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Application of Genomics in Agriculture

  • Chapter
Molecular Analysis of Plant Adaptation to the Environment

Part of the book series: Springer Handbook Series of Plant Ecophysiology ((KLEC,volume 1))

Abstract

The goals of agricultural plant science are to increase crop productivity and the quality of agricultural products and to protect the environment by maintaining a system of sustainable agriculture that preserves the ecological basis of plant production. These goals have significant economic implications, which are affected by environmental conditions. The inherent diversity among plant species demonstrates clearly that plants are able to adapt to environmental stresses using genetically based programs Crop improvement, i.e. the optimisation of plant features and performance according to agricultural needs, has been undertaken for hundred’s of years: agronomists, breeders, and gardeners have used classical plant breeding methods based on selection of natural variants to improve genetic sources. Methods and techniques developed in molecular biology in recent years, especially reliable transformation systems for essentially all crops and growing numbers of complete genome sequences of higher plants, are providing tools to support plant breeding strategies and allowing scientists to tackle as yet unsolved problems or to speed up breeding programmes. Such tools will extend plant breeding by introducing new, unanticipated traits, in order to develop plants in which both crop productivity and stress tolerance are enhanced.

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References

  • Aharoni, A., Keizer, L.C.P., Bouwmeester, H.J., Sun, Z.K., Alvarez-Huerta, M., Verhoeven, H.A., Blaas, J., van Houwelingen, A.M.M.L., 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 flavor biogenesis by use of DNA micro-arrays. Plant Cell 12, 7–661.

    Google Scholar 

  • Azevedo, E. and Fereres, E. 1993. “Resistance to abiotic stresses”. In: Plant Breeding, eds. M.D. Hayward, N.O. Bosemark and I. Romagosa, pp. 406–412. Chapman and Hall, London.

    Chapter  Google Scholar 

  • Azpiroz-Leehan, R. and Feldmann, K.A. 1997. T-DNA insertion mutagenesis in Arabidopsis: going back and forth. Trends Genet. 13, 2–156.

    Article  Google Scholar 

  • Bachem, C.W.B., Vanderhoeven, R.S., Debruijn, 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.

    Article  PubMed  CAS  Google Scholar 

  • Baldwin, D., Crane, V. and Rice, D. 1999. A comparison of gel-based, nylon filter and micro-array techniques to detect differential RNA expression in plants. Curr. Opin. Plant Biol 2, 96–103.

    Article  PubMed  CAS  Google Scholar 

  • Bassett, D.E., Eisen, M.B. and Boguski, M.S. 1999. Gene expression informatics–it’s all in your mine. Nature Genet. 21, 51–55.

    Article  PubMed  CAS  Google Scholar 

  • Bevan, M., Bancroft, I., Bent, E., Love, K., Goodman, H., Dean, C., Bergkamp, R., Dirkse, W., Vanstaveren, M., Stiekema, W., Drost, L., Ridley, P., Hudson, S.A., Patel, K., Murphy, G., Piffanelli, P., et al,1998. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391, 485–488.

    Google Scholar 

  • Blaszczyk, A., Brodzik, R and Sirko, A. 1999. Increased resistance to oxidative stress in transgenic tobacco plants overexpressing bacterial serine acetyltransferase. Plant J. 20, 237–243.

    Article  PubMed  CAS  Google Scholar 

  • Bohnert, H.J. and Sheveleva, E. 1998. Plant stress adaptations–making metabolism move. Curr. Opin. Plant Biol 1, 267–274.

    Article  PubMed  CAS  Google Scholar 

  • Boyer, J.S. 1982. Plant productivity and environment. Science 218, 443–448.

    Article  PubMed  CAS  Google Scholar 

  • Cooke, R., Raynal, M., Laudie, M., Grellet, F., Delseny, M., Moms, P.C., Guerrier, D., Giraudat, J., Quigley, F., Clabault, G., Li, Y.F., Mache, R., Krivitzky, M., Gy, I.J.J., Kreis, M., Lecharny, A., Parmentier, Y., Marbach, J., Fleck, J., Clement, B., Philipps, G., Herve, C., Bardet, C., Tremousaygue, D., Lescure, B., Lacomme, C., Roby, D., Jourjon, M-F., Chabrier, P., Charpenteau, J-L., Desprez, T., Amselem, J., Chiapello, H. and Höfte, H. 1996. Further progress towards a catalogue of all Arabidopsis genes–analysis of a set of 5000 non-redundant ESTs. Plant J. 9, 101–124.

    Article  PubMed  CAS  Google Scholar 

  • Burke, D.T., Carle, G.F. and Olson, M.V. 1987. Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236, 806–12.

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • DellaPenna, D. 1999. Nutritional genomics: manipulating plant micronutrients to improve human health. Science 285, 375–379.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Eisen, M.B. and Brown, P.O. 1999. DNA arrays for analysis of gene expression. Methods Enzymol. 303, 179–205.

    Article  PubMed  CAS  Google Scholar 

  • Ermolaeva, O., Rastogi, M., Pruitt, K.D., Schuler, G.D., Bittner, M.L., Chen, Y.D., Simon, R., Meltzer, P., Trent, J.M. and Boguski, M.S. 1998. Data management and analysis for gene expression arrays. Nature Genet. 20, 19–23.

    Article  PubMed  CAS  Google Scholar 

  • Ewing, R.M., Ben Kahla, A., Poirot, O., Lopez, F., Audic, S. and Claverie, J.M. 1999. Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9, 950–959.

    Article  PubMed  CAS  Google Scholar 

  • Flowers, T.J. and Yeo, A.R. 1995. Breeding for salinity resistance in crop plants: where next? Aust. J. Plant Physiol 22, 875–884.

    Article  Google Scholar 

  • Foodlad, M.R. 1999. Comparison of salt tolerance during seed germination and vegetative growth in tomato by QTL mapping. Genome 42, 727–734.

    Article  Google Scholar 

  • Frova, C., Krajewski, P., di Fonzo, N., Villa, M. and San-Gorla, M. 1999. Genetic analysis of drought tolerance in maize by molecular markers. 1. Yield components. Theor. Appl. Genet 99, 280–288.

    Article  Google Scholar 

  • Frova, C., Caffulli, A. and Pallavera, E. 1999. Mapping quantitative trait loci for tolerance to abiotic stresses in maize. J. Exp. Zool 282, 164–170.

    Article  Google Scholar 

  • Granjeaud, S., Bertucci, F. and Jordan, B.R. 1999. Expression profiling: DNA arrays in many guises. Bioessays 21, 781–790.

    Article  PubMed  CAS  Google Scholar 

  • Guyer, D., Patton, D. and Ward, E. 1995. Evidence for cross-pathway regulation of metabolic gene expression in plants. Proc. Natl. Acad. Sci. USA 92, 4997–5000.

    Article  PubMed  CAS  Google Scholar 

  • Harms, K., von Ballmoos, P., Brunold, C., Höfgen, R. and Hesse, H. 2000. Expression of a bacterial serine acetyltransferase in transgenic potato plants leads to increased levels of cysteine and glutathione. Plant J. 22, 335–343.

    Article  PubMed  CAS  Google Scholar 

  • Hawkesford, M.J. 2000. Plant responses to sulphur deficiency and the genetic manipulation of sulphate transporters to improve S-utilization efficiency. J. Exp. Bot 51, 131–138.

    Article  PubMed  CAS  Google Scholar 

  • Holmberg, N. and Bülow, L. 1998. Improving stress tolerance in plants by gene transfer.Trends Plant Sci 3, 61–66.

    Article  Google Scholar 

  • Ingram, J., and Bartels, D. 1996. The molecular basis of dehydration tolerance in plants. Ann. Rev. Plant Physiol. Plant Mol. Biol 47, 377–403.

    Article  CAS  Google Scholar 

  • Kasuga, M., Liu. Q., Miura, S., Yamaguchi-Shinozaki, K. and Shinozaki, K. 1999. Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nature Biotech 17, 287–291.

    CAS  Google Scholar 

  • Kozian, D.H. and Kirschbaum, B.J. 1999. Comparative gene-expression analysis. Trends in Biotech. 17, 73–78.

    Article  CAS  Google Scholar 

  • Kehoe, D.M., Villand, P. and Somerville, S. 1999. DNA micro-arrays for studies of higher plants and other photosynthetic organisms. Trends Plant Sci. 4, 38–41.

    Article  PubMed  Google Scholar 

  • Kush, G.S. 1999. Green revolution: preparing for the 215` century. Genome 42, 646–655. Liang. P. and Pardee, A,B, 1992. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257, 967–71.

    Google Scholar 

  • Lemieux, B., Aharoni, A. and Schena, M. 1998. Overview of DNA chip technology. Mol. Breed 4, 277–289.

    Article  CAS  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, 20–24.

    Article  PubMed  CAS  Google Scholar 

  • Malik, M.K., Slovin, J.P., Hwang, C.H. and Zimmerman, J.L. 1999. Modified expression of a carrot small heat shock protein gene, Hsp17.7, results in increased or decreased thermotolerance. Plant J. 20, 89–99.

    Article  PubMed  CAS  Google Scholar 

  • Martienssen, R.A. 1998. Functional genomics–probing plant gene function and expression with transposons. Proc. Natl. Acad. Sci. USA 95, 2021–2026.

    Article  PubMed  CAS  Google Scholar 

  • Mazur, B., Krebbers, E. and Tingey, S. 1999 Gene discovery and product development for grain quality traits. Science 285, 372–375.

    Article  PubMed  CAS  Google Scholar 

  • McNeil, S.D., Nuccio, M.L. and Hanson, A.D. 1999. Betaines and related osmoprotectants.

    Google Scholar 

  • Targets for metabolic engineering of stress resistance. Plant Physiol 120, 945–949. Meinke, D.W., Cherry, J.M., Dean, C., Rounsley, S.D. and Koornneef, M. 1998. Arabidopsis thaliana a model plant for genome analysis. Science 282, 678–682.

    Google Scholar 

  • Mekhedov, S., de Ilarduyam O.M. and Ohlrogge, J. 2000. Toward a functional catalog of the plant genome. A survey of genes for lipid biosynthesis. Plant Physiol. 122, 389–401.

    Article  PubMed  CAS  Google Scholar 

  • Michelmore, R. 2000. Genomic approaches to plant disease resistance. Curr. Opin. Plant Biol 3, 125–131.

    Article  PubMed  CAS  Google Scholar 

  • Mozo, T., Fischer, S., Meier-Ewert, S., Lehrach, H. and Altmann, T. 1998. Use of the IGF BAC library fo* ohysical mapping of the Arabidopsis thaliana genome. Plant J. 16, 377384.

    Google Scholar 

  • Mozo, T., Dewar, K., Dunn, P., Ecker, J.R., Fischer, S., Kloska, S., Lehrach, H., Marra, M., Martienssen, R., Meier-Ewert, S. and Altmann, T. 1999. A complete BAC-based physical map of the Arabidopsis thaliana genome. Nature Genet. 22, 271–275.

    Article  PubMed  CAS  Google Scholar 

  • Newman, T., de Bruijn, F.J., Green, P., Keegstra, K., Kende, H., McIntosh, L., Ohlrogge, J., Raikhel, N., Somerville, S., Thomashow, M., Retzel, E. and Somerville, C. 1994. Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol. 106, 1241–55.

    Article  PubMed  CAS  Google Scholar 

  • Noctor, G. and Foyer, C.H. 1998. Ascorbate and glutathione–keeping active oxygen under control. Annu. Rev. Plant Physiol. Plant Mol. Biol 49, 249–279.

    Article  PubMed  CAS  Google Scholar 

  • Nuccio, M.L., Rhodes, D., McNeil, S.D. and Hanson, A.D. 1999. Metabolic engineering of plants for osmotic stress resistance. Curr. Opin. Plant. Biol 2, 128–34.

    Article  PubMed  CAS  Google Scholar 

  • Pilon-Smits, E.A.H., Hwang, S.B., Lytle, C.M., Zhu, Y.L., Tai, J.C., Bravo, R.C., Chen, Y.C., Leustek, T. and Terry, N. 1999. Overexpression of ATP sulfurylase in Indian mustard leads to increased selenate uptake, reduction, and tolerance. Plant Physiol. 119, 123–132.

    Article  PubMed  CAS  Google Scholar 

  • Pruitt, R.E. and Meyerowitz, E.M. 1986. Characterization of the genome of Arabidopsis thaliana. J. Mol. Biol. 187, 169–183.

    Article  CAS  Google Scholar 

  • Ribaut, J.M., Hoisington, D.A., Deutsch, J.A., Jiang, C. and Gonzalez-de-Leon, D. 1996. Identification of quantitative trait loci under drought conditions in tropical maize. 1. Flowering parameters and the anthesis-silking interval. Theor. Appl. Genet 92, 905–914.

    Article  CAS  Google Scholar 

  • Ribaut, J.M., Jiang, C., Gonzalez-de-Leon, D., Edmeades, G.O. and Hoisington, D.A. 1997. Identification of quantitative trait loci under drought conditions in tropical maize. 2. Yield components and marker-assisted selection strategies. Theor. Appl. Genet 94, 887896.

    Google Scholar 

  • Ruan, Y., Gilmore, J. and Conner, T. 1998. Towards Arabidopsis genome analysis–monitoring expression profiles of 1400 genes using cDNA micro-arrays. Plant J. 15, 821–833.

    Article  PubMed  CAS  Google Scholar 

  • Richmond, T. and Somerville, S. 2000. Chasing the dream: plant EST micro-arrays. Curr. Opin. Plant Biol 3, 108–116.

    Article  PubMed  CAS  Google Scholar 

  • Schachtmann, D.P., Reid, R.J. and Ayling, S.L. 1998. Phosphorus uptake by plants: from the soil to cells. Plant Physiol. 116, 447–453.

    Article  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Schena, M. and Davis, R.W. 1999. “Genes, genomes, and chips”. In: DNA micro-arrays: a practical approach. New York, Oxford University Press, 205: 1–16.

    Google Scholar 

  • Shizuya, H., Birren, B., Kim, U-J., Mancino, V., Slepak, T., Tachiiri, Y. and Simon, M. 1992. Cloning and stable maintenance of 300 kilobase pair fragments of human DNA in Escherichia coli using a F-factor based vector. Proc. Natl. Acad. Sci. USA 89, 87948797.

    Google Scholar 

  • Smimoff, N. 1998. Plant resistance to environmental stress. Curr. Opin. Biotech 9, 214–219.

    Article  Google Scholar 

  • Sterky, F., Regan, S., Karlsson, J., Hertzberg, M., Rohde, A., Holmberg, A., Amini, B., Bhalerao, R., Larsson, M., Villarroel, R., van Montagu, M., Sandberg, G., Olsson, O., Teed, T.T., Boerjan, W., Gustafsson, P., Uhlen, M., Sundberg, B. and Lundeberg, J. 1998. Gene discovery in the wood-forming tissues of poplar-analysis of 5,692 expressed sequence tags. Proc. Natl. Acad. Sci. USA 95, 13330–13335.

    Article  PubMed  CAS  Google Scholar 

  • Tanksley, S.D., Ganal, M.W. and Martin, G.B. 1995. Chromosome landing–a paradigm for map-based gene cloning in plants with large genomes. Trends Genet. 11, 63–68.

    Article  PubMed  CAS  Google Scholar 

  • Terryn, N., Heijnen, L., De Keyser, A., van Asseldonck, M., De Clercq, R., Verbakel, H., Gielen, J., Zabeau, M., Villarroel, R., Jesse, T., Neyt, P., Hogers, R., van den Daele, H., Ardiles, W., Schueller, C., Mayer, K., Dehais, P., Rombauts, S., Van Montagu, M., Rouze, P. and Vos, P. 1999. Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4. FEBS Lett. 445, 237–245.

    Article  PubMed  CAS  Google Scholar 

  • Thomashow, M.F. 1999. Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu. Rev. Plant Physiol. Plant Mol. Biol 50, 571–599.

    Article  PubMed  CAS  Google Scholar 

  • The C. elegans sequencing consortium 1998. Genome sequence of the nematode C. elegans a platform for investigating biology. Science 282, 2012–2018.

    Google Scholar 

  • Vos, P., Hogers, R., Bleeker, M., Reijans, M., Vandelee, T., Homes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M. and Zabeau, M. 1995. AFLP–a new technique for DNA fingerprinting. Nucleic Acids Res. 23, 4407–4414.

    Article  PubMed  CAS  Google Scholar 

  • Vos, P., Simons, G., Jesse, T., Wijbrandi, J., Heinen, L„ Hogers, R., Frijters, A., Groenendijk, J., Diergaarde, P., Reijans, M., Fierensonstenk, J., Deboth, M., Peleman, J., Liharska, T., Hontelez, J. and Zabeau, M. 1998. The tomato MI-1 gene confers resistance to both root-knot nematodes and potato aphids. Nature Biotech. 16, 1365–1369.

    Article  CAS  Google Scholar 

  • Wodicka, L., Dong, H.L., Mittmann, M., Ho, M.H. and Lockhart, D.J. 1997. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nature Biotech. 15, 1359–1367.

    Article  CAS  Google Scholar 

  • Walbot, V. 1999. Genes, genomes, genomics. What can plant biologists expect from the 1998 National Science Foundation Plant Genome Research Program? Plant Physiol. 119, 1151–1155.

    Article  PubMed  CAS  Google Scholar 

  • Yamamoto, K. and Sasaki, T. 1997. Large-scale EST sequencing in rice. Plant Mol. Biol 35, 135–144.

    Article  PubMed  CAS  Google Scholar 

  • Zhao, J.M., Williams, C.C. and Last, R.L. 1998. Induction of Arabidopsis tryptophan pathway enzymes and camalexin by amino acid starvation, oxidative stress, and an abiotic elicitor. Plant Cell 10, 359–370.

    PubMed  CAS  Google Scholar 

  • Zhu, Y.L., Pilon-Smits, E.A.H., Jouanin, L. and Terry, N. 1999a. Overexpression of glutathione synthetase in Indian mustard enhances cadmium accumulation and tolerance. Plant Physiol. 119, 73–79.

    Article  CAS  Google Scholar 

  • Zhu, Y.L., Pilon-Smits, E.A.H., Tarun, A.S., Weber, S.U., Jouanin, L. and Terry, N. 1999b. Cadmium tolerance and accumulation in Indian mustard is enhanced by overexpressing gamma-glutamylcysteine synthetase. Plant Physiol. 121, 1169–1177.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Institut für Biologie, Angewandte Genetik, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany

    Holger Hesse

  2. Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Golm, Germany

    Rainer Höfgen

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  1. Holger Hesse
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  1. Agriculture and Environment Division, Institute of Arable Crop Research, Harpenden, UK

    Malcolm J. Hawkesford  & Peter Buchner  & 

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Hesse, H., Höfgen, R. (2001). Application of Genomics in Agriculture. In: Hawkesford, M.J., Buchner, P. (eds) Molecular Analysis of Plant Adaptation to the Environment. Springer Handbook Series of Plant Ecophysiology, vol 1. Springer, Dordrecht. https://doi.org/10.1007/978-94-015-9783-8_4

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  • DOI: https://doi.org/10.1007/978-94-015-9783-8_4

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