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.
Similar content being viewed by others
References
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):1017–1027
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):1363–1371
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 20:2324–2326
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 111:370–377
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 45:1142–1149
Bowers JE, Dangl GS, Meredith CP (1999) Development and characterization of additional microsatellite DNA markers for grape. Am J Enol Vit 50:243–246
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 39:418–432
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 168:2169–2185
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 167:1301–1305
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 15:11–20
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):1249–1263
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 104:610–618
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):1178–1187
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 105:780–795
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 113:369–382
Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus Biotech 12:13–15
Faes G (2004) Analisi della struttura del genoma di Vitis vinifera. Ph.D. dissertation, University of Udine, Italy, 100 pp
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 111:658–664
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 108:501–515
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 106:1213–1224
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 90:933–947
Hou DX (2003) Potential mechanisms of cancer chemoprevention by anthocyanins. Curr Mol Med 3(2):149–159
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 449:463–467
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 12:712–719
Karp A, Jones RN (1983) Cytogenetics of Lolium perenne. Part 2. Chiasma distribution. Theor Appl Genet 64:137–145
Kahkonen MP, Heinonen M (2003) Antioxidant activity of anthocyanins and their aglycons. J Agric Food Chem 51(3):628–633
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):2707–2718
Kobayashi S, Ishimaru M, Hiraoka K, Honda C (2002) Myb-related genes of Kyoho grape (Vitis labruscana) regulate anthocyanin biosynthesis. Planta 215:924–933
Kobayashi S, Yamamoto NG, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 14;304(5673):982
Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403–410
Kortekamp A, Zyprian E (2003) Characterization of Plasmopara-resistance in grapevine using in vitro plants. J Plant Physiol 160(11):1393–1400
Kosamby DD (1944) The estimation of map distance from recombination values. Ann. Eugen 12:172–175
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):1532–1534
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 171:291–303
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 1:174–181
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):427–435
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 8:424
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):1582–1592
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 15:349–366
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 5:208–217
Navindra PS, Yanjun Z, Muraleedharan GN (2003) Inhibition of proliferation of human cancer and cyclooxygenase enzymes by anthocyanidins and chatechins. Nutr Cancer 46(1):101–106
Neff MM, Turk E, Kalishman M (2002) Web-based primer design for single nucleotide polymorphism analysis. Trends Genet 18:613–615
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 86:2766–2770
Passamonti S, Vrhovsek U, Vanzo A, Mattivi F (2003) The stomach as a site for anthocyanins absorption from food. FEBS Lett 544:210–213
Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol (2):94–100
Riaz S, Dangl GS, Edwards KJ, Meredith CJ (2004) A microsatellite marker based framework linkage map of Vitis vinifera L. Theor Appl Genet 108:864–872
Rieseberg LH, Van Fossen C, Desrochers AM (1995) Hybrid speciation accompanied by genomic reorganization in wild sunflower. Nature 375:713–727
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 365–386
Salmaso M (2003) Analysis of genome diversity and construction of a functional map in Vitis spp. Ph.D. Dissertation, University of Padova, Italy, 108 pp
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 14:385–395
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):515–524
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 100:723–726
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 42:367–373
Simianer H, Szyda J, Ramon G, Lien S (1997) Evidence for individual and between-family variability of the recombination rate in cattle. Mamm Genome 8:830–835
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):743–755
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 8:684–692
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 103:30–36
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 114:723–730
Thomas MR, Scott NS (1993) Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theor Appl Genet 86:985–99l
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):2637–2650
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):21–30
Van Ooijen JW, Voorrips RE (2001) JoinMap 3.0. Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The Netherlands
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):e1326
Weeden NF (1993) Approaches to mapping in horticultural crops. Plant genome analysis. CRC Press Inc., Boca Raton, pp 7–68
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 308:1310–1314
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.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by E. Guiderdoni.
Marzia Salmaso and Giulia Malacarne contributed equally to the present work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Salmaso, M., Malacarne, G., Troggio, M. et al. A grapevine (Vitis vinifera L.) genetic map integrating the position of 139 expressed genes. Theor Appl Genet 116, 1129–1143 (2008). https://doi.org/10.1007/s00122-008-0741-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-008-0741-3