Hostname: page-component-7b7567c8c-fvjsw Total loading time: 0 Render date: 2026-11-14T04:51:46.898Z Has data issue: false hasContentIssue false
  • English
  • Français

Seed genomics: germinating opportunities

Published online by Cambridge University Press:  22 February 2007

A. (Lonneke) and
H.M. van der Geest
A. (Lonneke)
Affiliation:
Business Unit Plant Development and Reproduction, Plant Research International B.V., PO Box 16, 6700 AA Wageningen, The Netherlands
H.M. van der Geest*
Affiliation:
Business Unit Plant Development and Reproduction, Plant Research International B.V., PO Box 16, 6700 AA Wageningen, The Netherlands
*
*Correspondence Tel: +31 317 476990 Email: a.h.m.vandergeest@plant.wag-ur.nl
Rights & Permissions [Opens in a new window]

Abstract

Core share and HTML view are not available for this content. However, as you have access to this content, a full PDF is available via the 'Save PDF' action button.

With the sequencing of the Arabidopsis thaliana genome, the field of plant biology has made a quantum leap. The sequence information available to the community has greatly facilitated the identification of genes responsible for mutant phenotypes and the large-scale analysis of gene expression in Arabidopsis. High-throughput laboratory tools for DNA sequencing (genomics), mutant analysis (functional genomics), mRNA quantification (transcriptomics) and protein analysis (proteomics) are being used to scrutinize this model plant. For seed physiologists, the challenge lies in translating this information into physiological processes in seeds from other plant species. Combining more traditional seed biology with the new high-throughput molecular tools should yield breakthroughs in seed science.

Keywords

functional genomicsproteomicsseed biologytranscriptomics

Information

Type
Research Perspective
Information
Seed Science Research , Volume 12 , Issue 3 , September 2002, pp. 145 - 153
Copyright
Copyright © Cambridge University Press 2002

References

Aalen, R.B. (1999) Peroxiredoxin antioxidants in seed physiology. Seed Science Research 9, 285–295.Google Scholar
Aharoni, A. and Vorst, O. (2002) DNA microarrays for functional plant genomics. Plant Molecular Biology 48, 99–118.CrossRefGoogle ScholarPubMed
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 microarrays. Plant Cell 12, 647–661.Google Scholar
Arabidopsis GenomeInitiative Intiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815.Google Scholar
Assaad, F.F. (2001) Of weeds and men: what genomes teach us about plant biology. Current Opinion in Plant Biology 4, 478–487.Google Scholar
Barnes, S. (2002) Comparing Arabidopsis to other flowering plants. Current Opinion in Plant Biology 5, 128–133.CrossRefGoogle ScholarPubMed
Bentsink, L., Alonso-Blanco, C., Vreugdenhil, D., Tesnier, K., Groot, S.P.C. and Koornneef, M. (2000) Genetic analysis of seed soluble oligosaccharides in relation to seed storability of Arabidopsis. Plant Physiology 124, 1595–1604.CrossRefGoogle ScholarPubMed
Bergervoet, J.H.W., Kraak, H.L., de Vos, C.H.R. and Bino, R.J. (1994) Two-dimensional protein patterns of tomato (Lycopersicon esculentum Mill.) seeds; effects of isolation procedure and imbibition. Seed Science Research 4, 275–283.CrossRefGoogle Scholar
Bradford, K.J., Chen, F., Cooley, M.B., Dahal, P., Downie, B., Fukunaga, K.K., Gee, O.H., Gurusinghe, S., Mella, R.A., Nonagaki, H., Wu., C.-T., Yang, H. and Yim, K.-O. (2000) Gene expression prior to radicle emergence in imbibed tomato seeds. pp 231–251. in Black, M., Bradford, K.J. and Vásquez-Ramos, J., (Eds) Seed biology: advances and applications. Wallingford, UK, CABI International.Google Scholar
Coca, M.A., Almoguera, C. and Jordano, J. (1994) Expression of sunflower low-molecular-weight heat-shock proteins during embryogenesis and persistence after germination: localization and possible functional implications. Plant Molecular Biology 25, 479–492.CrossRefGoogle ScholarPubMed
Cuming, A.C. (1999) LEA proteins. pp 753–780. in Shewry, P.R.; and Casey, R. (Eds). Seed proteins. Dordrecht, The Netherlands, Kluwer Academic Publishers.CrossRefGoogle Scholar
de Castro, R.D., Zheng, X., Bergervoet, J.H.W., de Vos, C.H.R. and Bino, R.J. (1995) β-tubulin accumulation and DNA replication in imbibing tomato seeds. Plant Physiology 109, 499–504.Google Scholar
Finkelstein, R.R. (1994) Mutations at two new Arabidopsis ABA response loci are similar to the abi3 mutations. Plant Journal 5, 765–771.Google Scholar
Finkelstein, R.R. and Lynch, T.J. (2000) The Arabidopsis abscisic acid response gene ABI5 encodes a basic leucine zipper transcription factor. Plant Cell 12, 599–609.Google Scholar
Finkelstein, R.R., Wang, M.L., Lynch, T.J., Rao, S. and Goodman, H.M. (1998) The Arabidopsis abscisic acid response locus ABI4 encodes an APETALA2 domain protein. Plant Cell 10, 1043–1054.Google Scholar
Galau, G.A., Hughes, D.W. and Dure, L. (1986) Abscisic acid induction of cloned cotton late embryogenesis abundant (LEA) messenger RNAs. Plant Molecular Biology 7, 155–170.CrossRefGoogle Scholar
Gallardo, K., Job, C., Groot, S.P.C., Puype, M., Demol, H., Vandenkerckhove, J. and Job, D. (2001) Proteomic analysis of Arabidopsis seed germination and priming. Plant Physiology 126, 835–848.Google Scholar
Giraudat, J., Hauge, B.M., Valon, C., Smalle, J., Parcy, F. and Goodman, H.M. (1992) Isolation of the Arabidopsis ABI3 gene by positional cloning. Plant Cell 4, 1251–1261.Google Scholar
Girke, T., Todd, J., Ruuska, S., White, J., Benning, C. and Ohlrogge, J. (2000) Microarray analysis of developing Arabidopsis seeds. Plant Physiology 124, 1570–1581.Google Scholar
Hall, T.C., Chandrasekharan, M.B. and Li, G. (1999) Phaseolin: its past, properties, regulation and future. pp 209–240. Shewry, P.R. and Casey, R. (Eds) Seed proteins. Dordrecht, The Netherlands, Kluwer Academic Publishers.CrossRefGoogle Scholar
Hilhorst, H.W.M. (1995) A critical update on seed dormancy. I. Primary dormancy. Seed Science Research 5, 61–73.CrossRefGoogle Scholar
Holdsworth, M., Kurup, S. and McKibbin, R. (1999) Molecular and genetic mechanisms regulating the transition from embryo development to germination. Trends in Plant Science 4, 275–280.Google Scholar
Holdsworth, M., Lenton, J., Flintham, J., Gale, M., Kurup, S., McKibbin, R., Bailey, P., Larner, V. and Russell, L. (2001) Genetic control mechanisms regulating the initiation of germination. Journal of Plant Physiology 158, 439–445.CrossRefGoogle Scholar
Jing, H.-C., van Lammeren, A.A.M., de Castro, R.D., Bino, R.J., Hilhorst, H.W.M. and Groot, S.P.C. (1999) β-tubulin accumulation and DNA synthesis are sequentially resumed in embryo organs of cucumber (Cucumis sativus L.) seeds during germination. Protoplasma 208, 230–239.Google Scholar
Job, D., Capron, I., Job, C., Dacher, F., Corbineau, F. and Come, D. (2000) Identification of germination specific protein markers and their use in seed priming technology. pp 449–460. in Black, M., Bradford, K.J. and Vásquez-Ramos, J. (Eds) Seed biology: advances and applications. Wallingford, UK, CABI International.Google Scholar
Karssen, C.M., Brinkhorst-van, der, Swan, D.L.C., Breekland, A.E. and Koornneef, M. (1983) Induction of dormancy during seed development by endogenous abscisic acid: studies on abscisic acid deficient genotypes of Arabidopsis thaliana (L.) Heynh. Planta 157, 158–165.Google Scholar
Kersten, B., Burkle, L., Kuhn, E.J., Giavalisco, P., Konthur, Z., Lueking, A., Walter, G., Eickhoff, H. and Schneider, U. (2002) Large-scale plant proteomics. Plant Molecular Biology 48, 133–141.Google Scholar
Koornneef, M. and Karssen, C.M. (1994) Seed dormancy and germination. pp 313–334. in Meyerowitz, E.M. and Somerville, C.R. (Eds) Arabidopsis. Cold Spring Harbor, NY, Cold Spring Harbor Laboratory Press.Google Scholar
Koornneef, M. and van der Veen, J.H. (1980) Induction and analysis of gibberellin sensitive mutants in Arabidopsis thaliana (L.) Heynh. Theoretical and Applied Genetics 58, 257–263.Google Scholar
Koornneef, M., Reuling, G. and Karssen, C.M. (1984) The isolation and characterization of abscisic acid-insensitive mutants of Arabidopsis thaliana. Physiologia Plantarum 61, 377–383.CrossRefGoogle Scholar
Koornneef, M., Bentsink, L. and Hilhorst, H. (2002) Seed dormancy and germination. Current Opinion in Plant Biology 5, 33–36.Google Scholar
Leung, J., Bouvier-Durand, M., Morris, P.C., Guerrier, D., Chefdor, F. and Giraudat, J. (1994) Arabidopsis ABA response gene ABI1 features of a calcium-modulated protein phosphatase. Science 264. 1448–1452.CrossRefGoogle Scholar
Leung, J., Merlot, S. and Giraudat, J. (1997) The Arabidopsis ABSCISIC ACID-INSENSITIVE2 (ABI2) and ABI1 genes encode homologous protein phosphatases 2C involved in abscisic acid signal transduction. Plant Cell 9, 759–771.Google Scholar
Li, B. and Foley, M.E. (1997) Genetic and molecular control of seed dormancy. Trends in Plant Science 2, 384–389.CrossRefGoogle Scholar
Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittman, M., Wang, C., Kobayashi, M., Horton, H. and Brown, E.L. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology 14, 1675–1680.Google Scholar
Lotan, T., Ohto, M., Yee, K.M., West, M.A.L., Lo, R., Kwong, R.W., Yamagishi, K., Fischer, R.L., Goldberg, R.B. and Harada, J.J. (1998) Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells. Cell 93, 1195–1205.Google Scholar
Luerßen, K., Kirik, V., Herrmann, P. and Miséra, S. (1998) FUSCA3 encodes a protein with a conserved VP1/ABI3-like B3 domain which is of functional importance for the regulation of seed maturation in Arabidopsis thaliana. Plant Journal 15, 755–764.Google Scholar
McCarty, D.R. (1995) Genetic control and integration of maturation and germination pathways in seed development. Annual Review of Plant Physiology and Plant Molecular Biology 46, 71–93.CrossRefGoogle Scholar
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, 679–682.CrossRefGoogle Scholar
Mendel, G. (1866) Versuche über Pflanzen-Hybriden. Verhandlungen des naturforschenden Vereines in Brünn (Abhandlungen) 4, 3–47.Google Scholar
Meyer, K., Leube, M.P. and Grill, E. (1994) A protein phosphatase 2C involved in ABA signal-transduction in Arabidopsis thaliana. Science 264, 1452–1455.Google Scholar
Osborne, T.B. (1894) The proteins of kidney bean. Journal of the American Chemical Society 16, 633–664.Google Scholar
Osterlund, M.T. and Paterson, A.H. (2002) Applied plant genomics: the secret is integration. Current Opinion in Plant Biology 5, 141–145.Google Scholar
Parcy, F., Valon, C., Kohara, A., Miséra, S. and Giraudat, J. (1997) The ABSCISIC ACID-INSENSITIVE3, FUSCA3, and LEAFY COTYLEDON1 loci act in concert to control multiple aspects of Arabidopsis seed development. Plant Cell 9, 1265–1277.Google ScholarPubMed
Reidt, W., Ellerström, M., Kölle, K., Tewes, A., Tiedemann, J., Altshmied, L. and Bäumlein, H. (2001) FUS3-dependent gene regulation during late embryogenesis. Journal of Plant Physiology 158, 411–418.Google Scholar
Richards, D.E., King, K.E., Ait-ali, T. and Harberd, N.P. (2001) How gibberellin regulates plant growth and development: A molecular genetic analysis of gibberellin signaling. Annual Review of Plant Physiology and Plant Molecular Biology 52, 67–88.Google Scholar
Ritchie, S. and Gilroy, S. (1998) Gibberellins: regulating genes and germination. New Phytologist 140, 363–383.CrossRefGoogle ScholarPubMed
Roberts, J.K.M. (2002) Proteomics and a future generation of plant molecular biologists. Plant Molecular Biology 48, 143–154.CrossRefGoogle Scholar
Ruan, Y., Gilmore, J. and Conner, T. (1998) Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. Plant Journal 15, 821–833.Google Scholar
Russell, L., Larner, V., Kurup, S., Bougourd, S. and Holdsworth, M. (2000) The Arabidopsis COMATOSE locus regulates germination potential. Development 127, 3759–3767.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.Google Scholar
Sun, T.P. (2000) Gibberellin signal transduction. Current Opinion in Plant Biology 3, 374–380.CrossRefGoogle ScholarPubMed
van der Geest, A.H.M., Konings, M.C.J.M., Soeda, Y. and Groot, S.P.C. (2001) Gene expression during Brassica napus seed germination. In First international congress on stress tolerance in seeds. Wageningen, The Netherlands, 4–8 April, 2001. Abstract.Google Scholar
van Wijk, K.J. (2001) Challenges and prospects of plant proteomics. Plant Physiology 126, 501–508.CrossRefGoogle ScholarPubMed
Vicient, C.M., Roscoe, T.J. and Delseny, M. (1998) Characterization of an Em-like gene of Brassica napus. Journal of Experimental Botany 49, 1061–1062.Google Scholar
Wehmeyer, N. and Vierling, E. (2000) The expression of small heat shock proteins in seeds responds to discrete developmental signals and suggests a general protective role in desiccation tolerance. Plant Physiology 122, 1099–1108.CrossRefGoogle ScholarPubMed
White, J.A. and Benning, C. (2001) Genomic approaches towards the engineering of oil seeds. Plant Physiology and Biochemistry 39, 263–270.Google Scholar
White, J.A., Todd, J., Newman, T., Focks, N., Girke, T., Martínez, de, Ilárduya, O., Jaworski, J.G., Ohlrogge, J.B. and Benning, C. (2000) A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil. Plant Physiology 124, 1582–1594.CrossRefGoogle ScholarPubMed
Wisman, E. and Ohlrogge, J. (2000) Arabidopsis microarray service facilities. Plant Physiology 124, 1468–1471.CrossRefGoogle ScholarPubMed
Wobus, U. and Weber, H. (1999) Seed maturation: genetic programmes and control signals. Current Opinion in Plant Biology 2, 33–38.Google Scholar
Wu, C.-T., Leubner-Metzger, G., Meins, F. and Bradford, K.J. (2001) Class I β-1,3-glucanase and chitinase are expressed in the micropylar endosperm of tomato seeds prior to radicle emergence. Plant Physiology 126, 1299–1313.Google Scholar
Zhu, T. and Wang, X. (2000) Large-scale profiling of the Arabidopsis transcriptome. Plant Physiology 124, 1472–1476.Google Scholar
Zivy, M. and de Vienne, D. (2000) Proteomics, a link between genomics, genetics and physiology. Plant Molecular Biology 44, 575–580.CrossRefGoogle ScholarPubMed