Skip to main content

Identification of Strawberry Flavour Related Genes by the Use of DNA Microarrays

  • Chapter
Molecular Techniques in Crop Improvement

Abstract

RNA-based assessment of gene expression provides essential clues to the elucidation of gene function. The current availability of complete genome sequences and of large sets of Expressed Sequence Tags (ESTs) from numerous organisms has triggered the development of efficient and accurate methods for large-scale and genome-wide analyses of genetic variation and gene expression patterns. As a result, several novel methods either sequence-based (Brenner et al., 2000; Velculescu et al.,1995), fragment-based (Bachem et al.,1996; Shimkets et al., 1999) or hybridisation-based such as macro- and microarrays (Desprez et al., 1998; Lockhart et al.,1996; Schena et al., 1995) are currently available (see also Breyene and Zabeau, 2001).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 74.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Aharoni, A., Keizer, L.C.P., Bouwmeester, H.J., Sun, Z.K., Alvarez Huerta, M., Verhoeven, H.A., Blaas, J., van Houwelingen, A., De Vos, R.C.H., van der Voet, H., Jansen, R.C., Guis, M., Mol, J., Davis, R.W., Schena, M., van Tunen, A.J., and O’Connell A.P. 2000. Identification of the SAAT gene involved in strawberry flavour biogenesis by use of DNA microarrays. Plant Cell 12: 647–661.

    PubMed  CAS  Google Scholar 

  • Alizadeh, A.A., Eisen, M.B., Davis, R.E., Ma, C., Lossos, I.S., Rosenwald, A., Boldrick, J.G., Sabet, H., Tran, T., Yu, X., Powell, J.1., Yang, L.M., Marti, G.E., Moore, T., Hudson, J., Lu, L.S., Lewis, D.B., Tibshirani, R., Sherlock, G., Chan, W.C., Greiner, T.C., Weisenburger, D.D., Armitage, J.O., Warnke, R., Levy, R., Wilson, W., Grever, M.R., Byrd, J.C., Botstein, D., Brown, P.O., and Staudt, L.M. 2000. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403: 503–511.

    Article  PubMed  CAS  Google Scholar 

  • Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403–410.

    Google Scholar 

  • Arimura, G., Tashiro, K., Kuhara, S., Nishioka, T., Ozawa, R., and Takabayashi, J. 2000. Gene responses in bean leaves induced by herbivory and by herbivore-induced volatiles. Biochem. Biophys. Res. Commun. 277: 305–310.

    Google Scholar 

  • Bachem, C.W.B., Van Der Hoeven, R.S., De Bruijn, S.M., Vreugdenhil, D., Zabeau, M., and Visser, R.G.F. 1996. Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: Analysis of gene expression during potato tuber development. Plant J. 9: 745–753.

    Google Scholar 

  • Bauchot, A.D., Mottram, D.S., Dodson, A.T., and John, P. 1998. Effect of aminocyclopropane-l-carboxylic acid oxidase antisense gene on the formation of volatile esters in Cantaloupe Charentais melon (cv. Vedrandais). J. Agric. Food Chem. 46: 4787–4792.

    Google Scholar 

  • Bojorquez G., and Gomez-Lim M.A. 1995. Peroxisomal thiolase mRNA is induced during mango fruit ripening. Plant Mol. Biol. 28: 811–820.

    CAS  Google Scholar 

  • Bouwmeester, H.J., Verstappen, F.W.A., Posthumus M.A., and Dicke, M. 1999. Spider mite-induced (3S)-(E)-nerolĂ¯dol synthase activity in cucumber and lima bean. The first dedicated step in acyclic Cl l-homoterpene biosynthesis. Plant Physiol. 121: 173–180.

    Google Scholar 

  • Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D.H., Johnson, D., Luo, S.J., McCurdy, S., Foy, M., Ewan, M., Roth, R., George, D., Eletr, S., Albrecht, G., Vermaas, E., Williams, S.R., Moon, K., Burcham, T., Pallas, M., DuBridge, R.B., Kirchner, J., Fearon, K., Mao, J., and Corcoran, K. 2000. Gene expression analysis by massively parallel signature sequencing ( MPSS) on microbead arrays. Nature Biotech. 18: 630–634.

    Google Scholar 

  • Breyne, P., and Zabeau, M. 2001. Genome-wide expression analysis of plant cell cycle modulated genes. Curr. Opin. Plant Biol. 4: 136–142.

    Google Scholar 

  • Brown, P.O., and Botstein, D. 1999. Exploring the new world of the genome with DNA microarrays. Nature Genet. 21 Suppl.: 33–37.

    Google Scholar 

  • Croteau R., and Karp F. 1994. Origin of Natural Odorants. In: Muller PM and Lamparsky D (eds.) Perfumes: art, science, and technology. Blackie Academic and Professional, an imprint of Chapman and Hall, Glasgow.

    Google Scholar 

  • DeRisi, J.L., lyer, V.R., and Brown, P.O. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680–686.

    Article  PubMed  CAS  Google Scholar 

  • Desprez, T., Amselem, J., Caboche, M., and Hofte, H. 1998. Differential gene expression in Arabidopsis monitored using cDNA arrays. Plant J. 14: 643–652.

    Article  PubMed  CAS  Google Scholar 

  • Diatchenko, L., Lau, Y.F.C., Campbell, A.P., Chenchik, A., Moqadam, F., Huang, B., Lukyanov, S., Lukyanov, K., Gurskaya, N., Sverdlov, E.D., and Siebert, P.D. 1996. Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93: 6025–6030.

    Google Scholar 

  • Dudareva, N., D’Auria, 1.C., Nam, K.H., Raguso, R.A., and Pichersky, E. 1998. AcetylCoA:benzylalcohol acetyltransferase–an enzyme involved in floral scent production in Clarkia breweri. Plant J. 14: 297–304.

    CAS  Google Scholar 

  • Duggan, D.J., Bittner, M., Chen, Y.D., Meltzer, P., and Trent, J.M. 1999. Expression profiling using cDNA microarrays. Nature Genet. 21 Suppl.: 10–14.

    Google Scholar 

  • Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 96: 10943.

    Google Scholar 

  • Fodor, S.P.A., Read, J.L., Pirrung, M.C., Stryer, L., Lu, A.T., and Solas, D. 1991. Light-directed, spatially addressable parallel chemical synthesis. Science 251: 767–773.

    Article  PubMed  CAS  Google Scholar 

  • Fujii, T., Nagasawa, N., Iwamatsu, A., Bogaki, T., Tamai, Y., and Hamachi, M. 1994. Molecular cloning, sequence analysis, and expression of the yeast alcohol acetyltransferase gene. Appl. Environ. Microbiol. 60: 2786–2792.

    Google Scholar 

  • Fujii, T., Yoshimoto, H., Nagasawa, N., Bogaki, T., Tamai, Y., and Hamachi, M. 1996. Nucleotide sequences of alcohol acetyltransferase genes from lager brewing yeast, Saccharomyces carlsbergensis. Yeast 12: 593–598.

    Google Scholar 

  • Girke, T., Todd, J., Ruuska, S., White, J., Benning, C., and Ohlrogge, J. 2000. Microarray analysis of developing Arabidopsis seeds. Plant Physiol. 124: 1570–1581.

    Article  PubMed  CAS  Google Scholar 

  • Given, N.K., Venis, M.A., and Grierson, D. 1988. Hormonal regulation of ripening in the strawberry, a non-climacteric fruit. Planta 174: 402–406.

    Article  CAS  Google Scholar 

  • Harada, M., Ueda, Y., and Iwata, T. 1985. Purification and some properties of alcohol acetyltransferase from banana fruit. Plant Cell Physiol. 26: 1067–1074.

    CAS  Google Scholar 

  • Harmer, S.L., Hogenesch, L.B., Straume, M., Chang, H.S., Han, B., Zhu, T., Wang, X., Kreps, J.A., and Kay, S.A. 2000. Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290: 2110–2113.

    Article  PubMed  CAS  Google Scholar 

  • Harpster, M.H., Brummell, D.A., and Dunsmuir, P. 1998. Expression analysis of a ripening-specific, auxin-repressed endo-1, 4-beta-glucanase gene in strawberry. Plant Physiol. 118: 1307–1316.

    CAS  Google Scholar 

  • Hertzberg, M., Sievertzon, M., Aspeborg, H., Nilsson, P., Sandberg, G., and Lundeberg, J. 2001. cDNA microarray analysis of small plant tissue samples using a cDNA tag target amlification protocol. Plant J. 25: 585–591.

    Google Scholar 

  • Honkanen, E., and Hirvi, T. 1990. The flavour of berries. Dev. Food Sci. Amsterdam: Elsevier Scientific Publications.

    Google Scholar 

  • Jiang, M., Ryu, J., Kiraly, M., Duke, K., Reinke, V., and Kim, S.K. 2001. Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proc. Natl Acad. Sci. USA 98: 218–223.

    Google Scholar 

  • Kane, M.D., Jatkoe, T.A., Stumpf, C.R., Lu, J., Thomas, J.D., and Madore, S.J. 2000. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucl. Acids Res. 28: 4552–4557.

    Google Scholar 

  • Lander, E.S. 1999. Array of hope. Nature Genet. 21 Suppl.: 3–4.

    Google Scholar 

  • Lashkari, D.A., DeRisi, J.L., McCusker, J.H., Namath, A.F., Gentile, C., Hwang, S.Y., Brown, P.O., and Davis, R.W. 1997. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl Acad. Sci. USA 94: 13057–13062.

    Google Scholar 

  • Lipshutz, R.J., Fodor, S.P.A., Gingeras, T.R., and Lockhart, D.J. 1999. High density synthetic oligonucleotide arrays. Nature Genet. 21 Suppl.: 20–24.

    Google Scholar 

  • Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H., and Brown, E.L. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotech. 14: 1675–1680.

    Article  CAS  Google Scholar 

  • Maarse, H. 1991. Volatile compounds in foods and beverages. Marcel Dekker, Inc., New York.

    Google Scholar 

  • Maleck, K., Levine, A., Eulgem, T., Morgan, A., Schmid, J., Lawton, K.A., Dangl, J.L., and Dietrich, R.A. 2000. The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nature Genet. 26: 403–410.

    Article  PubMed  CAS  Google Scholar 

  • Manning, K. 1994. Changes in gene expression during strawberry fruit ripening and their regulation by auxin. Planta 194: 62–68.

    Article  CAS  Google Scholar 

  • Manning, K. 1998. Isolation of a set of ripening-related genes from strawberry: their identification and possible relationship to fruit quality traits. Planta 205: 622–631.

    Article  PubMed  CAS  Google Scholar 

  • Mir, K.U., and Southern, E.M. 1999. Determining the influence of structure on hybridization using oligonucleotide arrays. Nature Biotech. 17: 788–792.

    Article  CAS  Google Scholar 

  • Moyano, E., Portero-Robles, I., Medina-Escobar, N., Valpuesta, V., Munoz-Blanco, J., and Caballero J.L. 1998. A fruit-specific putative dihydroflavonol 4-reductase gene is differentially expressed in strawberry during the ripening process. Plant Physiol. 117: 711–716.

    Article  PubMed  CAS  Google Scholar 

  • Okamoto, T., Suzuki, T., and Yamamoto, N. 2000. Microarray fabrication with covalent attachment of DNA using Bubble Jet technology. Nature Biotech. 18: 438–441.

    Article  CAS  Google Scholar 

  • Olias, J.M., Sanz, C., Rios, J.J., and Perez, A.G. 1995. Substrate specificity of alcohol acyltransferase from strawberry and banana fruits. ACS symposium series.

    Google Scholar 

  • Perez, A.G., Rios, J.J., Sanz, C., and Olias, J.M.. 1992. Aroma components and free amino acids in strawberry variety Chandler during ripening. J. Agric. Food Chem. 40; 22322235.

    Google Scholar 

  • Perez, A.G., Sanz, C., and Olias. J.M. 1993. Partial purification and some properties of alcohol acyltransferase from strawberry fruits. J. Agric. Food Chem. 41: 1462–1466.

    Google Scholar 

  • Perez, A.G., Sanz, C., Olias, R., Rios, J.J. and Olias, J.M. 1996. Evolution of strawberry alcohol acyltransferase activity during fruit development and storage. J. Agric. Food Chem. 44: 3286–3290.

    Google Scholar 

  • Perez, A,G., Sanz, C., Olias, R., and Olias, J.M. 1999. Lipoxygenase and hydroperoxide lyase activities in ripening strawberry fruits. J. Agric. Food Chem. 47: 249–253.

    Google Scholar 

  • Reymond, P., Weber, H., Damond, M., and Farmer E.E. 2000. Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis. Plant Cell 12: 707–719.

    PubMed  CAS  Google Scholar 

  • Roscher, R., Schreier, P., and Schwab. W. 1997. Metabolism of 2,5-dimethyl-4-hydroxy3(2H)-furanone in detached ripening strawberry fruits. J. Agric. Food Chem. 45: 3202–3205.

    Google Scholar 

  • Ruan, Y., Gilmore, J., and Conner, T. 1998. Towards Arabidopsis genome analysis: Monitoring expression profiles of 1400 genes using cDNA microarrays. Plant J. 15: 821–833.

    Article  PubMed  CAS  Google Scholar 

  • Schaffer, R., Landgraf, J., Accerbi, M., Simon, V., Larson, M., and Wisman, E. 2001. Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell 13: 113–123.

    PubMed  CAS  Google Scholar 

  • Scharpf, L.G.Jr., and Chandan, R.C. 1989. Biotechnology and natural flavours for yogurt. National Yogurt Association, Virginia, USA.

    Google Scholar 

  • Schena, M., Shalon, D., Davis, R.W., and Brown, P.O. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467–470.

    Article  PubMed  CAS  Google Scholar 

  • Schenk, P.M., Kazan, K., Wilson, I., Anderson, J.P., Richmond, T., Somerville, S.C., and Manners, J.M. 2000. Coordinated plant defense responses in Arabidopsis revealed by microarray analysis. Proc. Natl Acad. Sci. USA 97: 11655–11660.

    Google Scholar 

  • Schwab, W. 1998. Application of stable isotope ratio analysis explaining the bioformation of 2,5-dimethyl-4-hydroxy-3(2H)-furanone in plants by a biological Maillard reaction. J. Agric. Food Chem. 46: 2266–2269.

    Google Scholar 

  • Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Shinozaki, K., Carninci, P., Hayashizaki, Y., and Shinozaki, K. 2001. Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13: 61–72.

    PubMed  CAS  Google Scholar 

  • Seymour, G.B., Taylor, J.E., and Tucker, G.A. 1993. Biochemistry of fruit ripening. Chapman and Hall, London.

    Book  Google Scholar 

  • Shimkets, R.A., Lowe, D.G., Tai, J.T., Sehl, P., Jin, H., Yang, R., Predki, P.F., Rothberg, B.E., Murtha, M.T., Roth, M.E., Shenoy, S.G., Windemuth, A., Simpson, J.W., Simons, J.F., Daley, M.P., Gold, S.A., McKenna, M.P., Hillan, K., Went, G.T., and Rothberg, J.M. 1999. Gene expression analysis by transcript profiling coupled to a gene database query. Nature Biotech. 17: 798–803.

    Article  CAS  Google Scholar 

  • St-Pierre, B., Laflamme, P., Alarco, A.M., De-Luca, V. 1998. The terminal Oacetyltransferase involved in vindoline biosynthesis defines a new class of proteins responsible for coenzyme A-dependent acyl transfer. Plant J. 14: 703–713.

    Article  PubMed  CAS  Google Scholar 

  • Ueda, Y., Tsuda, A., Bai, J.H., Fujishita, N., and Chachin, K. 1992. Characteristic pattern of aroma ester formation from banana, melon, and strawberry with reference to the substrate specificity of ester synthetase and alcohol contents in pulp. J. Jpn. Soc. Food Sci. Technol.: 183–187.

    Google Scholar 

  • Velculescu, V.E., Zhang, L., Vogelstein, B., and Kinzler, K.W. 1995. Serial analysis of gene expression. Science 270: 484–487.

    Article  PubMed  CAS  Google Scholar 

  • Wang, C.L., Chin, C.K., Ho, C.T., Hwang, C.F., Polashock, J.J., and Martin, C.E. 1996. Changes of fatty acids and fatty acid-derived flavour compounds by expressing the yeast Delta-9 desaturase gene in tomato. J. Agric. Food Chem. 44: 3399–3402.

    Google Scholar 

  • Wang, R., Guegler, K., LaBrie Samuel, T., and Crawford N.M. 2000. Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate. Plant Cell 12: 1491–1509.

    PubMed  CAS  Google Scholar 

  • Welford, S.M., Gregg, J., Chen, E., Garrison, D., Sorensen, P.H., Denny, C.T., and Nelson, S.F. 1998. Detection of differentially expressed genes in primary tumor tissues using representation differences analysis coupled to microarray hybridization. Nucl. Acids Res. 26: 3059–3065.

    Google Scholar 

  • Wintoch, H., Krammer, G., and Schreier, P. 1991. Glycosidically bound aroma compounds from two strawberry fruit species, Fragaria vesca f. semperflorens and Fragaria ananassa, cultivar Korona. Flavour Fragrance J. 6: 209–216.

    Article  CAS  Google Scholar 

  • Wisman, E., and Ohlrogge, J. 2000. Arabidopsis microarray service facilities. Plant Physiol. 124: 1468–1471.

    Google Scholar 

  • Woodward, J.R. 1972. Physical and chemical changes in developing strawberry fruits. J Sci. Food Agric. 23: 465–473.

    Google Scholar 

  • Yamakawa. Y., Goto, S., and Yokotsuka, I. 1978. Fractionation and some properties of acetic-ester synthesizing enzyme from Cladosporium cladosporioides No.9. Agric. Biol. Chem. 42: 269–274.

    Google Scholar 

  • Yang, G.P., Ross, D.T., Kuang, W.W., Brown, P.O. and Weigel, R.J. 1999. Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes. Nucl. Acids Res. 27: 1517–1523.

    Google Scholar 

  • Yoshioka, K., and Hashimoto, N. 1984. Ester formation by brewers’ yeast during sugar fermentation. Agric. Biol. Chem. 45: 333–340.

    Google Scholar 

  • Zabetakis I and Holden MA (1997) Strawberry flavour: analysis and biosynthesis. J. Sci. Food Agric. 74: 431–434.

    Article  Google Scholar 

  • Zhu, T. and Wang, X. 2000. Large-scale profiling of the Arabidopsis transcriptome. Plant Physiol. 124: 1472–1476.

    Article  PubMed  CAS  Google Scholar 

  • Zou, S., Meadows, S., Sharp, L., Jan, L.Y. and Jan, Y.N. 2000. Genome-wide study of aging and oxidative stress response in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 97: 13726–13731.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2002 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Aharoni, A., O’Connell, A.P. (2002). Identification of Strawberry Flavour Related Genes by the Use of DNA Microarrays. In: Jain, S.M., Brar, D.S., Ahloowalia, B.S. (eds) Molecular Techniques in Crop Improvement. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-2356-5_17

Download citation

  • DOI: https://doi.org/10.1007/978-94-017-2356-5_17

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-90-481-5982-6

  • Online ISBN: 978-94-017-2356-5

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics