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Grape Transcriptomics and Viticulture

  • Mélanie Massonnet
  • Marianna Fasoli
  • Amanda M. Vondras
  • Sara Zenoni
  • Silvia Dal Santo
  • Alessandro Vannozzi
  • Simone D. Castellarin
  • Mario Pezzotti
  • Dario CantuEmail author
Chapter
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

A major goal of viticulture is to exert control over ripening and produce fruit of reproducible yield and quality. This implies developing effective viticultural practices, breeding cultivars with improved characteristics, and requires considering the numerous variables that can influence development and ripening, like cultivar-specific traits, regional climate, and stresses. Molecular tools aid these efforts. Among them, transcriptome measurements that capture expression across the genome allow monitoring which genomic features are transcribed given the aforementioned variables. The technologies used to study the transcriptome have rapidly improved and become less expensive since the early 2000s, increasing the feasibility of developing molecular marker-driven practices. This chapter briefly reviews the history and state of transcriptomic technologies since they have been applied to grapevine, reviews the seminal publications that have used these tools, and proposes a direction for this field in the future.

Keywords

Transcriptomics Viticultural practices Terroir Abiotic stress Biotic stress Molecular viticulture 

References

  1. Abbà S, Galetto L, Carle P, Carrère S, Delledonne M, Foissac X, Palmano S, Veratti F, Marzachì C (2014) RNA-Seq profile of flavescence dorée phytoplasma in grapevine. BMC Genom 15(1):1088.  https://doi.org/10.1186/1471-2164-15-1088CrossRefGoogle Scholar
  2. Abdel-Ghany SE, Hamilton M, Jacobi JL, Ngam P, Devitt N, Schilkey F, Ben-Hur A, Reddy AS (2016) A survey of the sorghum transcriptome using single-molecule long reads. Nat Commun 7:11706.  https://doi.org/10.1038/ncomms11706CrossRefPubMedPubMedCentralGoogle Scholar
  3. Ablett E, Seaton G, Scott K, Shelton D, Graham MW, Baverstock P, Lee LS, Henry R (2000) Analysis of grape ESTs: global gene expression patterns in leaf and berry. Plant Sci 159(1):87–95.  https://doi.org/10.1016/S0168-9452(00)00335-6CrossRefPubMedGoogle Scholar
  4. Agudelo-Romero P, Erban A, Rego C, Carbonell-Bejerano P, Nascimento T, Sousa L, Martínez-Zapater JM, Kopka J, Fortes AM (2015) Transcriptome and metabolome reprogramming in Vitis vinifera cv. Trincadeira berries upon infection with Botrytis cinerea. J Exp Bot 66(7):1769–1785.  https://doi.org/10.1093/jxb/eru517CrossRefPubMedPubMedCentralGoogle Scholar
  5. Alston JM, Fuller K, Kaplan J, Tumber K (2013) The economic consequences of pierce’s disease and related policy in the California Winegrape Industry. J Agric Resour Econ 38(2):269–297Google Scholar
  6. Amrine KC, Blanco-Ulate B, Riaz S, Pap D, Jones L, Figueroa-Balderas R, Walker MA, Cantu D (2015) Comparative transcriptomics of Central Asian Vitis vinifera accessions reveals distinct defense strategies against powdery mildew. Hortic Res 2:15037.  https://doi.org/10.1038/hortres.2015.37CrossRefPubMedPubMedCentralGoogle Scholar
  7. Anderson K, Aryal NR (2013) Which winegrape varieties are grown where? A global empirical picture. University of Adelaide Press, Adelaide.  https://doi.org/10.20851/winegrapesCrossRefGoogle Scholar
  8. Armijo G, Schlechter R, Agurto M, Muñoz D, Nuñez C, Arce-Johnson P (2016) Grapevine pathogenic microorganisms: understanding infection strategies and host response scenarios. Front Plant Sci 7:382.  https://doi.org/10.3389/fpls.2016.00382CrossRefPubMedPubMedCentralGoogle Scholar
  9. Baudoin A, Olaya G, Delmotte F, Colcol JF, Sierotzki H (2008) QoI resistance of Plasmopara viticola and Erysiphe necator in the mid-atlantic United States. Plant Health Progress 122:122.  https://doi.org/10.1094/PHP-2008-0211-02-RSCrossRefGoogle Scholar
  10. Berdeja M, Nicolas P, Kappel C, Dai ZW, Hilbert G, Peccoux A, Lafontaine M, Ollat N, Gomès E, Delrot S (2015) Water limitation and rootstock genotype interact to alter grape berry metabolism through transcriptome reprogramming. Hortic Res 2:15012.  https://doi.org/10.1038/hortres.2015.12CrossRefPubMedPubMedCentralGoogle Scholar
  11. Bertsch C, Ramirez-Suero M, Magnin-Robert M, Larignon P, Chong J, Abou-Mansour E, Spagnolo A, Clément C, Fontaine F (2013) Grapevine trunk diseases: complex and still poorly understood. Plant Pathol 62:243–265.  https://doi.org/10.1111/j.1365-3059.2012.02674.xCrossRefGoogle Scholar
  12. Bindon KA, Dry PR, Loveys BR (2007) Influence of plant water status on the production of C13-norisoprenoid precursors in Vitis vinifera L. Cv. Cabernet Sauvignon grape berries. J Agric Food Chem 55(11):4493–4500.  https://doi.org/10.1021/jf063331pCrossRefPubMedGoogle Scholar
  13. Bisson L (2001) In search of optimal grape maturity. Pract Winery Vineyard J 23:32–43Google Scholar
  14. Blanco-Ulate B, Morales-Cruz A, Amrine KC, Labavitch JM, Powell AL, Cantu D (2014) Genome-wide transcriptional profiling of Botrytis cinerea genes targeting plant cell walls during infections of different hosts. Front Plant Sci 5:435.  https://doi.org/10.3389/fpls.2014.00435CrossRefPubMedPubMedCentralGoogle Scholar
  15. Blanco-Ulate B, Amrine KC, Collins TS, Rivero RM, Vicente AR, Morales-Cruz A, Doyle CL, Ye Z, Allen G, Heymann H, Ebeler SE, Cantu D (2015) Developmental and metabolic plasticity of white-skinned grape berries in response to Botrytis cinerea during noble rot. Plant Physiol 169(4):2422–2443.  https://doi.org/10.1104/pp.15.00852CrossRefPubMedPubMedCentralGoogle Scholar
  16. Blanco-Ulate B, Hopfer H, Figueroa-Balderas R, Ye Z, Rivero RM, Albacete A, Pérez-Alfocea F, Koyama R, Anderson MM, Smith RJ, Ebeler SE, Cantu D (2017) Red blotch disease alters grape berry development and metabolism by interfering with the transcriptional and hormonal regulation of ripening. J Exp Bot 68(5):1225–1238.  https://doi.org/10.1093/jxb/erw506CrossRefPubMedPubMedCentralGoogle Scholar
  17. Bock A, Sparks TH, Estrella N, Menzel A (2013) Climate-induced changes in grapevine yield and must sugar content in Franconia (Germany) between 1805 and 2010. PLoS ONE 8:10.  https://doi.org/10.1371/journal.pone.0069015CrossRefPubMedCentralGoogle Scholar
  18. Bradshaw AD, Caspari EW, Thoday JM (1965) Evolutionary significance of phenotypic plasticity in plants. Adv Genet 13:115–155.  https://doi.org/10.1016/S0065-2660(08)60048-6CrossRefGoogle Scholar
  19. Brilli M, Asquini E, Moser M, Bianchedi PL, Perazzolli M, Si-Ammour A (2018) A multi-omics study of the grapevine-downy mildew (Plasmopara viticola) pathosystem unveils a complex protein coding- and noncoding-based arms race during infection. Sci Rep 8(1):757.  https://doi.org/10.1038/s41598-018-19158-8CrossRefPubMedPubMedCentralGoogle Scholar
  20. Buonassisi D, Colombo M, Migliaro D, Dolzani C, Peressotti E, Mizzotti C, Velasco R, Masiero S, Perazzolli M, Vezzulli S (2017) Breeding for grapevine downy mildew resistance: a review of “omics” approaches. Euphytica 213:103.  https://doi.org/10.1007/s10681-017-1882-8CrossRefGoogle Scholar
  21. Burger AL, Botha FC (2004) Ripening-related gene expression during fruit ripening in Vitis vinifera L. cv. Cabernet Sauvignon and Clairette blanche. Vitis 43(2):59–63Google Scholar
  22. Camps C, Kappel C, Lecomte P, Léon C, Gomès E, Coutos-Thévenot P, Delrot S (2010) A transcriptomic study of grapevine (Vitis vinifera cv. Cabernet-Sauvignon) interaction with the vascular ascomycete fungus Eutypa lata. J Exp Bot 61(6):1719–1737.  https://doi.org/10.1093/jxb/erq040CrossRefPubMedPubMedCentralGoogle Scholar
  23. Castellarin SD, Matthews MA, Di Gaspero G, Gambetta GA (2007a) Water deficits accelerate ripening and induce changes in gene expression regulating flavonoid biosynthesis in grape berries. Planta 227:101–112.  https://doi.org/10.1007/s00425-007-0598-8CrossRefPubMedGoogle Scholar
  24. Castellarin SD, Pfeiffer A, Sivilotti P, Degan M, Peterlunger E, Di Gaspero G (2007b) Transcriptional regulation of anthocyanin biosynthesis in ripening fruits of grapevine under seasonal water deficit. Plant Cell Environ 30:1381–1399.  https://doi.org/10.1111/j.1365-3040.2007.01716.xCrossRefPubMedGoogle Scholar
  25. Charrier G, Delzon S, Domec JC, Zhang L, Delmas CEL, Merlin I, Corso D, King A, Ojeda H, Ollat N, Prieto JA, Scholach T, Skinner P, van Leeuwen C, Gambetta GA (2018) Drought will not leave your glass empty: low risk of hydraulic failure revealed by long-term drought observations in world’s top wine regions. Sci Adv 4:eaao6969.  https://doi.org/10.1126/sciadv.aao6969CrossRefPubMedPubMedCentralGoogle Scholar
  26. Chaves MM, Zarrouk O, Francisco R, Costa JM, Santos T, Regalado AP, Rodrigues ML, Lopes CM (2010) Grapevine under deficit irrigation: hints from physiological and molecular data. Ann Bot 105:661–676.  https://doi.org/10.1093/aob/mcq030CrossRefPubMedPubMedCentralGoogle Scholar
  27. Cheng B, Furtado A, Henry RJ (2017) Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts. Gigascience 6(11):1–13.  https://doi.org/10.1093/gigascience/gix086CrossRefPubMedPubMedCentralGoogle Scholar
  28. Choi HK, Iandolino A, da Silva FG, Cook DR (2013) Water deficit modulates the response of Vitis vinifera to the Pierce’s disease pathogen Xylella fastidiosa. Mol Plant Microbe Interact 26(6):643–657.  https://doi.org/10.1094/MPMI-09-12-0217-RCrossRefPubMedGoogle Scholar
  29. Clavijo BJ, Venturini L, Schudoma C et al (2017) An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Res 27(5):885–896.  https://doi.org/10.1101/gr.217117.116CrossRefPubMedPubMedCentralGoogle Scholar
  30. Cochetel N, Escudié F, Cookson SJ, Dai Z, Vivin P, Bert PF, Muñoz MS, Delrot S, Klopp C, Ollat N, Lauvergeat V (2017) Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype. J Exp Bot 68(15):4339–4355.  https://doi.org/10.1093/jxb/erx224CrossRefPubMedPubMedCentralGoogle Scholar
  31. Cookson SJ, Clemente Moreno MJ, Hevin C, Nyamba Mendome LZ, Delrot S, Trossat-Magnin C, Ollat N (2013) Graft union formation in grapevine induces transcriptional changes related to cell wall modification, wounding, hormone signalling, and secondary metabolism. J Exp Bot 64:2997–3008.  https://doi.org/10.1093/jxb/ert144CrossRefPubMedPubMedCentralGoogle Scholar
  32. Cookson SJ, Clemente Moreno MJ, Hevin C, Nyamba Mendome LZ, Delrot S, Magnin N, Trossat-Magnin C, Ollat N (2014) Heterografting with nonself rootstocks induces genes involved in stress responses at the graft interface when compared with autografted controls. J Exp Bot 65:2473–2481.  https://doi.org/10.1093/jxb/eru145CrossRefPubMedPubMedCentralGoogle Scholar
  33. Corso M, Vannozzi A, Maza E, Vitulo N, Meggio F, Pitacco A, Telatin A, D’Angelo M, Feltrin E, Negri AS, Prinsi B, Valle G, Ramina A, Bouzayen M, Bonghi C, Lucchin M (2015) Comprehensive transcript profiling of two grapevine rootstock genotypes contrasting in drought susceptibility links the phenylpropanoid pathway to enhanced tolerance. J Exp Bot 66(19):5739–5752.  https://doi.org/10.1093/jxb/erv274CrossRefPubMedPubMedCentralGoogle Scholar
  34. Corso M, Vannozzi A, Ziliotto F, Zouine M, Maza E, Nicolato T, Vitulo N, Meggio F, Valle G, Bouzayen M, Müller M, Munné-Bosch S, Lucchin M, Bonghi C (2016) Grapevine rootstocks differentially affect the rate of ripening and modulate auxin-related genes in Cabernet Sauvignon berries. Front Plant Sci 7:69.  https://doi.org/10.3389/fpls.2016.00069CrossRefPubMedPubMedCentralGoogle Scholar
  35. Cozzolino D, Dambergs RG (2010) Instrumental analysis of grape, must and wine. In: Reynolds A (ed) Managing wine quality, vol 1. Viticulture and wine quality. Woodhead Publishing, Cambridge, pp 134–161.  https://doi.org/10.1533/9781845699284.2.134CrossRefGoogle Scholar
  36. Czemmel S, Galarneau ER, Travadon R, McElrone AJ, Cramer GR, Baumgartner K (2015) Genes expressed in grapevine leaves reveal latent wood infection by the fungal pathogen Neofusicoccum parvum. PLoS ONE 10(3):e0121828.  https://doi.org/10.1371/journal.pone.0121828CrossRefPubMedPubMedCentralGoogle Scholar
  37. Czotter N, Molnar J, Szabó E, Demian E, Kontra L, Baksa I, Szittya G, Kocsis L, Deak T, Bisztray G, Tusnady GE, Burgyan J, Varallyay E (2018) NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of hungarian vineyards. Front Microbiol 9:122.  https://doi.org/10.3389/fmicb.2018.00122CrossRefPubMedCentralGoogle Scholar
  38. Dai ZW, Ollat N, Gomès E, Decroocq S, Tandonnet J-P, Bordenave L, Pieri P, Hilbert G, Kappel C, van Leeuwen C, Vivin P, Delrot S (2011) Ecophysiological, genetic, and molecular causes of variation in grape berry weight and composition: a review. Am J Enol Vitic 62:413–425.  https://doi.org/10.5344/ajev.2011.10116CrossRefGoogle Scholar
  39. Dal Santo S, Tornielli GB, Zenoni S, Fasoli M, Farina L, Anesi A, Guzzo F, Delledonne M, Pezzotti M (2013) The plasticity of the grapevine berry transcriptome. Genome Biol 14(6):r54.  https://doi.org/10.1186/gb-2013-14-6-r54CrossRefGoogle Scholar
  40. Dal Santo S, Fasoli M, Negri S, D’Incà E, Vicenzi N, Guzzo F, Tornielli GB, Pezzotti M, Zenoni S (2016) Plasticity of the berry ripening program in a white grape variety. Front Plant Sci 7:970.  https://doi.org/10.3389/fpls.2016.00970CrossRefGoogle Scholar
  41. Dal Santo S, Zenoni S, Sandri M, De Lorenzis G, Magris G, De Paoli E, Di Gaspero G, Del Fabbro C, Morgante M, Brancadoro L, Grossi D, Fasoli M, Zuccolotto P, Tornielli GB, Pezzotti M (2018) Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G × E) on the berry transcriptome. Plant J 93(6):1143–1159.  https://doi.org/10.1111/tpj.13834CrossRefGoogle Scholar
  42. Da Silva C, Zamperin G, Ferrarini A, Minio A, Dal Molin A, Venturini L, Buson G, Tononi P, Avanzato C, Zago E, Boido E, Dellacassa E, Gaggero C, Pezzotti M, Carrau F, Delledonne M (2013) The high polyphenol content of grapevine cultivar tannat berries is conferred primarily by genes that are not shared with the reference genome. Plant Cell 25(12):4777–4788.  https://doi.org/10.1105/tpc.113.118810CrossRefPubMedPubMedCentralGoogle Scholar
  43. Davies C, Robinson SP (2000) Differential screening indicates a dramatic change in mRNA profiles during grape berry ripening. Cloning and characterization of cDNAs encoding putative cell wall and stress response proteins. Plant Physiol 122(3):803–812.  https://doi.org/10.1104/pp.122.3.803CrossRefPubMedPubMedCentralGoogle Scholar
  44. Deluc LG, Grimplet J, Wheatley MD, Tillett RL, Quilici DR, Osborne C, Schooley DA, Schlauch KA, Cushman JC, Cramer GR (2007) Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development. BMC Genom 8:429.  https://doi.org/10.1186/1471-2164-8-429CrossRefGoogle Scholar
  45. Deluc LG, Quilici DR, Decendit A, Grimplet J, Wheatley MD, Schlauch KA, Mérillon JM, Cushman JC, Cramer GR (2009) Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay. BMC Genom 10:212.  https://doi.org/10.1186/1471-2164-10-212CrossRefGoogle Scholar
  46. Dokoozlian NK (2009) Integrated canopy management: a twenty year evolution in California. In: Proceedings of recent advances in grapevine canopy management. Davis, California, July 16 2009, pp 43–52Google Scholar
  47. Dokoozlian NK, Hirschfelt DJ (1995) The influence of cluster thinning at various stages of fruit development on flame seedless table grapes. Am J Enol Vitic 46:429–436Google Scholar
  48. Duchêne E, Huard F, Dumas V, Schneider C, Merdinoglu D (2010) The challenge of adapting grapevine varieties to climate change. Clim Res 41:193–204.  https://doi.org/10.3354/cr00850CrossRefGoogle Scholar
  49. Erbs G, Newman MA (2012) The role of lipopolysaccharide and peptidoglycan, two glycosylated bacterial microbe-associated molecular patterns (MAMPs), in plant innate immunity. Mol Plant Pathol 13(1):95–104.  https://doi.org/10.1111/j.1364-3703.2011.00730.xCrossRefPubMedGoogle Scholar
  50. Espinoza C, Medina C, Somerville S, Arce-Johnson P (2007) Senescence-associated genes induced during compatible viral interactions with grapevine and Arabidopsis. J Exp Bot 58(12):3197–3212.  https://doi.org/10.1093/jxb/erm165CrossRefPubMedGoogle Scholar
  51. Fallot J, Ruchaud C, Durquety PM, Gazeau JP (1979) The clone and its reaction to grafting. III. The transmission of incompatibility when grafting 5 BB and Vitis vinifera. Progrès Agricole et Viticole 96(10):211–216Google Scholar
  52. Fasoli M, Dal Santo S, Zenoni S, Tornielli GB, Farina L, Zamboni A, Porceddu A, Venturini L, Bicego M, Murino V, Ferrarini A, Delledonne M, Pezzotti M (2012) The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program. Plant Cell 24(9):3489–3505.  https://doi.org/10.1105/tpc.112.100230CrossRefPubMedPubMedCentralGoogle Scholar
  53. Fasoli M, Richter CL, Zenoni S, Bertini E, Vitulo N, Dal Santo S, Green EA, Dokoozlian NK, Pezzotti M, Tornielli GB (2018a) Unraveling the key molecular events of grape berry ripening under varying crop loads. In: XII international conference on grapevine breeding and genetics. Bordeaux, France, p 56Google Scholar
  54. Fasoli M, Richter CL, Zenoni S, Bertini E, Vitulo N, Dal Santo S, Dokoozlian NK, Pezzotti M, Tornielli GB (2018b) The timing and order of the molecular events that mark the onset of berry ripening in grapevine. Plant Physiol 178(3):1187–1206.  https://doi.org/10.1104/pp.18.00559CrossRefPubMedPubMedCentralGoogle Scholar
  55. Fisarakis I, Chartzoulakis K, Stavrakas D (2001) Response of Sultana vines (V. vinifera L.) on six rootstocks to NaCl salinity exposure and recovery. Agric Water Manag 51:13–27.  https://doi.org/10.1016/S0378-3774(01)00115-9CrossRefGoogle Scholar
  56. Forcato C (2010) Gene prediction and functional annotation in the Vitis vinifera genome. PhD Thesis, Universita’ Degli Studi Di Padova, ItalyGoogle Scholar
  57. Fuller KB, Alston JM, Sambucci OS (2014) The value of powdery mildew resistance in grapes: evidence from California. Wine Econ Policy 3:90–107.  https://doi.org/10.1016/j.wep.2014.09.001CrossRefGoogle Scholar
  58. Fung RW, Gonzalo M, Fekete C, Kovacs LG, He Y, Marsh E, McIntyre LM, Schachtman DP, Qiu W (2008) Powdery mildew induces defense-oriented reprogramming of the transcriptome in a susceptible but not in a resistant grapevine. Plant Physiol 146(1):236–249.  https://doi.org/10.1104/pp.107.108712CrossRefPubMedPubMedCentralGoogle Scholar
  59. Gambetta GA, Matthews MA, Shaghasi TH, McElrone AJ, Castellarin SD (2010) Sugar and abscisic acid signaling orthologs are activated at the onset of ripening in grape. Planta 232:219–234.  https://doi.org/10.1007/s00425-010-1165-2CrossRefPubMedPubMedCentralGoogle Scholar
  60. Gambetta GA, Manuck CM, Drucker ST, Shaghasi T, Fort K, Matthews MA, Walker MA, McElrone AJ (2012) The relationship between root hydraulics and scion vigour across Vitis rootstocks: what role do root aquaporins play? J Exp Bot 63:6445–6455.  https://doi.org/10.1093/jxb/ers312CrossRefPubMedPubMedCentralGoogle Scholar
  61. Gambino G, Cuozzo D, Fasoli M, Pagliarani C, Vitali M, Boccacci P, Pezzotti M, Mannini F (2012) Co-evolution between Grapevine rupestris stem pitting-associated virus and Vitis vinifera L. leads to decreased defence responses and increased transcription of genes related to photosynthesis. J Exp Bot 63(16):5919–5933.  https://doi.org/10.1093/jxb/ers244CrossRefPubMedGoogle Scholar
  62. Gambino G, Dal Molin A, Boccacci P, Minio A, Chitarra W, Avanzato CG, Tononi P, Perrone I, Raimondi S, Schneider A, Pezzotti M, Mannini F, Gribaudo I, Delledonne M (2017) Whole-genome sequencing and SNV genotyping of ‘Nebbiolo’ (Vitis vinifera L.) clones. Sci Rep 7(1):17294.  https://doi.org/10.1038/s41598-017-17405-yCrossRefPubMedPubMedCentralGoogle Scholar
  63. Gessler C, Pertot I, Perazzolli M (2011) Plasmopara viticola: a review of knowledge on downy mildew of grapevine and effective disease management. Phytopathol Mediterr 50:3–44.  https://doi.org/10.14601/Phytopathol_Mediterr-9360CrossRefGoogle Scholar
  64. Giampetruzzi A, Roumi V, Roberto R, Malossini U, Yoshikawa N, La Notte P, Terlizzi F, Credi R, Saldarelli P (2012) A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in Cv Pinot gris. Virus Res 163:262–268.  https://doi.org/10.1016/j.virusres.2011.10.010CrossRefPubMedGoogle Scholar
  65. Gisi U, Sierotzki H (2008) Fungicide modes of action and resistance in downy mildews. Eur J Plant Pathol 122:157–167.  https://doi.org/10.1007/s10658-008-9290-5CrossRefGoogle Scholar
  66. Gramaje D, Úrbez-Torres JR, Sosnowski MR (2018) Managing grapevine trunk diseases with respect to etiology and epidemiology: current strategies and future prospects. Plant Dis 102:12–39.  https://doi.org/10.1094/PDIS-04-17-0512-FECrossRefPubMedGoogle Scholar
  67. Gramazio P, Blanca J, Ziarsolo P, Herraiz FJ, Plazas M, Prohens J, Vilanova S (2016) Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding. BMC Genom 17:300.  https://doi.org/10.1186/s12864-016-2631-4CrossRefGoogle Scholar
  68. Gregory PJ, Atkinson CJ, Bengough AG, Else MA, Fernández-Fernández F, Harrison RJ, Schmidt S (2013) Contributions of roots and rootstocks to sustainable, intensified crop production. J Exp Bot 64:1209–1222.  https://doi.org/10.1093/jxb/ers385CrossRefPubMedPubMedCentralGoogle Scholar
  69. Grimplet J, Deluc LG, Tillett RL, Wheatley MD, Schlauch KA, Cramer GR, Cushman JC (2007) Tissue-specific mRNA expression profiling in grape berry tissues. BMC Genom 8:187.  https://doi.org/10.1186/1471-2164-8-187CrossRefGoogle Scholar
  70. Gubler WD, Ypema HL, Ouimette DE, Bettiga LJ (1996) Occurrence of resistance in Uncinula necator to triadimefon, myclobutanil, and fenarimol in California grapevines. Plant Dis 80(8):902–909.  https://doi.org/10.1094/PD-80-0902CrossRefGoogle Scholar
  71. Guidoni S, Allara P, Schubert A (2002) Effect of cluster thinning on berry skin anthocyanin composition of Vitis vinifera cv. Nebbiolo. Am J Enol Vitic 53:224–226Google Scholar
  72. Guidoni S, Ferrandino A, Novello V (2008) Effects of seasonal and agronomical practices on skin anthocyanin profile of Nebbiolo grapes. Am J Enol Vitic 59:22–29Google Scholar
  73. Han N, Ji XL, Du YP, He X, Zhao XJ, Zhai H (2017) Identification of a novel alternative splicing variant of VvPMA1 in grape root under salinity. Front Plant Sci 8:605.  https://doi.org/10.3389/fpls.2017.00605CrossRefPubMedPubMedCentralGoogle Scholar
  74. Herrera JC, Castellarin SD (2016) Preveraison water deficit accelerates berry color change in merlot grapevines. Am J Enol Vitic 67:356–360.  https://doi.org/10.5344/ajev.2016.15083CrossRefGoogle Scholar
  75. Herrera JC, Hochberg U, Degu A, Sabbatini P, Lazarovitch N, Castellarin SD, Fait A, Alberti G, Peterlunger E (2017) Grape metabolic response to postveraison water deficit is affected by interseason weather variability. J Agric Food Chem 65(29):5868–5878.  https://doi.org/10.1021/acs.jafc.7b01466CrossRefPubMedGoogle Scholar
  76. Hochberg U, Rockwell FE, Holbrook NM, Cochard H (2018) Iso/anisohydry: a plant-environment interaction rather than a simple hydraulic trait. Trends Plant Sci 23(2):112–120.  https://doi.org/10.1016/j.tplants.2017.11.002CrossRefPubMedGoogle Scholar
  77. Hunter JJ, De Villiers OT, Watts JE (1991) The effect of partial defoliation on quality characteristics of Vitis vinifera L. cv. Cabernet Sauvignon grapes. II. Skin color, skin sugar and wine quality. Am J Enol Vitic 42:13–18Google Scholar
  78. Hren M, Nikolić P, Rotter A, Blejec A, Terrier N, Ravnikar M, Dermastia M, Gruden K (2009) ‘Bois noir’ phytoplasma induces significant reprogramming of the leaf transcriptome in the field grown grapevine. BMC Genom 10:460.  https://doi.org/10.1186/1471-2164-10-460CrossRefGoogle Scholar
  79. Jackson DI, Lombard PB (1993) Environmental and management practices affecting grape composition and wine quality: a review. Am J Enol Vitic 44:409–430Google Scholar
  80. Jaillon O, Aury JM, Noel B, The French–Italian Public Consortium for Grapevine Genome Characterization et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467.  https://doi.org/10.1038/nature06148CrossRefPubMedPubMedCentralGoogle Scholar
  81. Jiang J, Liu X, Liu C, Liu G, Li S, Wang L (2017) Integrating omics and alternative splicing reveals insights into grape response to high temperature. Plant Physiol 173(2):1502–1518.  https://doi.org/10.1104/pp.16.01305CrossRefPubMedPubMedCentralGoogle Scholar
  82. Jones GV, Reid R, Vilks A (2012) Climate, grapes, and wine: structure and suitability in a variable and changing climate. In: Dougherty P (ed) The geography of wine. Springer, Dordrecht, pp 109–133.  https://doi.org/10.1007/978-94-007-0464-0_7CrossRefGoogle Scholar
  83. Jones JD, Dangl JL (2006) The plant immune system. Nature 444:323–329.  https://doi.org/10.1038/nature05286CrossRefPubMedPubMedCentralGoogle Scholar
  84. Kelloniemi J, Trouvelot S, Héloir MC, Simon A, Dalmais B, Frettinger P, Cimerman A, Fermaud M, Roudet J, Baulande S, Bruel C, Choquer M, Couvelard L, Duthieuw M, Ferrarini A, Flors V, Le Pêcheur P, Loisel E, Morgant G, Poussereau N, Pradier JM, Rascle C, Trdá L, Poinssot B, Viaud M (2015) Analysis of the molecular dialogue between gray mold (Botrytis cinerea) and grapevine (Vitis vinifera) reveals a clear shift in defense mechanisms during berry ripening. Mol Plant Microbe Interact 28(11):1167–1180.  https://doi.org/10.1094/MPMI-02-15-0039-RCrossRefPubMedGoogle Scholar
  85. Kim MA, Rhee JS, Kim TH, Lee JS, Choi AY, Choi BS, Choi IY, Sohn YC (2017) Alternative splicing profile and sex-preferential gene expression in the female and male Pacific Abalone Haliotis discus hannai. Genes 8(3):99.  https://doi.org/10.3390/genes8030099CrossRefPubMedCentralGoogle Scholar
  86. Kliewer WM, Dokoozlian NK (2005) Leaf area/crop weight ratios of grapevines: influence on fruit composition and wine quality. Am J Enol Vitic 56:170–181Google Scholar
  87. Li J, Harata-Lee Y, Denton MD, Feng Q, Rathjen JR, Qu Z, Adelson DL (2017a) Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis. Cell Discov 3:17031.  https://doi.org/10.1038/celldisc.2017.31CrossRefPubMedPubMedCentralGoogle Scholar
  88. Li X, Wu J, Yin L, Zhang Y, Qu J, Lu J (2015) Comparative transcriptome analysis reveals defense-related genes and pathways against downy mildew in Vitis amurensis grapevine. Plant Physiol Biochem 95:1–14.  https://doi.org/10.1016/j.plaphy.2015.06.016CrossRefPubMedGoogle Scholar
  89. Li Y, Wei W, Feng J, Luo H, Pi M, Liu Z, Kang C (2017b) Genome re-annotation of the wild strawberry Fragaria vesca using extensive Illumina- and SMRT-based RNA-seq datasets. DNA Res 25(1):61–70.  https://doi.org/10.1093/dnares/dsx038CrossRefPubMedCentralGoogle Scholar
  90. Lider LA, Ferrari NL, Bowers KW (1978) A study of longevity of graft combinations in California vineyards, with special interest in the vinifera X rupestris hybrids. Am J Enol Vitic 29:18–24Google Scholar
  91. Liu J, Chen X, Liang X, Zhou X, Yang F, Liu J, He SY, Guo Z (2016) Alternative splicing of rice WRKY62 and WRKY76 transcription factor genes in pathogen defense. Plant Physiol 171(2):1427–1442.  https://doi.org/10.1104/pp.15.01921CrossRefPubMedPubMedCentralGoogle Scholar
  92. Lovisolo C, Perrone I, Carra A, Ferrandino A, Flexas J, Medrano H, Schubert A (2010) Drought-induced changes in development and function of grapevine (Vitis spp.) organs and in their hydraulic and non-hydraulic interactions at the whole-plant level: a physiological and molecular update. Funct Plant Biol 37:98–116.  https://doi.org/10.1071/FP09191CrossRefGoogle Scholar
  93. Lowe R, Shirley N, Bleackley M, Dolan S, Shafee T (2017) Transcriptomics technologies. PLoS Comput Biol 13(5):e1005457.  https://doi.org/10.1371/journal.pcbi.1005457CrossRefPubMedPubMedCentralGoogle Scholar
  94. Madden LV, Wheelis M (2003) The threat of plant pathogens as weapons against U.S. crops. Annu Rev Phytopathol 41:155–176.  https://doi.org/10.1146/annurev.phyto.41.121902.102839CrossRefPubMedGoogle Scholar
  95. Marguerit E, Brendel O, Lebon E, van Leeuwen C, Ollat N (2012) Rootstock control of scion transpiration and its acclimation to water deficit are controlled by different genes. New Phytol 194:416–429.  https://doi.org/10.1111/j.1469-8137.2012.04059.xCrossRefPubMedGoogle Scholar
  96. Martelli GP (2014) Directory of virus and virus-like diseases of the grapevine and their agents. J Plant Pathol 96:1–136Google Scholar
  97. Massonnet M, Fasoli M, Tornielli GB, Altieri M, Sandri M, Zuccolotto P, Paci P, Gardiman M, Zenoni S, Pezzotti M (2017a) Ripening transcriptomic program in red and white grapevine varieties correlates with berry skin anthocyanin accumulation. Plant Physiol 174(4):2376–2396.  https://doi.org/10.1104/pp.17.00311CrossRefPubMedPubMedCentralGoogle Scholar
  98. Massonnet M, Figueroa-Balderas R, Galarneau ERA, Miki S, Lawrence DP, Sun Q, Wallis CM, Baumgartner K, Cantu D (2017b) Neofusicoccum parvum colonization of the grapevine woody stem triggers asynchronous host responses at the site of infection and in the leaves. Front Plant Sci 8:1117.  https://doi.org/10.3389/fpls.2017.01117CrossRefPubMedPubMedCentralGoogle Scholar
  99. Massonnet M, Morales-Cruz A, Figueroa-Balderas R, Lawrence DP, Baumgartner K, Cantu D (2018) Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum. Mol Plant Pathol 19(1):21–34.  https://doi.org/10.1111/mpp.12491CrossRefPubMedGoogle Scholar
  100. Matthews MA, Nuzzo V (2007) Berry size and yield paradigms on grapes and wines quality. Acta Hortic.  https://doi.org/10.17660/ActaHortic.2007.754.56CrossRefGoogle Scholar
  101. Meggio F, Prinsi B, Negri AS, Simone Di Lorenzo G, Lucchini G, Pitacco A, Failla O, Scienza A, Cocucci M, Espen L (2014) Biochemical and physiological responses of two grapevine rootstock genotypes to drought and salt treatments. Aust J Grape Wine Res 20:310–323.  https://doi.org/10.1111/ajgw.1207CrossRefGoogle Scholar
  102. Meng B, Martelli GP, Golino DA, Fuchs M (eds) (2017) Grapevine viruses: molecular biology, diagnostics and management. Springer, HeidelbergGoogle Scholar
  103. Milien M, Renault-Spilmont AS, Cookson SJ, Sarrazin A, Verdeil JL (2012) Visualization of the 3D structure of the graft union of grapevine using X-ray tomography. Sci Hortic 144:130–140.  https://doi.org/10.1016/j.scienta.2012.06.045CrossRefGoogle Scholar
  104. Minio A, Massonnet M, Figueroa-Balderas R, Vondras AM, Blanco-Ulate B, Cantu D (2019) Iso-Seq allows genome-independent transcriptome profiling of grape berry development. G3 (Bethesda, MD).  https://doi.org/10.1534/g3.118.201008CrossRefGoogle Scholar
  105. Mittler R (2006) Abiotic stress, the field environment and stress combination. Trends Plant Sci 11:15–19.  https://doi.org/10.1016/j.tplants.2005.11.002CrossRefPubMedGoogle Scholar
  106. Morales-Cruz A, Allenbeck G, Figueroa-Balderas R, Ashworth VE, Lawrence DP, Travadon R, Smith RJ, Baumgartner K, Rolshausen PE, Cantu D (2018) Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk disease complex. Mol Plant Pathol 19(2):490–503.  https://doi.org/10.1111/mpp.12544CrossRefPubMedGoogle Scholar
  107. Mori K, Goto-Yamamoto N, Kitayama M, Hashizume K (2007) Loss of anthocyanins in red-wine grape under high temperature. J Exp Bot 58(8):1935–1945.  https://doi.org/10.1093/jxb/erm055CrossRefPubMedGoogle Scholar
  108. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods 5(7):621–628.  https://doi.org/10.1038/nmeth.1226CrossRefPubMedPubMedCentralGoogle Scholar
  109. 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 Genom 5(4):208–217.  https://doi.org/10.1007/s10142-005-0143-4CrossRefGoogle Scholar
  110. Navarro B, Pantaleo V, Gisel A, Moxon S, Dalmay T, Bisztray G, Di Serio F, Burgyán J (2009) Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant–viroid interaction. PLoS ONE 4:e7686.  https://doi.org/10.1371/journal.pone.0007686CrossRefPubMedPubMedCentralGoogle Scholar
  111. Oerke E-C (2006) Crop losses to pests. J Agric Sci 144:31–43.  https://doi.org/10.1017/S0021859605005708CrossRefGoogle Scholar
  112. Ollat N, Bordenave L, Tandonnet JP, Boursiquot JM, Marguerit E (2016) Grapevine rootstocks: origins and perspectives. Acta Hort 1136:11–22.  https://doi.org/10.17660/ActaHortic.2016.1136.2CrossRefGoogle Scholar
  113. Østergård H, Finckh M, Fontaine L, Goldringer I, Hoad S, Kristensen K, Lammerts van Bueren E, Mascher F, Munk L, Wolfe M (2009) Time for a shift in crop production: Embracing complexity through diversity at all levels. J Sci Food Agric 89:1439–1445.  https://doi.org/10.1002/jsfa.3615CrossRefGoogle Scholar
  114. Palliotti A, Cartechini A (2000) Cluster thinning effects on yield and grape composition in different grapevine cultivars. Acta Hortic.  https://doi.org/10.17660/ActaHortic.2000.512.11CrossRefGoogle Scholar
  115. Pandey MK, Roorkiwal M, Singh VK, Ramalingam A, Kudapa H, Thudi M, Chitikineni A, Rathore A, Varshney RK (2016) Emerging genomic tools for legume breeding: current status and future prospects. Front Plant Sci 7:455.  https://doi.org/10.3389/fpls.2016.00455CrossRefPubMedPubMedCentralGoogle Scholar
  116. Pantaleo V, Saldarelli P, Miozzi L, Giampetruzzi A, Gisel A, Moxon S, Dalmay T, Bisztray G, Burgyan J (2010) Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine. Virology 408:49–56.  https://doi.org/10.1016/j.virol.2010.09.001CrossRefPubMedGoogle Scholar
  117. Parkinson J, Blaxter M (2009) Expressed sequence tags: an overview. Methods Mol Biol 533:1–12.  https://doi.org/10.1007/978-1-60327-136-3_1CrossRefPubMedGoogle Scholar
  118. Pastore C, Zenoni S, Tornielli GB, Allegro G, Dal Santo S, Valentini G, Intrieri C, Pezzotti M, Filippetti I (2011) Increasing the source/sink ratio in Vitis vinifera (cv Sangiovese) induces extensive transcriptome reprogramming and modifies berry ripening. BMC Genom 12:631.  https://doi.org/10.1186/1471-2164-12-631CrossRefGoogle Scholar
  119. Pastore C, Zenoni S, Fasoli M, Pezzotti M, Tornielli GB, Filippetti I (2013) Selective defoliation affects plant growth, fruit transcriptional ripening program and flavonoid metabolism in grapevine. BMC Plant Biol 13:30.  https://doi.org/10.1186/1471-2229-13-30CrossRefPubMedPubMedCentralGoogle Scholar
  120. Pilati S, Perazzolli M, Malossini A, Cestaro A, Demattè L, Fontana P, Dal Ri A, Viola R, Velasco R, Moser C (2007) Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at véraison. BMC Genom 8:428.  https://doi.org/10.1186/1471-2164-8-428CrossRefGoogle Scholar
  121. Pina A, Errea P (2005) A review of new advances in mechanism of graft compatibility–incompatibility. Sci Hortic 106:1–11.  https://doi.org/10.1016/j.scienta.2005.04.003CrossRefGoogle Scholar
  122. Polesani M, Bortesi L, Ferrarini A, Zamboni A, Fasoli M, Zadra C, Lovato A, Pezzotti M, Delledonne M, Polverari A (2010) General and species-specific transcriptional responses to downy mildew infection in a susceptible (Vitis vinifera) and a resistant (V. riparia) grapevine species. BMC Genom 11:117.  https://doi.org/10.1186/1471-2164-11-117CrossRefGoogle Scholar
  123. Poni S, Gatti M (2017) Affecting yield components and grape composition through manipulations of the source-sink balance. Acta Hortic 1188:21–34.  https://doi.org/10.17660/ActaHortic.2017.1188.4CrossRefGoogle Scholar
  124. Poni S, Casalini L, Bernizzoni F, Civardi S, Intrieri C (2006) Effects of early defoliation on shoot photosynthesis, yield components, and grape composition. Am J Enol Vitic 57:397–407Google Scholar
  125. Poni S, Gatti M, Palliotti A, Dai Z, Duchêne E, Truong T-T, Ferrara G, Matarrese AMS, Gallotta A, Bellincontro A, Mencarelli F, Tombesi S (2018) Grapevine quality: a multiple choice issue. Sci Hortic 234:445–462.  https://doi.org/10.1016/j.scienta.2017.12.035CrossRefGoogle Scholar
  126. Qiu W, Feechan A, Dry I (2015) Current understanding of grapevine defense mechanisms against the biotrophic fungus (Erysiphe necator), the causal agent of powdery mildew disease. Hortic Res 2:15020.  https://doi.org/10.1038/hortres.2015.20CrossRefPubMedPubMedCentralGoogle Scholar
  127. Rapicavoli JN, Blanco-Ulate B, Muszyński A, Figueroa-Balderas R, Morales-Cruz A, Azadi P, Dobruchowska JM, Castro C, Cantu D, Roper MC (2018) Lipopolysaccharide O-antigen delays plant innate immune recognition of Xylella fastidiosa. Nat Commun 9(1):390.  https://doi.org/10.1038/s41467-018-02861-5CrossRefPubMedPubMedCentralGoogle Scholar
  128. Renouf V, Tregoat O, Roby JP, van Leeuwen C (2010) Soils, rootstocks and grapevine varieties in prestigious bordeaux vineyards and their impact on yield and quality. Journal International des sciences de la vigne et du vin 44:127–134.  https://doi.org/10.20870/oeno-one.2010.44.3.1471CrossRefGoogle Scholar
  129. Ruel JJ, Walker MA (2006) Resistance to Pierce’s disease in muscadinia rotundifolia and other native grape species. Am J Enol Vitic 57:158–165Google Scholar
  130. Saltz JB, Bell AM, Flint J, Gomulkiewicz R, Hughes KA, Keagy J (2018) Why does the magnitude of genotype-by-environment interaction vary? Ecol Evolut 8(12):6342–6353.  https://doi.org/10.1002/ece3.4128CrossRefGoogle Scholar
  131. Savoi S, Wong DC, Arapitsas P, Miculan M, Bucchetti B, Peterlunger E, Fait A, Mattivi F, Castellarin SD (2016) Transcriptome and metabolite profiling reveals that prolonged drought modulates the phenylpropanoid and terpenoid pathway in white grapes (Vitis vinifera L.). BMC Plant Biol 16:67.  https://doi.org/10.1186/s12870-016-0760-1CrossRefPubMedPubMedCentralGoogle Scholar
  132. Savoi S, Wong DCJ, Degu A, Herrera JC, Bucchetti B, Peterlunger E, Fait A, Mattivi F, Castellarin SD (2017) Multi-omics and integrated network analyses reveal new insights into the systems relationships between metabolites, structural genes, and transcriptional regulators in developing grape berries (Vitis vinifera L.) exposed to water deficit. Front Plant Sci 8:1124.  https://doi.org/10.3389/fpls.2017.01124CrossRefPubMedPubMedCentralGoogle Scholar
  133. Schultz HR (2003) Differences in hydraulic architecture account for near- isohydric and anisohydric behaviour of two eld-grown. Plant Cell Environ 26:1393–1406.  https://doi.org/10.1046/j.1365-3040.2003.01064.xCrossRefGoogle Scholar
  134. Seguin G (1988) Ecosystems of the great red wines produced in the maritime climate of Bordeaux. In: Fuller-Perrine L (ed) Proceedings of the symposium on maritime climate winegrowing. Department of Horticultural Sciences, Cornell University, Geneva, NY, pp 36–53Google Scholar
  135. Suzuki N, Rivero RM, Shulaev V, Blumwald E, Mittler R (2014) Abiotic and biotic stress combinations. New Phytol 203(1):32–43.  https://doi.org/10.1111/nph.12797CrossRefPubMedGoogle Scholar
  136. Terrier N, Ageorges A, Abbal P, Romieu C (2001) Generation of ESTs from grape berry at various developmental stages. J Plant Physiol 158(12):1575–1583.  https://doi.org/10.1078/0176-1617-00566CrossRefGoogle Scholar
  137. Terrier N, Glissant D, Grimplet J, Barrieu F, Abbal P, Couture C, Ageorges A, Atanassova R, Léon C, Renaudin JP, Dédaldéchamp F, Romieu C, Delrot S, Hamdi S (2005) Isogene specific oligo arrays reveal multifaceted changes in gene expression during grape berry (Vitis vinifera L.) development. Planta 222(5):832–847.  https://doi.org/10.1007/s00425-005-0017-yCrossRefPubMedPubMedCentralGoogle Scholar
  138. Todić S, Bešlić Z, Kuljančić I (2005) Varying degree of grafting compatibility between cv. Chardonnay, Merlot and different grapevine rootstocks. J Cent Eur Agric 6(2):115–120Google Scholar
  139. Vaillant-Gaveau N, Wojnarowiez G, Petit A-N, Jacquens L, Panigai L, Clement C, Fontaine F (2014) Relationships between carbohydrates and reproductive development in chardonnay grapevine: impact of defoliation and fruit removal treatments during four successive growing seasons. Journal International des sciences de la vigne et du vin 48(4):219–229.  https://doi.org/10.20870/oeno-one.2014.48.4.1694CrossRefGoogle Scholar
  140. van Leeuwen C, Seguin G (2006) The concept of terroir in viticulture. J Wine Res 17:1–10.  https://doi.org/10.1080/09571260600633135CrossRefGoogle Scholar
  141. van Leeuwen C, Friant PH, Choné X, Trégoat O, Koundouras S, Dubourdieu D (2004) The influence of climate, soil and cultivar on terroir. Am J Enol Vitic 55:207–217Google Scholar
  142. van Leeuwen C, Trégoat O, Choné X, Bois B, Pernet D, Gaudillère J-P (2009) Vine water status is a key factor in grape ripening and vintage quality for red Bordeaux wine. How can it be assessed for vineyard management purposes? Journal International des sciences de la vigne et du vin 43:121.  https://doi.org/10.20870/oeno-one.2009.43.3.798CrossRefGoogle Scholar
  143. Vannozzi A, Dry IB, Fasoli M, Zenoni S, Lucchin M (2012) Genome-wide analysis of the grapevine stilbene synthase multigenic family: genomic organization and expression profiles upon biotic and abiotic stresses. BMC Plant Biol 12:130.  https://doi.org/10.1186/1471-2229-12-130CrossRefPubMedPubMedCentralGoogle Scholar
  144. Vannozzi A, Donnini S, Vigani G, Corso M, Valle G, Vitulo N, Bonghi C, Zocchi G, Lucchin M (2017) Transcriptional characterization of a widely-used grapevine rootstock genotype under different iron-limited conditions. Front Plant Sci 7:1994.  https://doi.org/10.3389/fpls.2016.01994CrossRefPubMedPubMedCentralGoogle Scholar
  145. Vega A, Gutiérrez RA, Peña-Neira A, Cramer GR, Arce-Johnson P (2011) Compatible GLRaV-3 viral infections affect berry ripening decreasing sugar accumulation and anthocyanin biosynthesis in Vitis vinifera. Plant Mol Biol 77(3):261–274.  https://doi.org/10.1007/s11103-011-9807-8CrossRefPubMedPubMedCentralGoogle Scholar
  146. Velasco R, Zharkikh A, Troggio M et al (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2(12):e136.  https://doi.org/10.1371/journal.pone.0001326CrossRefGoogle Scholar
  147. Venter M, Burger AL, Botha FC (2001) Molecular analysis of fruit ripening: the identification of differentially expressed sequences in Vitis vinifera using cDNA-AFLP technology. Vitis 40(4):191–196Google Scholar
  148. Venturini L, Ferrarini A, Zenoni S, Tornielli GB, Fasoli M, Dal Santo S, Minio A, Buson G, Tononi P, Zago ED, Zamperin G, Bellin D, Pezzotti M, Delledonne M (2013) De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity. BMC Genom 14:41.  https://doi.org/10.1186/1471-2164-14-41CrossRefGoogle Scholar
  149. Viers JH, Williams JN, Nicholas KA, Barbosa O, Kotzé I, Spence L, Webb LB, Merenlender A, Reynolds M (2013) Vinecology: pairing wine with nature. Conserv Lett 6:287–299.  https://doi.org/10.1111/conl.12011CrossRefGoogle Scholar
  150. Vitulo N, Forcato C, Carpinelli EC, Telatin A, Campagna D, D’Angelo M, Zimbello R, Corso M, Vannozzi A, Bonghi C, Lucchin M, Valle G (2014) A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype. BMC Plant Biol 14:99.  https://doi.org/10.1186/1471-2229-14-99CrossRefPubMedPubMedCentralGoogle Scholar
  151. Vuylsteke M, Peleman JD, van Eijk MJ (2007) AFLP-based transcript profiling (cDNA-AFLP) for genome-wide expression analysis. Nat Protoc 2(6):1399–1413.  https://doi.org/10.1038/nprot.2007.174CrossRefPubMedGoogle Scholar
  152. Walker RR, Blackmore DH, Clingeleffer PR, Correll RL (2002) Rootstock effects on salt tolerance of irrigated field-grown grapevines (Vitis vinifera L. cv. Sultana). 1. Yield and vigour inter-relationships. Aust J Grape Wine Res 8(1):3–14.  https://doi.org/10.1111/j.1755-0238.2002.tb00206.xCrossRefGoogle Scholar
  153. Walker RR, Blackmore DH, Clingeleffer PR, Correll RL (2004) Rootstock effects on salt tolerance of irrigated field-grown grapevines (Vitis vinifera L. cv. Sultana) 2. Ion concentrations in leaves and juice. Aust J Grape Wine Res 10:90–99.  https://doi.org/10.1111/j.1755-0238.2004.tb00011.xCrossRefGoogle Scholar
  154. Wang B, Tseng E, Regulski M, Clark TA, Hon T, Jiao Y, Lu Z, Olson A, Stein JC, Ware D (2016) Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nat Commun 7:11708.  https://doi.org/10.1038/ncomms11708CrossRefPubMedPubMedCentralGoogle Scholar
  155. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63.  https://doi.org/10.1038/nrg2484CrossRefPubMedPubMedCentralGoogle Scholar
  156. Waters DLE, Holton TA, Ablet EM, Slade Lee L, Henry RJ (2005) cDNA microarray analysis of developing grape (Vitis vinifera cv. Shiraz) berry skin. Funct Integr Genom 5(1):40–58.  https://doi.org/10.1007/s10142-004-0124-zCrossRefGoogle Scholar
  157. Weng K, Li ZQ, Liu RQ, Wang L, Wang YJ, Xu Y (2014) Transcriptome of Erysiphe necator-infected Vitis pseudoreticulata leaves provides insight into grapevine resistance to powdery mildew. Hortic Res 1:14049.  https://doi.org/10.1038/hortres.2014.49CrossRefPubMedPubMedCentralGoogle Scholar
  158. Wilcox WF, Gubler WD, Uyemoto JK (2015) Diseases of Grape (Vitis vinifera L.). https://www.apsnet.org/publications/commonnames/Pages/Grape.aspx. Accessed 14 Dec 2018
  159. White MA, Whalen P, Jones GV (2009) Land and wine. Nat Geosci 2:82–84.  https://doi.org/10.1038/ngeo429CrossRefGoogle Scholar
  160. Wu J, Zhang Y, Zhang H, Huang H, Folta KM, Lu J (2010) Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa sequencing technology. BMC Plant Biol 10:234.  https://doi.org/10.1186/1471-2229-10-234CrossRefPubMedPubMedCentralGoogle Scholar
  161. Xu S, Wang J, Shang H, Huang Y, Yao W, Chen B, Zhang M (2018) Transcriptomic characterization and potential marker development of contrasting sugarcane cultivars. Sci Rep 8:1683.  https://doi.org/10.1038/s41598-018-19832-xCrossRefPubMedPubMedCentralGoogle Scholar
  162. Xu X, Zhang Y, Williams J, Antoniou E, McCombie WR, Wu S, Zhu W, Davidson NO, Denoya P, Li E (2013) Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets. BMC Bioinform 14(Suppl 9):S1.  https://doi.org/10.1186/1471-2105-14-S9-S1CrossRefGoogle Scholar
  163. Zaini PA, Nascimento R, Gouran H, Cantu D, Chakraborty S, Phu M, Goulart LR, Dandekar AM (2018) Molecular profiling of Pierce’s disease outlines the response circuitry of Vitis vinifera to Xylella fastidiosa Infection. Front Plant Sci 9:771.  https://doi.org/10.3389/fpls.2018.00771CrossRefPubMedPubMedCentralGoogle Scholar
  164. Zarrouk O, Costa JM, Francisco R et al (2016) Drought and water management in Mediterranean vineyards. In: Gerós H, Chaves M, Medrano H, Delrot S (eds) Grapevine in a changing environment: a molecular and ecophysiological perspective. Wiley, Hoboken, pp 38–67CrossRefGoogle Scholar
  165. Zenoni S, Ferrarini A, Giacomelli E, Xumerle L, Fasoli M, Malerba G, Bellin D, Pezzotti M, Delledonne M (2010) Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol 152(4):1787–1795.  https://doi.org/10.1104/pp.109.149716CrossRefPubMedPubMedCentralGoogle Scholar
  166. Zenoni S, Dal Santo S, Tornielli GB, D’Inca E, Filippetti I, Pastore C, Allegro G, Silvestroni O, Lanari V, Pisciotta A, Di Lorenzo R, Palliotti A, Tombesi S, Gatti M, Poni S (2017) Transcriptional responses to pre-flowering leaf defoliation in grapevine berry from different growing sites, years, and genotypes. Front Plant Sci 8:630.  https://doi.org/10.3389/fpls.2017.00630CrossRefPubMedPubMedCentralGoogle Scholar
  167. Zhao S, Fung-Leung W-P, Bittner A, Ngo K, Liu X (2014) Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS ONE 9(1):e78644.  https://doi.org/10.1371/journal.pone.0078644CrossRefPubMedPubMedCentralGoogle Scholar
  168. Zhu FY, Chen MX, Ye NH, Shi L, Ma KL, Yang JF, Cao YY, Zhang Y, Yoshida T, Fernie AR, Fan GY, Wen B, Zhou R, Liu TY, Fan T, Gao B, Zhang D, Hao GF, Xiao S, Liu YG, Zhang J (2017) Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings. Plant J 91(3):518–533.  https://doi.org/10.1111/tpj.13571CrossRefPubMedGoogle Scholar

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Mélanie Massonnet
    • 1
  • Marianna Fasoli
    • 2
  • Amanda M. Vondras
    • 1
  • Sara Zenoni
    • 3
  • Silvia Dal Santo
    • 3
  • Alessandro Vannozzi
    • 4
  • Simone D. Castellarin
    • 5
  • Mario Pezzotti
    • 3
  • Dario Cantu
    • 1
    Email author
  1. 1.Department of Viticulture and EnologyUniversity of California DavisDavisUSA
  2. 2.Viticulture, Chemistry and EnologyE. & J. Gallo WineryModestoUSA
  3. 3.Department of BiotechnologyUniversity of VeronaVeronaItaly
  4. 4.Department of Agronomy, Food, Natural Resources, Animals and EnvironmentUniversity of PadovaLegnaroItaly
  5. 5.Wine Research CentreThe University of British ColumbiaVancouverCanada

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