Theor Appl Genet 108:864–872PubMedCrossRefGoogle Scholar
  40. Riaz S, Krivanek AF, Xu K, Walker MA (2006) Refined mapping of the Pierce’s disease resistance locus, PdR1, and sex on an extended genetic linkage map of Vitis rupestris x V. arizonica. Theor Appl Genet 113:1317–1329PubMedCrossRefGoogle Scholar
  41. Salmaso M, Faes G, Segala C, Stefanini M, Salakhutdinov I, Zyprian E, Toepfer R, Grando MS, Velasco R (2004) Genome diversity and gene haplotypes in the grapevine (Vitis vinifera L.) as revealed by single nucleotide polymorphisms. Mol Breed 14:385–395CrossRefGoogle Scholar
  42. Salmaso M, Malacarne G, Troggio M, Faes G, Stefanini M, Grando MS, Velasco R (2008) A grapevine (Vitis vinifera L.) genetic map integrating the position of 139 expressed genes. Theor Appl Genet 116:1129–1143CrossRefGoogle Scholar
  43. Salse J, Piégu B, Cooke R, Delseny M (2002) New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome. Plant J 38:396–409CrossRefGoogle Scholar
  44. Scott KD, Eggler P, Seaton G, Rosetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726CrossRefGoogle Scholar
  45. Sefc KM, Regner F, Turetschek E, Glossl J, Steinkellner H (1999) Identification of microsatellite sequences in Vitis riparia and their applicability for genotyping of different Vitis species. Genome 42:367–373PubMedCrossRefGoogle Scholar
  46. Staub JE, Serquen FC, Gupta M (1996) Genetic markers, map construction, and their application in plant breeding. HortScience 31:729–741Google Scholar
  47. Tanksley SD, Ganal MW, Martin GB (1995) Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. Trends Genet 11:63–68PubMedCrossRefGoogle Scholar
  48. This P, Lacombe T, Thomas MR (2006) Historical origins and genetic diversity of wine grapes. Trends Genet 22:511–519PubMedCrossRefGoogle Scholar
  49. Thomas MR, Scott NS (1993) Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theor Appl Genet 86:985–990Google Scholar
  50. Thomas MR, Matsumoto S, Cain P, Scott N (1993) Repetitive DNA of grapevine: classes present and sequences suitable for cultivar identification. Theor Appl Genet 86:173–180Google Scholar
  51. Troggio M, Malacarne G, Coppola G, Segala C, Cartwright DA, Pindo M, Stefanini M, Mank R, Moroldo M, Morgante M, Grando MS, Velasco R (2007) A dense single-nucleotide-polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs. Genetics 176:2637–2650PubMedCrossRefGoogle Scholar
  52. Troggio M, Malacarne G, Vezzulli S, Salmaso M, Faes G, Velasco R (2008) Comparison of different methods for SNP detection in grapevine. Vitis 47:21–30Google Scholar
  53. Tuskan GA, Di Fazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen G-L, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, de Pamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé J-C, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui H, Sterky F, Terry A, Tsai C-J, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604PubMedCrossRefGoogle Scholar
  54. Van Ooijen JW, Voorrips RE (2001) JoinMap® version 3.0: software for the calculation of genetic linkage maps. Plant Research International, WageningenGoogle Scholar
  55. Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, FitzGerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, Macalma TM, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Demattè L, Mraz A, Battilana J, Stormo K, Costa F, Tao Q, Si-Ammour A, Harkins T, Lackey A, Perbost C, Taillon B, Stella A, Solovyev V, Fawcett JA, Sterck L, Vandepoele K, Grando MS, Toppo S, Moser C, Lanchbury J, Bogden R, Skolnick M, Sgaramella V, Bhatnagar SK, Fontana P, Gutin A, Van de Peer Y, Salamini F, Viola R (2007) High quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2:e1326PubMedCrossRefGoogle Scholar
  56. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78PubMedCrossRefGoogle Scholar
  57. Walsh PS, Erlich HA, Higuchi R (1992) Preferential PCR amplification of alleles: mechanisms and solutions. Genome Res 1:241–250CrossRefGoogle Scholar
  58. Welter L, Göktürk-Baydar N, Akkurt M, Maul E, Eibach R, Töpfer R, Zyprian E (2007) Genetic mapping and localization of quantitative trait loci affecting fungal disease resistance and leaf morphology in grapevine (Vitis vinifera L.). Mol Breed 20:359–374CrossRefGoogle Scholar
  59. Xu K, Riaz S, Roncoroni NC, Jin Y, Hu R, Zhou R, Walker MA (2008) Genetic and QTL analysis of resistance to Xiphinema index in a grapevine cross. Theor Appl Genet 116:305–311PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Silvia Vezzulli
    • 1
    Email author
  • Michela Troggio
    • 1
  • Giuseppina Coppola
    • 1
  • Angelica Jermakow
    • 2
  • Dustin Cartwright
    • 3
  • Andrey Zharkikh
    • 3
  • Marco Stefanini
    • 1
  • M. Stella Grando
    • 1
  • Roberto Viola
    • 1
  • Anne-Françoise Adam-Blondon
    • 4
  • Mark Thomas
    • 2
  • Patrice This
    • 5
  • Riccardo Velasco
    • 1
  1. 1.IASMA Research CentreSan Michele a/AdigeItaly
  2. 2.CSIRO Plant IndustryGlen OsmondAustralia
  3. 3.Myriad Genetics Inc.Salt Lake CityUSA
  4. 4.UMR 1165, INRA-CNRS-Université d Evry Génomique VégétaleParis CedexFrance
  5. 5.UMR 1097, DIA-PC Equipe génétique Vigne, INRA SupagroMontepellierFrance

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