Application of genomics to grapevine improvement

Australian Journal of Grape and Wine Research

Volumn 16, Issue SUPPL. 1, 2010, Pages 122-130

  di Gaspero, Gabriele ^a,b   Cattonaro, F ^a  

^a Istituto di Genomica Applicata   (Italy)

^b UNIVERSITY OF UDINE   (Italy)

Author keywords

Breeding; DNA technology; Genotyping; Phenotyping; Sequencing

Indexed keywords

VITACEAE; VITIS;

EID: 79952479530     PISSN: 13227130     EISSN: 17550238     Source Type: Journal    
DOI: 10.1111/j.1755-0238.2009.00072.x     Document Type: Article

References (55)

1. Agati, G., Meyer, S., Matteini, P. and Cerovic, Z.G. (2007) Assessment of anthocyanins in grape (Vitis vinifera L.) berries using a noninvasive chlorophyll fluorescence method. Joumal of Agricultural and Food Chemistry 55, 1053-1061.
2. Akkurt, M., Welter, L., Maul, E., Töpfer, R. and Zyprian, E. (2006) Development of SCAR markers linked to powdery mildew (Uncinula necator) resistance in grapevine (Vitis vinifera L. and Vitis sp.). Molecular Breeding 19, 103-111.
3. Alleweldt, G., Spiegel-Roy, P. and Reisch, E. (1990) Grapes (Vitis). In: Genetic resources of temperate fruits and nut crops, Vol. 1. Eds. J.N. Moore and J.R. Ballington (International Society of Horticultural Science: Wageningen, the Netherlands) pp. 291-327.
4. Baker, N.R. and Rosenqvist, E. (2004) Applications of chlorophyll fluorescence can improve crop production strategies: an examination of future possibilities. Journal of Experimental Botany 55, 1607-1621.
5. Barker, C.L., Donald, T., Pauquet, J., Ratnaparkhe, M.E., Bouquet, A., Adam-Blondon, A.F., Thomas, M.R. and Dry, I. (2005) Genetic and physical mapping of the grapevine powdery mildew resistance gene, Run1, using a bacterial artificial chromosome library. Theoretical and Applied Genetics 111, 370-377.
6. Battilana, J., Costantini, L., Emanuelli, F., Sevini, F., Segala, C., Moser, S., Velasco, R., Versini, G. and Grando, M.S. (2009) The l-deoxy-D:-xylulose 5-phosphate synthase gene co-localizes with a major QTL affecting monoterpene content in grapevine. Theoretical and Applied Genetics 118, 653-669.
7. Bisson, L.F., Waterhouse, A.L., Ebeler, S.E., Walker, M.A. and Lapsley, J.T. (2002) The present and future of the international wine industry. Nature 418, 696-699.
8. Bouquet, A. and Danglot, Y. (1996) Inheritance of seedlessness in grapevine (Vitis vinifera L.). Vitis 35, 35-42.
9. Bowers, J., Boursiquot, J.M., This, P., Chu, K., Johansson, H. and Meredith, C. (1999) Historical genetics: the parentage of Chardonnay, Gamay, and other wine grapes of Northeastern France. Science 285, 1562-1565.
10. Bowers, J.E. and Meredith, C.P. (1997) The parentage of a classic wine grape, Cabernet Sauvignon. Nature Genetics 16, 84-87.
11. Cabezas, J.A., Cervera, M.T., Ruiz-Garcia, L., Carreno, J. and Martinez-Zapater, J.M. (2006) A genetic analysis of seed and berry weight in grapevine. Genome 49, 1572-1585.
12. Chaerle, L., Leinonen, L., Jones, H.G. and Van Der Straeten, D. (2007) Monitoring and screening plant populations with combined thermal and chlorophyll fluorescence imaging. Joumal of Experimental Botany 58, 773-784.
13. Cipriani, G., Di Gaspero, G., Canaguier, A., Jusseaumes, J., Tassin, J., Lemainque, A., Roux, C., Adam-Blondon, A.-F. and Testolin, R. (2009) Molecular linkage maps: strategies, resources and achievements. In: Grapes. Eds. Zapater M.M., Adam-Blondon A.F. In: Series on genomics of fruit and vegetables crops. Series ed. Chittaranjan Kole (Science Publishers: Enfield, NH, USA).
14. Clarke, J., Wu, H.C., Jayasinghe, L., Patel, A., Reid, S. and Bayley, H. (2009) Continuous base identification for single-molecule nan-opore DNA sequencing. Nature Nanotechnology 4, 265-270.
15. Costantini, L., Battilana, J., Lamaj, F., Fanizza, G. and Grando, M.S. (2008) Berry and phenology-related traits in grapevine (Vitis vinifera L.): from quantitative trait loci to underlying genes. BMC Plant Biology 8, 38.
16. Cséfalvay, L., Di Gaspero, G., Matouš, K., Bellin, D., Ruperti, B. and Olejničková, J. (2009) Pre-symptomatic detection of Plasmo-para viticola infection in grapevine leaves using chlorophyll fluorescence imaging. European Journal of Plant Pathology 125, 291-302.
17. Dalbò, M.A., Ye, G.-N., Weeden, N.F., Steinkellner, H., Sefc, K.M. and Reisch, B.I. (2000) A gene controlling sex in grapevines placed on a molecular marker-based genetic map. Genome 43, 333-340.
18. Dalbò, M.A., Ye, G.N., Weeden, N.F., Wilcox, W.F. and Reisch, B.I. (2001) Marker-assisted selection for powdery mildew resistance in grapes. Journal of the American Society for Horticultural Science 26, 83-89.
19. Deluc, L.G., Grimplet, J., Wheatley, M.D., Tillett, R.L., Quilici, D.R., Osborne, C., Schooley, D.A., Schlauch, K.A., Cushman, J.C. and Cramer, G.R. (2007) Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development. BMC Genomics 8, 429.
20. Di Gaspero, G., Cipriani, G., Adam-Blondon, A.F. and Testolin, R. (2007) Linkage maps of grapevine displaying the chromosomal locations of 420 microsatellite markers and 82 markers from R-gene candidates. Theoretical and Applied Genetics 114, 1249-1263.
21. Doligez, A., Bouquet, A., Danglot, Y., Lahogue, F., Riaz, S., Meredith, C.P., Edwards, K.J. and This, P. (2002) Genetic mapping of grapevine (Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight. Theoretical and Applied Genetics 105, 780-795.
22. Duchêne, E., Butterlin, G., Claudel, P., Dumas, V., Jaegli, N. and Merdinoglu, D. (2009) A grapevine (Vitis vinifera L.) deoxy-D-xylulose synthase gene colocates with a major quantitative trait loci for terpenol content. Theoretical and Applied Genetics 118, 541-552.
23. Ehlert, B. and Hincha, D.K. (2008) Chlorophyll fluorescence imaging accurately quantifies freezing damage and cold acclimation responses in Arabidopsis leaves. Plant Methods 4, 12.
24. Eibach, R., Zyprian, E., Welter, L. and Töpfer, R. (2007) The use of molecular markers for pyramiding resistance genes in grapevine breeding. Vitis 46, 120-124.
25. Fernandez, L., Doligez, A., Lopez, G., Thomas, M.R., Bouquet, A. and Torregrosa, L. (2006) Somatic chimerism, genetic inheritance, and mapping of the fleshless berry (flb) mutation in grapevine (Vitis vinifera L.). Genome 49, 721-728.
26. Fernandez, L., Torregrosa, L., Terrier, N., Sreekantan, L., Grimplet, J., Davies, C., Thomas, M.R., Romieu, C. and Ageorges, A. (2007) Identification of genes associated with flesh morphogenesis during grapevine fruit development. Plant Molecular Biology 63, 307-323.
27. Fernie, A.R. and Schauer, N. (2009) Metabolomics-assisted breeding: a viable option for crop improvement? Trends in Genetics 25, 39-48.
28. Fischer, B.M., Salakhutdinov, I., Akkurt, M., Eibach, R., Edwards, K.J., Töpfer, R. and Zyprian, E.M. (2004) Quantitative trait locus analysis of fungal disease resistance factors on a molecular map of grapevine. Theoretical and Applied Genetics 108, 501-515.
29. Frisch, M. and Melchinger, A.E. (2005) Selection theory for marker-assisted backcrossing. Genetics 170, 909-917.
30. Hoffmann, S., Di Gaspero, G., Kovacs, L., Howard, S., Kiss, E., Galbacs, Z., Testolin, R. and Kozma, P. (2008) Resistance to Erysiphe necator in the grapevine 'Kishmish vatkana' is controlled by a single locus through restriction of hyphal growth. Theoretical and Applied Genetics 116, 427-438.
31. Holland, J.B. (2001) Epistasis and plant breeding. Plant Breeding Reviews 21, 27-92.
32. Hospital, F., Chevalet, C. and Mulsant, P. (1992) Using markers in gene introgression breeding programs. Genetics 132, 1199-1210.
33. Jaillon, O., Aury, J.-M., 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.E., Valle, G., Morgante, M., Caboche, M., Adam-Blondon, A.F., Weissenbach, J., Quétier, F. and Wincker, P. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463-468.
34. Jansen, R.C., van Ooijen, J.W., Stam, P., Lister, C. and Dean, C. (1995) Genotype-by-environment interaction in genetic mapping of multiple quantitative trait loci. Theoretical and Applied Genetics 91, 33-37.
35. Keurentjes, J.J. (2009) Genetical metabolomics: closing in on phe-notypes. Current Opinion in Plant Biology 12, 1-8.
36. Kobayashi, S., Goto-Yamamoto, N. and Hirochika, H. (2004) Retrotransposon-induced mutations in grape skin color. Science 304, 982.
37. Le Cunff, L., Fournier-Level, A., Laucou, V., Vezzulli, S., Lacombe, T., Adam-Blondon, A.F., Boursiquot, J.M. and This, P. (2008) Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp. sativa. BMC Plant Biology 8, 31.
38. Lijavetzky, D., Cabezas, J.A., Ibáñez, A., Rodríguez, V. and Martinez-Zapater, J.M. (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.
39. Mardis, E.R. (2008) The impact of next-generation sequencing technology on genetics. Trends in Genetics 24, 133-141.
40. Mattivi, F., Guzzon, R., Vrhovsek, U., Stefanini, M. and Velasco, R. (2006) Metabolite profiling of grape: flavonols and anthocyanins. Journal of Agricultural and Food Chemistry 54, 7692-7702.
41. Morgante, M. and Salamini, F. (2003) From plant genomics to breeding practice. Current Opinion in Biotechnology 14, 214-219.
42. Morgante, M., De Paoli, E. and Radovic, S. (2007) Transposable elements and the plant pangenomes. Current Opinion in Plant Biology 10, 149-155.
43. Moroldo, M., Paillard, S., Marconi, R., Fabrice, L., Canaguier, A., Cruaud, C., De Berardinis, V., Guichard, C., Brunaud, V., Le Clainche, L., Scalabrin, S., Testolin, R., Di Gaspero, G., Morgante, M. and Adam-Blondon, A.F. (2008) A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance. BMC Plant Biology 8, 66.
44. Ossowski, S., Schneeberger, K., Clark, R.M., Lanz, C., Warthmann, N. and Weigel, D. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research 18, 2024-2033.
45. Pauquet, J., Bouquet, A., This, P. and Adam-Blondon, A.F. (2001) Establishment of a local map of AFLP markers around the powdery mildew resistance gene Run1 in grapevine and assessment of their usefulness for marker assisted selection. Theoretical and Applied Genetics 103, 1201-1210.
46. Pindo, M., Vezzulli, S., Coppola, G., Cartwright, D.A., Zharkikh, A., Velasco, R. and Troggio, M. (2008) SNP high-throughput screening in grapevine using the SNPlex genotyping system. BMC Plant Biology 8, 12.
47. Polášková, P., Herszage, J. and Ebeler, S.E. (2008) Wine flavor: chemistry in a glass. Chemical Society Reviews 37, 2478-2489.
48. Riaz, S., Krivanek, A.F., Xu, K. and Walker, M.A. (2006) Refined mapping of the Pierce's disease resistance locus, PdR1, and sex on the extended genetic map of Vitis rupestris x V. arizonica. Theoretical and Applied Genetics 113, 1317-1329.
49. Riaz, S., Tenscher, A.C., Rubin, J., Graziani, R., Pao, S.S. and Walker, M.A. (2008) Fine-scale genetic mapping of two Pierce's disease resistance loci and a major segregation distortion region on chromosome 14 of grape. Theoretical and Applied Genetics 117, 671-681.
50. Stratton, M. (2008) Genome resequencing and genetic variation. Nature Biotechnology 26, 65-66.
51. Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D.A., Cestaro, A., Pruss, D., Pindo, M., Fitzgerald, L.M., Vezzulli, S., Reid, J., Malacarne, G., Iliev, D., Coppola, G., Wardell, B., Micheletti, D., Macalma, T., Facci, M., Mitchell, J.T., 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, J.A., Sterck, L., Vandepoele, K., Grando, S.M., Toppo, S., Moser, C., Lanchbury, J., Bogden, R., Skolnick, M., Sgaramella, V., Bhatnagar, S.K., Fontana, P., Gutin, A., Van de Peer, Y., Salamini, F. and Viola, R. (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PloS One 2, e1326.
52. Welter, L.J., Göktürk-Baydar, N., Akkurt, M., Maul, E., Eibach, R., Töpfer, R. and Zyprian, E.M. (2007) Genetic mapping and localization of quantitative trait loci affecting fungal disease resistance and leaf morphology in grapevine (Vitis vinifera L). Molecular Breeding 20, 359-374.
53. Woo, N.S., Badger, M.R. and Pogson, B.J. (2008) A rapid, non-invasive procedure for quantitative assessment of drought survival using chlorophyll fluorescence. Plant Methods 4, 27.
54. Xu, K., Riaz, S., Roncoroni, N.C., Jin, Y., Hu, R., Zhou, R. and Walker, M.A. (2008) Genetic and QTL analysis of resistance to Xiphinema index in a grapevine cross. Theoretical and Applied Genetics 116, 305-311.
55. Zhu, C., Gore, M., Buckler, E.S. and Yu, J. (2008) Status and prospects of association mapping in plants. The Plant Genome 1, 5-20.