Abstract
Genetic maps functionally oriented towards disease resistance have been constructed in grapevine by analysing with a simultaneous maximum-likelihood estimation of linkage 502 markers including microsatellites and resistance gene analogs (RGAs). Mapping material consisted of two pseudo-testcrosses, ‘Chardonnay’ × ‘Bianca’ and ‘Cabernet Sauvignon’ × ‘20/3’ where the seed parents were Vitis vinifera genotypes and the male parents were Vitis hybrids carrying resistance to mildew diseases. Individual maps included 320–364 markers each. The simultaneous use of two mapping crosses made with two pairs of distantly related parents allowed mapping as much as 91% of the markers tested. The integrated map included 420 Simple Sequence Repeat (SSR) markers that identified 536 SSR loci and 82 RGA markers that identified 173 RGA loci. This map consisted of 19 linkage groups (LGs) corresponding to the grape haploid chromosome number, had a total length of 1,676 cM and a mean distance between adjacent loci of 3.6 cM. Single-locus SSR markers were randomly distributed over the map (CD = 1.12). RGA markers were found in 18 of the 19 LGs but most of them (83%) were clustered on seven LGs, namely groups 3, 7, 9, 12, 13, 18 and 19. Several RGA clusters mapped to chromosomal regions where phenotypic traits of resistance to fungal diseases such as downy mildew and powdery mildew, bacterial diseases such as Pierce’s disease, and pests such as dagger and root-knot nematode, were previously mapped in different segregating populations. The high number of RGA markers integrated into this new map will help find markers linked to genetic determinants of different pest and disease resistances in grape.
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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
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 19:103–111
Aradhya MK, Dangl GS, Prins BH, Boursiquot J-M, Walker MA, Meredith CP, Simon CJ (2003) Genetic structure and differentiation in cultivated grape, Vitis vinifera L. Genet Res 81:179–192
Axtell MJ, McNellis TW, Mudgett MB, Hsu CS, Staskawicz BJ (2001) Mutational analysis of the Arabidopsis RPS2 disease resistance gene and the corresponding Pseudomonas syringae avrRpt2 avirulence gene. Mol Plant Microbe Interact 14:181–188
Bai J, Pennill LA, Ning J, Lee SW, Ramalingam J, Webb CA, Zhao B, Sun Q, Nelson JC, Leach JE, Hulbert SH (2002) Diversity in nucleotide binding site-leucine-rich repeat genes in cereals. Genome Res 12:1871–1884
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 11:370–377
Baumgarten A, Cannon S, Spangler R, May G (2003) Genome-level evolution of resistance genes in Arabidopsis thaliana. Genetics 165:309–319
Cannon SB, Zhu H, Baumgarten AM, Spangler R, May G, Cook DR, Young ND (2002) Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS–LRR resistance gene subfamilies. J Mol Evol 54:548–562
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
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
Cindric P, Korac N, Kovac V (2000) Grape breeding in the vojvodina province. Acta Hortic 528:499–504
Csizmazia J, Bereznai L (1968) A szõlõ Plasmopara viticola és a Viteus vitifolii elleni rezisztencia nemesités eredményei. Orsz Szõl Bor Kut Int Évkönyve, Budapest, pp 191–200
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
Dalbó MA, Ye GN, Weeden NF, Wilcox WF, Reisch BI (2001) Marker-assisted selection for powdery mildew resistance in grapes. J Am Soc Hortic 126:83–89
de Givry S, Bouchez M, Chabrier P, Milan D, Schiex T (2005) CarthaGene: multipopulation integrated genetic and radiation hybrid mapping. Bioinformatics 21:1703–1704
Di Gaspero G, Cipriani G (2002) Resistance gene analogs are candidate markers for disease-resistance genes in grape (Vitis spp.). Theor Appl Genet 106:163–172
Di Gaspero G, Cipriani G (2003) Nucleotide binding site/leucine-rich repeats, Pto-like and receptor-like kinases related to disease resistance in grapevine. Mol Genet Genomics 269:612–623
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
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
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 109:1178–1187
Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15
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
Frisch M, Quint M, Lübberstedt T, Melchinger AE (2004) Duplicate marker loci can result in incorrect locus orders on linkage maps. Theor Appl Genet 109:305–316
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, 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
Grube RC, Radwanski ER, Jahn M (2000) Comparative genetics of disease resistance within the Solanaceae. Genetics 155:873–887
Jander G (2006) Gene identification and cloning by molecular marker mapping. Methods Mol Biol 323:115–126
Koleda I (1975) Ergebnise von kreuzungen zwischen Vitis amurensis und Vitis vinifera in der zuechtung frostwiederstandfaechiger Reben. Vitis 14:1–5
Kozma P Jr (2000) Winegrape breeding for fungus disease resistance. Acta Hortic 528:505–510
Krivanek AF, Riaz S, Walker MA (2006) Identification and molecular mapping of PdR1, a primary resistance gene to Pierce’s disease in Vitis. Theor Appl Genet 112:1125–1131
Lamoureux D, Bernole A, Le Clainche I, Tual S, Thareau V, Paillard S, Legeai F, Dossat C, Wincker P, Oswald M, Merdinoglu D, Vignault C, Delrot S, Caboche M, Chalhoub B, Adam-Blondon A-F (2006) Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome. Theor Appl Genet 113:344–356
Lodhi MA, Daly MJ, Ye GN, Weeden NF, Reisch BI (1995) A molecular marker based linkage map of Vitis. Genome 38:786–794
Lowe KM, Walker MA (2006) Genetic linkage map of the interspecific grape rootstock cross Ramsey (Vitis champinii) × Riparia Gloire (Vitis riparia). Theor Appl Genet 112:1582–1592
Madsen LH, Collins NC, Rakwalska M, Backes G, Sandal N, Krusell L, Jensen J, Waterman EH, Jahoor A, Ayliffe M, Pryor AJ, Langridge P, Schulze-Lefert P, Stougaard J (2003) Barley disease resistance gene analogs of the NBS-LRR class: identification and mapping. Theor Appl Genet 269:150–161
McDowell JM, Dhandaydham M, Long TA, Aarts MG, Goff S, Holub EB, Dangl JL (1998) Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis. Plant Cell 10:1861–1874
Merdinoglu D, Wiedemann-Merdinoglu S, Coste P, Dumas V, Haetty S, Butterlin G, Greif C (2003) Genetic analysis of downy mildew resistance derived from Muscadinia rotundifolia. Acta Hortic 603:451–456
Meyers BC, Shen KA, Rohani P, Gaut BS, Michelmore RW (1998) Receptor-like genes in the major resistance locus of lettuce are subject to divergent selection. Plant Cell 10:1833–1846
Mondragon-Palomino M, Meyers BC, Michelmore RW, Gaut BS (2002) Patterns of positive selection in the complete NBS–LRR gene family of Arabidopsis thaliana. Genome Res 12:1305–1315
Monosi B, Wisser RJ, Pennill L, Hulbert SH (2004) Full-genome analysis of resistance gene homologues in rice. Theor Appl Genet 109:1434–1447
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
Richly E, Kurth J, Leister D (2002) Mode of amplification and reorganization of resistance genes during recent Arabidopsis thaliana evolution. Mol Biol Evol 19:76–84
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, NJ, pp 365–386
Takken FLW, Albrecht M, Tameling WIL (2006) Resistance proteins: molecular switches of plant defence. Curr Opin Plant Biol 9:383–390
Tian Y, Fan L, Thurau T, Jung C, Cai D (2004) The absence of TIR-type resistance gene analogues in the sugar beet (Beta vulgaris L.) genome. J Mol Evol 58:40–53
Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630
Voorips RE (2002) Mapchart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78
Zhu H, Cannon SB, Young ND, Cook DR (2002) Phylogeny and genomic organization of the TIR and non-TIR NBS-LRR resistance gene family in Medicago truncatula. Mol Plant Microbe Interact 15:529–539
Zyprian E, Akkurt M, Fischer B, Salakhutdinov I, Welter L, Kortekamp A, Eibach R, Töpfer R (2005) Fundamental research meets pratical breeding: genetics of disease resistance in grapevine. In: Proceedings of International Grape Genomics Symposium, St. Louis, USA, 12–14 July 2005
Acknowledgements
Authors thank A. Fiori, G. Comuzzo, R. Frezza, M. J. Prado Castro, R. Marconi, D. Andreetta, E. Balen for technical work, Friuli Venezia Giulia Regional Administration, Federazione Banche di Credito Cooperativo of FVG and Vivai Cooperativi Rauscedo for funding, M. A. Walker for sharing unpublished data.
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Communicated by A. Charcosset.
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Di Gaspero, G., Cipriani, G., Adam-Blondon, AF. et al. Linkage maps of grapevine displaying the chromosomal locations of 420 microsatellite markers and 82 markers for R-gene candidates. Theor Appl Genet 114, 1249–1263 (2007). https://doi.org/10.1007/s00122-007-0516-2
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DOI: https://doi.org/10.1007/s00122-007-0516-2