Skip to main content
SpringerLink
Log in

An integrated SSR map of grapevine based on five mapping populations

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

A grapevine (mainly Vitis vinifera L., 2n = 38) composite genetic map was constructed with CarthaGene using segregation data from five full-sib populations of 46, 95, 114, 139 and 153 individuals, to determine the relative position of a large set of molecular markers. This consensus map comprised 515 loci (502 SSRs and 13 other type PCR-based markers), amplified using 439 primer pairs (426 SSRs and 13 others) with 50.1% common markers shared by at least two crosses. Out of all loci, 257, 85, 74, 69 and 30 were mapped in 1, 2, 3, 4 and 5 individual mapping populations, respectively. Marker order was generally well conserved between maps of individual populations, with only a few significant differences in the recombination rate of marker pairs between two or more populations. The total length of the integrated map was 1,647 cM Kosambi covering 19 linkage groups, with a mean distance between neighbour loci of 3.3 cM. A framework-integrated map was also built, with marker order supported by a LOD of 2.0. It included 257 loci spanning 1,485 cM Kosambi with a mean inter-locus distance of 6.2 cM over 19 linkage groups. These integrated maps are the most comprehensive SSR-based maps available so far in grapevine and will serve either for choosing markers evenly scattered over the whole genome or for selecting markers that cover particular regions of interest. The framework map is also a useful starting point for the integration of the V. vinifera physical and genetic maps.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

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 109:1017–1027

    Article  PubMed  CAS  Google Scholar 

  • Arroyo-Garcia R, Martinez-Zapater JM (2004) Development and characterization of new microsatellite markers for grape. Vitis 4:175–178

    Google Scholar 

  • Bailey JA, Church DM, Ventura M, Rocchi M, Eichler EE (2004) Analysis of segmental duplications and genome assembly in the mouse. Genome Res 14:789–801

    Article  PubMed  CAS  Google Scholar 

  • Beavis WD, Grant D (1991) A linkage map based on information from four F2 populations of maize (Zea mays L.). Theor Appl Genet 82:636–644

    Article  CAS  Google Scholar 

  • Bouquet A, Danglot Y (1996) Inheritance of seedlessness in grapevine (Vitis vinifera L.). Vitis 35:35–42

    Google Scholar 

  • 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 39:628–633

    Article  PubMed  CAS  Google Scholar 

  • Bowers JE, Dangl GS, Meredith CP (1999) Development and characterization of additional microsatellite DNA markers for grape. Am J Enol Vitic 50:243–246

    CAS  Google Scholar 

  • Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4:10

    Article  PubMed  Google Scholar 

  • Castellarin SD, Di Gaspero G, Marconi R, Nonis A, Peterlunger E, Paillard S, Adam-Blondon A-F, Testolin R (2006) Colour variation in red grapevines (Vitis vinifera L.): genomic organisation, expression of flavonoid 3′-hydroxylase, flavonoid 3′,5′-hydroxylase genes and related metabolite profiling of red cyanidin-/blue delphinidin-based anthocyanins in berry skin. BMC Genomics 7:12

    Article  PubMed  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Cervera MT, Storme V, Ivens B, Gusmao J, Liu BH, Hostyn V, van Slycken J, van Montagu M, Boerjan W (2001) Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers. Genetics 158:787–809

    PubMed  CAS  Google Scholar 

  • Crespan M (2003) The parentage of Muscat of Hamburg. Vitis 42:193–197

    CAS  Google Scholar 

  • Dalbo MA, Ye GN, Weeden NF, Steinkellner H, Sefc KM, Reisch BI (2000) A gene controlling sex in grapevines placed on a molecular marker-based genetic map. Genome 43:333–340

    Article  PubMed  CAS  Google Scholar 

  • 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 106:912–922

    PubMed  CAS  Google Scholar 

  • Di Gaspero G, Peterlunger E, Testolin R, Edwards KJ, Cipriani G (2000) Conservation of microsatellite loci within the genus Vitis. Theor Appl Genet 101:301–308

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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 109:1178–1187

    Article  PubMed  CAS  Google Scholar 

  • Fatmi A, Poneleit CG, Pfeiffer TW (1993) Variability of recombination frequencies in the Iowa Stiff Stalk Synthetic (Zea mays L.). Theor Appl Genet 86:859–866

    Article  Google Scholar 

  • Fischer BM, Salakhutdinov I, Akkurt M, Eibach R, Edwards KJ, Töpfer R, Zyprian EM (2004) Quantitative trait locus analysis of fungal disease resistance factors on a molecular map of grapevine. Theor Appl Genet 108:501–515

    Article  PubMed  CAS  Google Scholar 

  • de Givry S, Bouchez M, Chabrier P, Milan D, Schiex T (2005) CarthaGene: multipopulation integrated genetic and radiation hybrid mapping. Bioinformatics 21:1703–1704

    Article  PubMed  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137:1121–1137

    PubMed  CAS  Google Scholar 

  • Haas HU, Alleweldt G (2000) The karyotype of grapevine (Vitis vinifera L.). Acta Hortic 528:247–255

    CAS  Google Scholar 

  • Krizsics Csikasz A, Kozma P Jr (2002) Characterization of fungus resistant grape varieties and candidate varieties in Pécs area. Acta Hortic 603:763–765

    Google Scholar 

  • Lefort F, Kyvelos CJ, Zervou M, Edwards KJ, Roubelakis-Angelakis KA (2002) Characterization of new microsatellite loci from Vitis vinifera and their conservation in some Vitis species and hybrids. Mol Ecol Notes 2:20–21

    Article  CAS  Google Scholar 

  • Lenormand T, Dutheil J (2005) Recombination difference between sexes: a role for haploid selection. PLOS Biol 3(e63):0396–0403

    CAS  Google Scholar 

  • Lodhi MA, Daly MJ, Ye GN, Weeden NF, Reisch BI (1995) A molecular marker based linkage map of Vitis. Genome 38:786–794

    Article  PubMed  CAS  Google Scholar 

  • Lombard V, Delourme R (2001) A consensus linkage map for rapeseed (Brassica napus L.): construction and integration of three individual maps from DH populations. Theor Appl Genet 103:491–507

    Article  CAS  Google Scholar 

  • Loridon K, McPhee K, Morin J, Dubreuil P, Pilet-Nayel ML, Aubert G, Rameau C, Baranger A, Coyne C, Lejeune-Hènaut I, Burstin J (2005) Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.). Theor Appl Genet 111:1022–1031

    Article  PubMed  CAS  Google Scholar 

  • Merdinoglu D, Butterlin G, Bevilacqua L, Chiquet V, Adam-Blondon AF, 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

    Article  CAS  Google Scholar 

  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200

    Article  PubMed  CAS  Google Scholar 

  • Patel GI, Olmo HP (1955) Cytogenetics of Vitis: I. The hybrid Vitis vinifera × V. rotundifolia. Am J Bot 42:141–159

    Article  Google Scholar 

  • Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101:9903–9908

    Article  PubMed  CAS  Google Scholar 

  • Pellerone FI, Edwards KJ, Thomas MR (2001) Grapevine microsatellite repeats: isolation, characterisation and use for genotyping of grape germplasm from Southern Italy. Vitis 40:179–186

    CAS  Google Scholar 

  • Riaz S, Dangl GS, Edwards KJ, Meredith CP (2004) A microsatellite marker based framework linkage map of Vitis vinifera L. Theor Appl Genet 108:864–872

    Article  PubMed  CAS  Google Scholar 

  • Schiex T, Gaspin C (1997) CarthaGene: constructing and joining maximum likelihood genetic maps. In: 5th international conference on intelligent systems for molecular biology, Porto Caras, Halkidiki, Greece, June 1997

  • Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Stam P, van Ooijen JW (1995) JoinMap (tm) version 2.0: software for the calculation of genetic linkage maps, Wageningen

  • Tesnière C, Verriès C (2000) Molecular cloning and expression of cDNAs encoding alcohol dehydrogenases from Vitis vinifera L. during berry development. Plant Sci 157:77–88

    Article  PubMed  Google Scholar 

  • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  • Thomas MR, Scott NS (1993) Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theor Appl Genet 86:985–990

    CAS  Google Scholar 

  • Tulseriam L, Compton WA, Morris R, Thomas-Compton M, Eskridge K (1992) Analysis of genetic recombination in maize populations using molecular markers. Theor Appl Genet 84:65–72

    Google Scholar 

  • Zhang LQ, Lu HSS, Chung WY, Yang J, Li WH (2005) Patterns of segmental duplication in the human genome. Mol Biol Evol 22:135–141

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

This research was funded by Génoplante grant C11999076 and INRA for genotyping the A1, A2 and D populations and for building the integrated map, by the Friuli Venezia Giulia Regional Administration for genotyping the population DG and by the American Vineyard Foundation and the United States Department of Agriculture Viticulture Consortium for genotyping the R population. We thank D. Claux, G. Butterlin, A. Fiori, M. Claverie, M. Dardé, C. Sauzet, C. Bisiaux, F. Lahogue for their participation in the genotyping of different populations, as well as R. Pratelli and M. Thomas for personal communication of primer sequences.

Author information

Author notes

  1. A. F. Adam-Blondon

    Present address: INRA-URGV, 2 rue Gaston Crémieux, CP 5708, 91057, Evry Cedex, France

Authors and Affiliations

  1. INRA, UMR DGPC 1097, équipe Génétique Vigne, bâtiment 6, 2 place Viala, 34060, Montpellier Cedex 1, France

    A. Doligez, A. F. Adam-Blondon, V. Laucou, C. Roux & P. This

  2. UMR Santé de la Vigne et Qualité du Vin, INRA-ULP, INRA, 28 rue Herrlisheim, 68021, Colmar Cedex, France

    D. Merdinoglu

  3. Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze, 208, 33100, Udine, Italy

    G. Cipriani & G. Di Gaspero

  4. Department of Viticulture and Enology, University of California, Davis, CA, 95616, USA

    C. P. Meredith & S. Riaz

Authors
  1. A. Doligez
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. F. Adam-Blondon
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. G. Cipriani
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. G. Di Gaspero
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. V. Laucou
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. D. Merdinoglu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. C. P. Meredith
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. S. Riaz
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. C. Roux
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. P. This
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to A. Doligez.

Additional information

Communicated by A. Charcosset

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Doligez, A., Adam-Blondon, A.F., Cipriani, G. et al. An integrated SSR map of grapevine based on five mapping populations. Theor Appl Genet 113, 369–382 (2006). https://doi.org/10.1007/s00122-006-0295-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-006-0295-1

Keywords

Search

Navigation