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Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics

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Abstract

The aim of the present work was to develop a microsatellite marker-based map of the Vitis vinifera genome (n=19), useful for genetic studies in this perennial heterozygous species, as SSR markers are highly transferable co-dominant markers. A total of 346 primer pairs were tested on the two parents (Syrah and Grenache) of a full sib population of 96 individuals (S × G population), successfully amplifying 310 markers. Of these, 88.4% markers were heterozygous for at least one of the two parents. A total of 292 primer pairs were then tested on Riesling, the parent of the RS1 population derived from selfing (96 individuals), successfully amplifying 299 markers among which 207 (62.9%) were heterozygous. Only 6.7% of the markers were homozygous in all three genotypes, stressing the interest of such markers in grape genetics. Four maps were constructed based on the segregation of 245 SSR markers in the two populations. The Syrah map was constructed from the segregations of 177 markers that could be ordered into 19 linkage groups (total length 1,172.2 cM). The Grenache map was constructed with the segregations of 178 markers that could be ordered into 18 linkage groups (total length 1,360.6 cM). The consensus S × G map was constructed with the segregations of 220 markers that were ordered into 19 linkage groups (total length 1,406.1 cM). One hundred and eleven markers were scored on the RS1 population, among them 27 that were not mapped using the S × G map. Out of these 111 markers, 110 allowed to us to construct a map of a total length of 1,191.7 cM. Using these four maps, the genome length of V. vinifera was estimated to be around 2,200 cM. The present work allowed us to map 123 new SSR markers on the V. vinifera genome that had not been ordered in a previous SSR-based map (Riaz et al. 2004), representing an average of 6.5 new markers per linkage group. Any new SSR marker mapped is of great potential usefulness for many applications such as the transfer of well-scattered markers to other maps for QTL detection, the use of markers in specific regions for the fine mapping of genes/QTL, or for the choice of markers for MAS.

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References

  • Bernole A, Adam-Blondon A-F, Caboche M, Chalhoub B (2004) PCR-anchoring of 700 markers and ESTs on a BAC library. Plant, animal and microbe genome conference XII, SanDiego, 10–14 January 2004 http://www.intl-pag.org/12/abstracts/P5 h_PAG12_604.htm

  • Bowers JE, Dangl GS, Vignani R, Meredith CP (1996) DNA fingerprint characterization of some California grape cultivars. Am J Enol Vitic 44:266–274

    Google Scholar 

  • Bowers J, Boursiquot J-M, This P, Chu K, JohanssonH, Meredith C (1999a) Historical genetics: the parentage of Chardonnay, Gamay and other wine grapes of northeastern France. Science 285:1562–1565

    Article  CAS  PubMed  Google Scholar 

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

    CAS  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Chabrier P, Gaspin C, Schiex T (2000) CarthaGene: a maximum likelihood multiple population genetic/radiated hybrid mapping software. Plant and animal genome VIII conference, San Diego, January 2000 http://www.intl-pag.org/pag/8/abstracts/pag8189.html

  • Chakravarti A, Lasher LK, Reefer JE (1991) A maximum likelihood method for estimating genome length using genetic linkage data. Genetics 128:175–182

    CAS  PubMed  Google Scholar 

  • Dalbó 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

    CAS  PubMed  Google Scholar 

  • Dalbó MA, Ye GN, Weeden NF, Wilcox WF, Reisch BI (2001) Marker-assisted selection for powdery mildew resistance in grapes. J Am Soc Sci 126:83–89

    Google Scholar 

  • Decroocq V, Favé M-G, 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

    CAS  PubMed  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  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  Google Scholar 

  • Doligez A, Bouquet A, Ballester J-F, Farnos M, Danglot Y, Adam-Blondon A-F, Roux C, Domergue P, This P (2003) QTLS for quality-related traits in table grapes. Plant and animal genome XI conference, San Diego, January 2003 http://www.intl-pag.org/pag/11/abstracts/P5 h_P533_XI.html

  • Eibach R, Diehl H, Alleweldt G (1989) Untersuchungen zur Vererbung von Resistenzeigenschaften bei Reben gegen Oidium tuckeri, Plasmopara viticola und Botrytis cinerea. Vitis 28:209–228

    Google Scholar 

  • 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 108:505–515

    Article  Google Scholar 

  • Gerber S, Rodolphe F (1994) An estimation of the genome length of maritime pine (Pinus pinaster Ait). Theor Appl Genet 88:289–292

    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

    CAS  PubMed  Google Scholar 

  • Hulbert SH, Ilott TW, Legg EJ, Lincoln SE, Lander ES, Michelmore RW (1988) Genetic analysis of the fungus Bremia lactucae, using restriction fragment length polymorphisms. Genetics 120:947–958

    CAS  PubMed  Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • Lange K, Boehnke M (1982) How many polymorphic genes will it take to span the human genome? Am J Hum Genet 34:842–845

    CAS  PubMed  Google Scholar 

  • Levadoux L (1956) Les populations sauvages et cultivées de Vitis vinifera L. Ann Amelior Plant 6:59–118

    Google Scholar 

  • Liebhardt R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, Van De Weg E, Gessler C (2002) Development and characterization of 140 new microsatellites in apple (Malus × domestica Borkh.). Mol Breed 10:217–241

    CAS  Google Scholar 

  • Lin H, Walker A (1998) Identifying grape rootstocks with simple sequence repeat (SSR) DNA markers. Am J Enol Vitic 49:403–407

    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

    CAS  PubMed  Google Scholar 

  • Loureiro MD, Martinez MC, Boursiquot JM, This P (1998) Molecular marker analysis of Vitis vinifera ‘Albariño’ and some similar grapevine cultivars. J Am Soc Hortic Sci 123:842–848

    CAS  Google Scholar 

  • Nelson CD, Kubisiak M, Stine M, Nance WL (1994) A genetic linkage map of the longleaf pine (Pinus palustris Mill.) based on random amplified polymorphic DNAs. Theor Appl Genet 87:145–151

    Google Scholar 

  • Olmo HP (1976) Grapes. In: Simmonds NW (ed) Evolution of crop plants. Longman, London, pp 294–298

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

    Article  CAS  PubMed  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Sefc KM, Regner F, Tureschek E, Glossl J, Steinkellner H (1999) Identification of microsatellite sequences in Vitis riparia and their application for genotyping of different Vitis species. Genome 42:367–373

    CAS  PubMed  Google Scholar 

  • Siret R (2001) Etude du polymorphisme génétique de la vigne cultivée (Vitis vinifera L.) à l’aide de marqueurs microsatellites: application à la caractérisation des cépages dans les vins. Dissertation, Université de Montpellier

  • 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 

  • Thomas MR, Cain P, Scott NS (1994) DNA typing for grapevine: a universal methodology and database for cultivar identification. Theor Appl Genet 86:173–180

    Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78

    Article  CAS  PubMed  Google Scholar 

  • Zyprian E, Eibach R, Töpfer R (2003) Comparartive molecular mapping in segregating populations of grapevine. Acta Hortic 603:71–77

    Google Scholar 

Download references

Acknowledgements

This research was funded by Génoplante grant CI1999076 and the INRA. The VMC primers were available through the VMC consortium coordinated by Agrogène. The authors are deeply indebted to Sumaira Riaz and Carole Meredith for helpful discussions, use of unpublished results (primer pairs and early versions of their map) and to Agnès Doligez for careful review of different versions of this paper. Many thanks to Mark Thomas for allowing us to test unpublished primer pairs developed at the CSIRO.

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Correspondence to A. -F. Adam-Blondon.

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Communicated by C. Möllers

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Adam-Blondon, A.F., Roux, C., Claux, D. et al. Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics. Theor Appl Genet 109, 1017–1027 (2004). https://doi.org/10.1007/s00122-004-1704-y

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