Theoretical and Applied Genetics

, Volume 116, Issue 8, pp 1129–1143 | Cite as

A grapevine (Vitis vinifera L.) genetic map integrating the position of 139 expressed genes

  • Marzia Salmaso
  • Giulia Malacarne
  • Michela Troggio
  • Giorgia Faes
  • Marco Stefanini
  • M. Stella Grando
  • Riccardo Velasco
Original Paper

Abstract

Grapevine molecular maps based on microsatellites, AFLP and RAPD markers are now available. SSRs are essential to allow cross-talks between maps, thus upgrading any growing grapevine maps. In this work, single nucleotide polymorphisms (SNPs) were developed from coding sequences and from unique BAC-end sequences, and nested in a SSR framework map of grapevine. Genes participating to flavonoids metabolism and defence, and signal transduction pathways related genes were also considered. Primer pairs for 351 loci were developed from ESTs present on public databases and screened for polymorphism in the “Merzling” (a complex genotype Freiburg 993–60 derived from multiple crosses also involving wild Vitis species) × Vitis vinifera (cv. Teroldego) cross population. In total 138 SNPs, 108 SSR markers and a phenotypic trait (berry colour) were mapped in 19 major linkage groups of the consensus map. In specific cases, ESTs with putatively related functions mapped near QTLs previously identified for resistance and berry ripening. Genes related to anthocyanin metabolism mapped in different linkage groups. A myb gene, which has been correlated with anthocyanin biosynthesis, cosegregated with berry colour on linkage group 2. The possibility of associating candidate genes to known position of QTL is discussed for this plant.

Notes

Acknowledgments

This work has been supported by the Cass di Risparmio di Trento e Rovereto Foundation. We thank Rosalba Grillo for providing technical support and Cinzia Segala for processing ESTs. Particular thanks to Francesco Salamini and Silvia Vezzulli for the critical reading of the manuscript.

Supplementary material

122_2008_741_MOESM1_ESM.ppt (316 kb)
Supplementary figure 1 (PPT 317 kb)

References

  1. Adam-Blondon AF, 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(5):1017–1027PubMedCrossRefGoogle Scholar
  2. Adam-Blondon AF, Bernole A, Faes G, Lamoureux D, Pateyron S, Grando MS, Caboche M, Velasco R, Chalhoub B (2005) Construction and characterization of BAC libraries from major grapevine cultivars. Theor Appl Genet 110(8):1363–1371PubMedCrossRefGoogle Scholar
  3. Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J (2004) BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 20:2324–2326PubMedCrossRefGoogle Scholar
  4. Barker CL, Donald T, Pauquet J, Ratnaparkhe MB, Bouquet A, Adam-Blondon AF, Thomas MR, Dry I (2005) Genetic and physical mapping of the grapevine powdery mildew resistance gene, Run1, using a bacterial artificial chromosome library. Theor Appl Genet 111:370–377PubMedCrossRefGoogle Scholar
  5. Bowers JE, Dangl GS, Vignani R, Meredith CP (1996) Isolation and characterization of the new polymorphic simple sequence repeat loci in grape (Vitis vinifera L.). Genome 45:1142–1149Google Scholar
  6. Bowers JE, Dangl GS, Meredith CP (1999) Development and characterization of additional microsatellite DNA markers for grape. Am J Enol Vit 50:243–246Google Scholar
  7. Causse M, Santoni S, Damerval C, Maurice A, Charcosset A, Deatrick J, de Vienne D (1996) A composite map of expressed sequences in maize. Genome 39:418–432Google Scholar
  8. Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L, Murignaux A, Charcossot A (2004) Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics 168:2169–2185PubMedCrossRefGoogle Scholar
  9. Chervin C, El-Kereamy1 E, Roustan JP, Latché A, Lamon J, Bouzayen M (2004) Ethylene seems required for the berry development and ripening in grape, a non-climacteric fruit. Plant Sci 167:1301–1305Google Scholar
  10. Di Gaspero G, Cipriani G, Marrazzo MT, Andreetta D, Prado Castro MJ, Peterlunger E, Testolin R (2005) Isolation of (AC)n-microsatellites in Vitis vinifera L. and analysis of genetic background in grapevines under marker assisted selection. Mol Breed 15:11–20CrossRefGoogle Scholar
  11. 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(7):1249–1263PubMedCrossRefGoogle Scholar
  12. Donald TM, Pellerone F, Adam-Blondon AF, Bouquet A, Thomas MR, Dry IB (2002) Identification of resistance gene analogs linked to a powdery mildew resistance locus in grapevine. Theor Appl Genet 104:610–618PubMedCrossRefGoogle Scholar
  13. Doucleff M, Jin Y, Gao F, Riaz S, Krivanek AF, Walker MA (2004) A genetic linkage map of grape, utilizing Vitis rupestris and Vitis arizonica. Theor Appl Genet 109(6):1178–1187PubMedCrossRefGoogle 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 AF, 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 mapping populations. Theor Appl Genet 113:369–382PubMedCrossRefGoogle Scholar
  16. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus Biotech 12:13–15Google Scholar
  17. Faes G (2004) Analisi della struttura del genoma di Vitis vinifera. Ph.D. dissertation, University of Udine, Italy, 100 ppGoogle Scholar
  18. 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
  19. 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
  20. 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
  21. Grattapaglia D, Bertolucci FL, Sederoff RR (1995) Genetic mapping of QTLs controlling vegetative propagation in Eucalyptus grandis and E. urophylla using a pseudo-testcross strategy and RAPD markers. Theor Appl Genet 90:933–947CrossRefGoogle Scholar
  22. Hou DX (2003) Potential mechanisms of cancer chemoprevention by anthocyanins. Curr Mol Med 3(2):149–159PubMedCrossRefGoogle Scholar
  23. Jaillon O, Aury J, 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 M, Valle G, Morgante M, Caboche M, Adam-Blondon A, Weissenbach J, Quétier F, Wincker P, The French–Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467Google Scholar
  24. Jakobek JL, Smith-Becker JA, Lindgren PB (1999) A bean cDNA expressed during a hypersensitive reaction encodes a putative calcium-binding protein. Mol Plant Microbe Interact 12:712–719PubMedCrossRefGoogle Scholar
  25. Karp A, Jones RN (1983) Cytogenetics of Lolium perenne. Part 2. Chiasma distribution. Theor Appl Genet 64:137–145CrossRefGoogle Scholar
  26. Kahkonen MP, Heinonen M (2003) Antioxidant activity of anthocyanins and their aglycons. J Agric Food Chem 51(3):628–633PubMedCrossRefGoogle Scholar
  27. Kim CY, Liu Y, Thorne ET, Yang H, Fukushige H, Gassmann W, Hildebrand D, Sharp RE, Zhang S (2003) Activation of a stress-responsive mitogen-activated protein kinase cascade induces the biosynthesis of ethylene in plants. Plant cell (11):2707–2718Google Scholar
  28. Kobayashi S, Ishimaru M, Hiraoka K, Honda C (2002) Myb-related genes of Kyoho grape (Vitis labruscana) regulate anthocyanin biosynthesis. Planta 215:924–933PubMedCrossRefGoogle Scholar
  29. Kobayashi S, Yamamoto NG, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 14;304(5673):982CrossRefGoogle Scholar
  30. Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403–410PubMedCrossRefGoogle Scholar
  31. Kortekamp A, Zyprian E (2003) Characterization of Plasmopara-resistance in grapevine using in vitro plants. J Plant Physiol 160(11):1393–1400PubMedCrossRefGoogle Scholar
  32. Kosamby DD (1944) The estimation of map distance from recombination values. Ann. Eugen 12:172–175Google Scholar
  33. Lai Z, Livingstone K, Zou Y, Church SA, Knapp SJ, Andrews J, Rieseberg LH (2005a) Identification and mapping of SNPs from ESTs in sunflower. Theor Appl Genet 111(8):1532–1534PubMedCrossRefGoogle Scholar
  34. Lai Z, Nakazato T, Salmaso M, Burke JM, Tang S, Knapp SJ, Rieseberg LH (2005b) Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species. Genetics 171:291–303PubMedCrossRefGoogle Scholar
  35. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newberg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181PubMedCrossRefGoogle Scholar
  36. Lijavetzky D, Ruiz-Garcia L, Cabezas JA, De Andres MT, Bravo G, Ibanez A, Martinez-Zapater J (2006) Molecular genetics of berry colour variation in table grape. Mol Genet Genomics 276(5):427–435PubMedCrossRefGoogle Scholar
  37. 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
  38. 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(8):1582–1592PubMedCrossRefGoogle Scholar
  39. Merdinoglu D, Butterlin G, Bevilacqua L, Chiquet A, Adam-Blondon A-F, Decroocq 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
  40. Moser C, Segala C, Fontana P, Salakhudtinov I, Gatto P, Pindo M, Zyprian E, Toepfer R, Grando MS, Velasco R (2005) Comparative analysis of expressed sequence tags from different organs of Vitis vinifera L. Funct Integr Genomics 5:208–217PubMedCrossRefGoogle Scholar
  41. Navindra PS, Yanjun Z, Muraleedharan GN (2003) Inhibition of proliferation of human cancer and cyclooxygenase enzymes by anthocyanidins and chatechins. Nutr Cancer 46(1):101–106CrossRefGoogle Scholar
  42. Neff MM, Turk E, Kalishman M (2002) Web-based primer design for single nucleotide polymorphism analysis. Trends Genet 18:613–615PubMedCrossRefGoogle Scholar
  43. Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single strand conformational polymorphisms. Proc Natl Acad Sci USA 86:2766–2770PubMedCrossRefGoogle Scholar
  44. Passamonti S, Vrhovsek U, Vanzo A, Mattivi F (2003) The stomach as a site for anthocyanins absorption from food. FEBS Lett 544:210–213PubMedCrossRefGoogle Scholar
  45. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol (2):94–100Google Scholar
  46. 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
  47. Rieseberg LH, Van Fossen C, Desrochers AM (1995) Hybrid speciation accompanied by genomic reorganization in wild sunflower. Nature 375:713–727CrossRefGoogle Scholar
  48. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  49. Salmaso M (2003) Analysis of genome diversity and construction of a functional map in Vitis spp. Ph.D. Dissertation, University of Padova, Italy, 108 ppGoogle Scholar
  50. 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
  51. Schneider K, Borchardt DC, Schafer-Pregl R, Nagl N, Glass C, Jeppsson A, Gebhardt C, Salamini F (1999) PCR-based cloning and segregation analysis of functional gene homologues in Beta vulgaris. Mol Gen Genet. 262(3):515–524PubMedCrossRefGoogle Scholar
  52. Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSR derived from grape ESTs. Theor Appl Genet 100:723–726CrossRefGoogle Scholar
  53. Sefc KM, Regner F, Turetschek E, Glössl 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
  54. Simianer H, Szyda J, Ramon G, Lien S (1997) Evidence for individual and between-family variability of the recombination rate in cattle. Mamm Genome 8:830–835PubMedCrossRefGoogle Scholar
  55. Sparvoli F, Martin C, Scienza A, Gavazzi G, Tonelli C (1994) Cloning and molecular analysis of structural genes involved in flavonoid and stilbene biosynthesis in grape (Vitis vinifera L.). Plant Mol Biol. 24(5):743–755PubMedCrossRefGoogle Scholar
  56. Syvanen AC, Aalto-Setala K, Harju L, Kontula K, Soderlund H (1990) A primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E. Genomics 8:684–692PubMedCrossRefGoogle Scholar
  57. Testolin R, Huang WG, Lain O, Messina R, Secchione A, Cipriani G. (2001) A kiwifruit (Actinidia spp.) linkage map based on microsatellites and integrated with AFLP markers. Theor Appl Genet 103:30–36CrossRefGoogle Scholar
  58. This P, Cadle-Davidson M, Lacombe T, Owens CL (2007). Wine grape (Vitis vinifera L.) color associates with allelic variation in the domestication gene VvmybA1. Theor Appl Genet 114:723–730PubMedCrossRefGoogle Scholar
  59. Thomas MR, Scott NS (1993) Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theor Appl Genet 86:985–99lGoogle Scholar
  60. 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(4):2637–2650PubMedCrossRefGoogle Scholar
  61. Troggio M, Malacarne G, Vezzulli S, Faes G, Salmaso M, Velasco R (2008) Methods for polymorphism detection and genotyping within expressed regions in grapevine genome. Vitis 47(1):21–30Google Scholar
  62. Van Ooijen JW, Voorrips RE (2001) JoinMap 3.0. Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The NetherlandsGoogle Scholar
  63. 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(12):e1326Google Scholar
  64. Weeden NF (1993) Approaches to mapping in horticultural crops. Plant genome analysis. CRC Press Inc., Boca Raton, pp 7–68Google Scholar
  65. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS (2005) The effects of artificial selection on the maize genome. Science 308:1310–1314PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Marzia Salmaso
    • 1
    • 4
  • Giulia Malacarne
    • 1
  • Michela Troggio
    • 1
  • Giorgia Faes
    • 1
    • 3
  • Marco Stefanini
    • 2
  • M. Stella Grando
    • 1
  • Riccardo Velasco
    • 1
  1. 1.Genetics and Molecular Biology DepartmentIstituto Agrario San Michele all’AdigeSan Michele a/A (TN)Italy
  2. 2.Agricultural Resources DepartmentIstituto Agrario San Michele all’AdigeSan Michele a/A (TN)Italy
  3. 3.Istituto Trentino di Cultura-IRSTPovo (TN)Italy
  4. 4.Department of Environmental Agronomy and Crop ProductionUniversity of PadovaLegnaro (PD)Italy

Personalised recommendations