, Volume 222, Issue 5, pp 832–847 | Cite as

Isogene specific oligo arrays reveal multifaceted changes in gene expression during grape berry (Vitis vinifera L.) development

  • Nancy Terrier
  • David Glissant
  • Jérôme Grimplet
  • François Barrieu
  • Philippe Abbal
  • Carole Couture
  • Agnès Ageorges
  • Rossitza Atanassova
  • Céline Léon
  • Jean-Pierre Renaudin
  • Fabienne Dédaldéchamp
  • Charles RomieuEmail author
  • Serge Delrot
  • Saïd Hamdi
Original Article


The transition from a green, hard, and acidic pericarp to a sweet, soft, coloured, and sugar-rich ripe fruit occurs in many unrelated fruit species. High throughput identification of differentially expressed genes in grape berry has been achieved by the use of 50-mers oligoarrays bearing a set of 3,200 Unigenes from Vitis vinifera to compare berry transcriptome at nine developmental stages. Analysis of transcript profiles revealed that most activations were triggered simultaneously with softening, occurring within only 24 h for an individual berry, just before any change in colouration or water, sugar, and acid content can be detected. Although most dramatically induced genes belong to unknown functional categories, numerous changes occur in the expression of isogenes involved in primary and secondary metabolism during ripening. Focusing on isogenes potentially significant in development regulation (hormonal control of transcription factor) revealed a possible role for several hormones (cytokinin, gibberellin, or jasmonic acid). Transcription factor analysis revealed the induction of RAP2 and WRKY genes at véraison, suggesting increasing biotic and abiotic stress conditions during ripening. This observation was strengthened by an increased expression of multiple transcripts involved in sugar metabolism and also described as induced in other plant organs during stress conditions. This approach permitted the identification of new isogenes as possible control points: a glutathione S-transferase exhibits the same expression profile as anthocyanin accumulation and a new putative sugar transporter is induced in parallel with sugar import.


Anthocyanin Fruit Ripening Sugar Vitis 



Expressed sequence tag


Grape ripening induced protein


UDP glucose-flavonoid 3-O-glucosyl transferase



This research was supported by a Genoplant grant n° CI 2001003 entitled “Grapevine genomics: Grape berry development and ripening, transcriptomic analysis and identification of interest genes”.

Supplementary material

425_2005_17_MOESM1_ESM.pdf (1.1 mb)
Supplementary material


  1. Ageorges A, Issaly N, Picaud S, Delrot S, Romieu C (2000) Identification and functional expression in yeast of a grape berry sucrose carrier. Plant Physiol Biochem 38:1–9CrossRefGoogle Scholar
  2. Aharoni A, Keizer LC, Bouwmeester HJ, Sun Z, Alvarez-Huerta M, Verhoeven, HA, Blaas J, Van Houwelingen AM, De Vos RC, Van Der Voet H, Jansen RC, Guis M, Mol J, Davis RW, Schena M, Van Tunen AJ, O’Connell AP (2000) Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. Plant Cell 12:647–662CrossRefPubMedGoogle Scholar
  3. Aharoni A, Keizer LC, Van Den Broeck HC, Blanco-Portales R, Munoz-Blanco J, Bois G, Smit P, De Vos RC, O’Connell AP (2002) Novel insight into vascular, stress, and auxin-dependent and -independent gene expression programs in strawberry, a non-climacteric fruit. Plant Physiol 129:1019–1031CrossRefPubMedGoogle Scholar
  4. Alfenito MR, Souer E, Goodman CD, Buell R, Mol J, Koes R, Walbot V (1998) Functional complementation of anthocyanin sequestration in the vacuole by widely divergent glutathione S-transferases. Plant Cell 10:1135–1149CrossRefPubMedGoogle Scholar
  5. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C, Heller C, Jeske A, Koesema E, Meyers CC, Parker H, Prednis L, Ansari Y, Choy N, Deen H, Geralt M, Hazari N, Hom E, Karnes M, Mulholland C, Ndubaku R, Schmidt I, Guzman P, Aguilar-Henonin L, Schmid M, Weigel D, Carter DE, Marchand T, Risseeuw E, Brogden D, Zeko A, Crosby WL, Berry CC and Ecker JR (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653–657CrossRefPubMedGoogle Scholar
  6. Arabidopsis Genome Initiative (2000) Analyse of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 403:503–511CrossRefGoogle Scholar
  7. Baiges I, Schaffner AR, Affenzeller MJ, Mas A (2002) Plant aquaporins. Physiol Plant 115:175–182CrossRefPubMedGoogle Scholar
  8. Barnavon L, Doco T, Terrier N, Ageorges A, Romieu C, Pellerin P (2000) Analysis of cell wall neutral sugar composition, β-galactosidase activity and a related cDNA clone throughout the development of Vitis vinifera grape berries. Plant Physiol Biochem 38:289–300CrossRefGoogle Scholar
  9. Baugh LR, Hill AA, Brown EL, Hunter CP (2001) Quantitative analysis of mRNA amplification by in vitro transcription. Nucl Acids Res 29:e29CrossRefPubMedGoogle Scholar
  10. Boss PK, Davies C, Robinson SP (1996a) Analysis of the expression of anthocyanin pathway genes in developing Vitis vinifera L. cv Shiraz grape berries and the implications for pathway regulation. Plant Physiol 111:1059–1066Google Scholar
  11. Boss PK, Davies C, Robinson SP (1996b) Expression of anthocyanin biosynthesis pathway genes in red and white grapes. Plant Mol Biol 32:565–569CrossRefGoogle Scholar
  12. Carystinos GD, MacDonald HR, Monroy AF, Dhindsa RS, Poole RJ (1995) Vacuolar H(+)-translocating pyrophosphatase is induced by anoxia or chilling in seedlings of rice. Plant Physiol 108:641–649CrossRefPubMedGoogle Scholar
  13. Coombe BG (1973) Regulation of set and development of the grape berry. Acta Hortic 34:261–269Google Scholar
  14. Dali N, Michaud D, Yelle S (1992) Evidence for xylem discontinuity in Pinot noir and Merlot grapes: dye uptake and mineral composition during berry maturation. Am J EnolVitic 44:187–192Google Scholar
  15. Darley CP, Davies JM, Sanders D (1995) Chill induced changes in the activity and abundance of the vacuolar proton-pumping pyrophosphatase from mung bean hypocotyls. Plant Physiol 109:659–665PubMedGoogle Scholar
  16. Davies C, Robinson SP (1996) Sugar accumulation in grape berries. Cloning of two putative vacuolar invertase cDNAs and their expression in grapevine tissues. Plant Physiol 111:275–283CrossRefPubMedGoogle Scholar
  17. 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 122:803–812CrossRefPubMedGoogle Scholar
  18. Davies C, Wolf T, Robinson SP (1999) Three putative sucrose transporters are differentially expressed in grapevine tissues. Plant Science 147:93–100CrossRefGoogle Scholar
  19. Didier G, Brézellec P, Remy E and Hénault A (2002) GeneANOVA-gene expression analysis of variance. Bioinformatics 18:490–491CrossRefPubMedGoogle Scholar
  20. Duval M, Hsieh TF, Kim SY, Thomas TL (2002) Molecular characterization of AtNAM: a member of the Arabidopsis NAC domain superfamily. Plant Mol Biol 50:237–248CrossRefPubMedGoogle Scholar
  21. Eberwise J, Yeh H, Miyashirao K, Cao Y, Nair S, Finnell R, Zettel M, Coleman P (1992) Analysis of gene expression in single live neurons. Proc Natl Acad Sci USA 89:3010–3014PubMedCrossRefGoogle Scholar
  22. Ehness R, Roitsch T (1997) Co-ordinated induction of mRNAs for extracellular invertase and a glucose transporter in Chenopodium rubrum by cytokinins. Plant J 11:539–548CrossRefPubMedGoogle Scholar
  23. Eulgem T, Rushton PJ, Robatzek S, Somssich IE (2000) The WRKY superfamily of plant transcription factors. Trends Plant Sci 5:199–206CrossRefPubMedGoogle Scholar
  24. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194PubMedGoogle Scholar
  25. Fillion L, Ageorges A, Picaud S, Coutos-Thévenot P, Lemoine R, Romieu C, Delrot S (1999) Cloning and expression of hexose transporter gene expressed during the ripening of grape berry. Plant Physiol 120:1083–1093CrossRefPubMedGoogle Scholar
  26. Finkelstein D, Ewing R, Gollub J, Sterky F, Cherry JM, Somerville S (2002) Microarray data quality analysis: lessons from the AFGC project. Arabidopsis Functional Genomics Consortium. Plant Mol Biol 48:119–131CrossRefPubMedGoogle Scholar
  27. Forsthoefel NR, Vernon DM, Cushman JC (1995a) A salinity-induced gene from the halophyte M. crystallinum encodes a glycolytic enzyme, cofactor-independent phosphoglyceromutase. Plant Mol Biol 29:213–226CrossRefGoogle Scholar
  28. Forsthoefel NR, Cushman MA, Cushman JC (1995b) Posttranscriptional and posttranslational control of enolase expression in the facultative Crassulacean acid metabolism plant Mesembryanthemum crystallinum L. Plant Physiol 108:1185–1195CrossRefGoogle Scholar
  29. Giovannoni J (2001) Molecular biology of fruit maturation and ripening. Annu Rev Plant Physiol Plant Mol Biol 52:725–749CrossRefPubMedGoogle Scholar
  30. Girke T, Todd J, White J, Benning C, Ohlrogge J (2000) Microarray analysis of developing Arabidopsis seeds. Plant Physiol 124:1570–1581CrossRefPubMedGoogle Scholar
  31. Hanson J, Johannesson H, Engtröm P (2001) Sugar-dependent alterations in cotyledon and leaf development in transgenic plants expressing the HDZhdip gene ATHB13. Plant Mol Biol 45:247–262CrossRefPubMedGoogle Scholar
  32. Hara K, Yagi M, Koizumi N, Kusano T, Sano H (2000) Screening of wound-responsive genes identifies an immediate-early expressed gene encoding a highly charged protein in mechanically wounded tobacco plants. Plant Cell Physiol 41:684–691CrossRefPubMedGoogle Scholar
  33. Hawker JS (1969) Changes in the activities of enzymes concerned with sugar metabolism during the development of grape berries. Phytochemistry 8:9–17CrossRefGoogle Scholar
  34. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877CrossRefPubMedGoogle Scholar
  35. Ishimaru M, Kobayashhi S (2002) Expression of a xyloglucan endo-transglycosylase gene is closely related to grape berry softening. Plant Science 162:621–628CrossRefGoogle Scholar
  36. Jaglo-Ottosen KR, Gilmour SJ, Zarka DG, Schabenberger O, Thomashow MF (1998) Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science 280:104–106CrossRefPubMedGoogle Scholar
  37. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci 123:403–405CrossRefGoogle Scholar
  38. Jeong ST, Goto-Yamamoto N, Kobayashi S, Esaka M (2004) Effects of plant hormones and shading on the accumulation of anthocyanins and the expression of anthocyanin biosynthetic genes in grape berry skins. Plant Science 167:247–252CrossRefGoogle Scholar
  39. Jimenez A, Creissen G, Kular B, Firmin J, Robinson S, Verhoeyen M, Mullineaux P (2002) Changes in oxidative processes and components of the antioxidant system during tomato fruit ripening. Planta 214:751–758CrossRefPubMedGoogle Scholar
  40. Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, Madore SJ (2000) Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 28:4552–4557PubMedCrossRefGoogle Scholar
  41. Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1999) Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nat Biotechnol 17:287–291CrossRefPubMedGoogle Scholar
  42. Kennedy JA, Hayasaka Y, Vidal S, Waters EJ, Jones GP (2001) Composition of grape skin proanthocyanidins at different stages of berry development. J Agric Food Chem 49:5348–5355CrossRefPubMedGoogle Scholar
  43. Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 304:982CrossRefPubMedGoogle Scholar
  44. Lal SK, Lee C, Sachs MM (1998) Differential regulation of enolase during anaerobiosis in maize. Plant Physiol 118:1285–1293CrossRefPubMedGoogle Scholar
  45. Lee H, Guo Y, Ohta M, Xiong L, Stevenson B, Zhu J (2002) LOS2, a genetic locus required for cold-responsive gene transcription encodes a bi-functional enolase. EMBO J 21:2692–2702CrossRefPubMedGoogle Scholar
  46. Lers A, Burd S, Lomaniec E, Droby S, Chalutz E (1998) The expression of a grapefruit gene encoding an isoflavone reductase-like protein is induced in response to UV. Plant Mol Biol 36:847–856CrossRefPubMedGoogle Scholar
  47. Martin C, Prescott A, Mackay S, Bartlett J, Vrijlandt E (1991) Control of anthocyanin biosynthesis in flowers of Antirrhinum majus. Plant J 1:37–49PubMedCrossRefGoogle Scholar
  48. Mellema S, Eichenberger W, Rawyler A, Suter M, Tadege M, Kuhlemeier C (2002) The ethanolic fermentation pathway supports respiration and lipid biosynthesis in tobacco pollen. Plant J 30:329–336CrossRefPubMedGoogle Scholar
  49. Nguyen-Quoc B, Foyer CH (2001) A role for ’futile cycles’ involving invertase and sucrose synthase in sucrose metabolism of tomato fruit. J Exp Bot 52:881–889CrossRefPubMedGoogle Scholar
  50. Nunan KJ, Davies C, Robinson SP, Fincher GB (2001) Expression patterns of cell wall-modifying enzymes during grape berry development. Planta 214:257–264PubMedCrossRefGoogle Scholar
  51. Ojeda H, Deloire A, Carbonneau A, Ageorges A, Romieu C (1999) Berry development of grapevines: Relation between the growth of berries and their DNA indicate cell multiplication and enlargement. Vitis 38:145–150Google Scholar
  52. Or E, Baybik J, Sadka A, Saks Y (2000) Isolation of mitochondrial malate dehydrogenase and phosphoenolpyruvate carboxylase cDNA clones from grape berries and analysis of their expression pattern throughout berry development. J Plant Physiol 157:527–534Google Scholar
  53. Park JM, Park CJ, Lee SB, Ham BK, Shin R, Paek KH (2001) Overexpression of the tobacco Tsi1 gene encoding an EREBP/AP2-type transcription factor enhances resistance against pathogen attack and osmotic stress in tobacco. Plant Cell 13:1035–1046CrossRefPubMedGoogle Scholar
  54. Picaud S, Becq F, Dédaldéchamp F, Ageorges A, Delrot S (2003) Cloning and expression ot two plasma membrane aquaporins expressed during the ripening of grape berry. Funct Plant Biol 30:621–630CrossRefGoogle Scholar
  55. Rajeevan MS, Ranamukhaarachchi DG, Vernon SD and Unger ER (2001) Use of real-Time quantitative PCR to validate the results of cDNA array and differential display PCR technologies. Methods 25:443–451CrossRefPubMedGoogle Scholar
  56. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277CrossRefPubMedGoogle Scholar
  57. Richmond T, Somerville S (2000) Chasing the dream: plant EST microarray. Curr Opin Plant Biol 3:108–116CrossRefPubMedGoogle Scholar
  58. Robinson SP, Jacobs AK, Dry IB (1997). A Class IV chitinase is highly expressed in grape berries during ripening. Plant Physiol 114:771–778CrossRefPubMedGoogle Scholar
  59. Salzman RA, Tikhonova I, Bordelon BP, Hasegawa PM, Bressan RA (1998) Coordinate accumulation of antifungal proteins and hexoses constitutes a developmentally controlled defence response during fruit ripening in grape. Plant Physiol 117:465–72CrossRefPubMedGoogle Scholar
  60. Sarni-Manchado P, Verries C, Tesnière C. (1997) Molecular characterization and structural analysis of one alcohol dehydrogenase gene (GV–Adh1) expressed during ripening of grapevine (Vitis vinifera L.) berry. Plant Sci 125:177–187CrossRefGoogle Scholar
  61. Sarry JE, Sommerer N, Sauvage FX, Bergoin A, Rossignol M, Albagnac G, Romieu C (2004) Grape berry biochemistry revisited upon proteomic analysis of the mesocarp. Proteomics 4:201–215CrossRefPubMedGoogle Scholar
  62. Sparvoli F, Martin C, Scienza A, Gavazzi G, Tonellin C (1994) Cloning and molecular analysis of structural genes involved in flavonoid biosynthesis in grape (Vitis vinifera L.). Plant Mol Biol 24:743–755CrossRefPubMedGoogle Scholar
  63. Tattersall DB, van Heeswijck R, Høj PB (1997) Identification and characterization of a fruit-specific, thaumatin-like protein that accumulates at very high level in conjunction with the onset of sugar accumulation and berry softening in grapes. Plant Physiol 114:759–769CrossRefPubMedGoogle Scholar
  64. Terrier N, Romieu C (2001) Grape berry acidity. In: K Roubelakis-Angelakis KA (ed) Molecular biology and biotechnology of the grapevine. Kluwer, Dordrecht, pp 35–57Google Scholar
  65. Terrier N, Sauvage FX, Ageorges A, Romieu C (2001a) Changes in acidity and in proton transport at the tonoplast of grape berries during development. Planta 213:20–28CrossRefGoogle Scholar
  66. Terrier N, Ageorges A, Abbal P, Romieu C (2001b) Generation of ESTs from grape berry at various developmental stages. J Plant Physiol 158:1575–1583CrossRefGoogle Scholar
  67. Tesnière C, Verries C (2000) Molecular cloning and expression of cDNAs encoding alcohol dehydrogenases from Vitis vinifera L. during berry development. Plant Sci 157:77–88CrossRefPubMedGoogle Scholar
  68. Tesnière C, Romieu C, Dugelay I, Nicol MZ, Flanzy C, Robin JP (1994) Partial recovery of grape energy metabolism upon aeration following anaerobic stress. J Exp Bot 45:145–151CrossRefGoogle Scholar
  69. Umeda M, Uchimiya H (1994) Differential transcript levels of genes associated with glycolysis and alcohol fermentation in rice plants (Oryza sativa L.) under submergence stress. Plant Physiol 106:1015–1022PubMedGoogle Scholar
  70. Vroemen CW, Mordhorst AP, Albrecht C, Kwaaitaal MA, de Vries SC (2003) The CUP-SHAPED COTYLEDON3 gene is required for boundary and shoot meristem formation in Arabidopsis. Plant Cell 15:1563–1577CrossRefPubMedGoogle Scholar
  71. Wang R, Okamoto M, Xing X, Crawford NM (2003) Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1000 rapidly responding genes and linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism. Plant Physiol 132:556–557CrossRefPubMedGoogle Scholar
  72. Weschke W, Panitz R, Gubatz S, Wang Q, Radchuk R, Weber H, Wobus U (2003) The role of invertases and hexose transporters in controlling sugar ratios in maternal and filial tissues of barley caryopses during early development. Plant J 33:395–411CrossRefPubMedGoogle Scholar
  73. White PJ (2002) Recent advances in fruit development and ripening: an overview. J Exp Bot 53:1995–2000CrossRefPubMedGoogle Scholar
  74. Yang YH, Speed T (2002) Design issues for cDNA microarray experiments. Nature Rev Gen 3:579–588Google Scholar

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Nancy Terrier
    • 1
  • David Glissant
    • 2
  • Jérôme Grimplet
    • 1
  • François Barrieu
    • 3
  • Philippe Abbal
    • 1
  • Carole Couture
    • 3
  • Agnès Ageorges
    • 1
  • Rossitza Atanassova
    • 2
  • Céline Léon
    • 3
  • Jean-Pierre Renaudin
    • 3
  • Fabienne Dédaldéchamp
    • 2
  • Charles Romieu
    • 1
    Email author
  • Serge Delrot
    • 2
  • Saïd Hamdi
    • 3
  1. 1.Unité Mixte de Recherche S.P.O.Biologie Intégrative de la Vigne et du Raisin, I.N.R.A.Montpellier Cedex 1France
  2. 2.Unité Mixte de Recherche C.N.R.S. 6161, Transport des AssimilatsUniversité de Poitiers, Laboratoire de Physiologie, Biochimie et Biologie Moléculaire VégétalesPoitiersFrance
  3. 3.UMR 619, Equipe Biologie de la VigneUniversité de Bordeaux 1Villenave d’Ornon CedexFrance

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