Computer Modelling of Seed Germination: The 'virtual SEED' European Network Project (vseed)

Transcription

1 PD Dr. Gerhard Leubner Computer Modelling of Seed Germination: The 'virtual SEED' European Network Project (vseed) Testa rupture and Endosperm rupture Lockhart-style model for radicle elongation

2 PD Dr. Gerhard Leubner Computer Modelling of Seed Germination: The 'virtual SEED' European Network Project (vseed) We propose that germination is an ideal exemplary subject for the integration of new technologies and for developing molecular plant biomechanics in conjunction with dynamic mathematical modelling. Mike Holdsworth (Nottingham) John King (Nottingham) Andy Wood (Nottingham) Nichola Everitt (Nottingham) Paul Knox (Leeds) Leonie Bentsink (Utrecht) Gerhard Leubner (Freiburg) Thomas Speck (Freiburg)

3 PD Dr. Gerhard Leubner Computer Modelling of Seed Germination: The 'virtual SEED' European Network Project (vseed) The vseed project aims to provide a dynamic mathematical description of seed dormancy, after-ripening and germination focussing on the key seed compartments the radicle and endosperm. This interdisciplinary project will analyse the comparative biology of the closely related Brassicaceae species Arabidopsis thaliana and Lepidium sativum (garden cress), using engineering, imaging, identification of key transcriptome networks, modelling, and post-genomics approaches to develop a virtual germinating seed. Mike Holdsworth (Nottingham) John King (Nottingham) Andy Wood (Nottingham) Nichola Everitt (Nottingham) Paul Knox (Leeds) Leonie Bentsink (Utrecht) Gerhard Leubner (Freiburg) Thomas Speck (Freiburg)

4 PD Dr. Gerhard Leubner Computer Modelling of Seed Germination: The 'virtual SEED' European Network Project (vseed) includ. abiotic stress

5 PD Dr. Gerhard Leubner Computer Modelling of Seed Germination: The 'virtual SEED' European Network Project (vseed) Book chapter: Hilhorst, Finch-Savage, Buitink, Bolingue, Leubner-Metzger (2010). Topics Curr Genetics 21: 43-67

6 PD Dr. Gerhard Leubner Computer Modelling of Seed Germination: The 'virtual SEED' European Network Project (vseed) WP1 Modelling transcriptome networks (leader Holdsworth): Identification and mathematical modelling of key transcriptome networks associated with radicle and endosperm function. WP2 Cell wall biology (leader Knox): Analysis of cell wall biology during embryo growth and endosperm weakening. WP3 Tissue/seed scale biophysical modelling (leader Leubner): Provision of tissue/seed scale biomechanical modelling through the use of novel engineering and imaging approaches. WP4 Multi-scale modelling and integration (leader King): Multi-scale modelling, integrating cross-species analysis, from transcriptomic networks through tissue biomechanical models to physiological seed behaviour (including abiotic stresses). WP5 Resource development and model validation (leader Bentsink): Resource development and model validation through use of unique, and development of novel genetic resources. Main PI vseed: Mike Holdsworth, Nottingham

7 1. Endosperm in mature seeds: Evolution, roles, diversity Seed structure and interaction between seed tissues control of germination timing, biodiversity, environmental adaptation! Tansley Review: Linkies et al. (2010) The evolution of seeds. New Phytologist 186:

8 1. Endosperm in mature seeds: Evolution, roles, diversity Seed structure: Thicker microp. endosperm (cap) Cotyledons Non-micropylar endosperm Endosperm Micropylar endosperm Darwin s tree of life (1837) Darwin s evidence: Structure Delphinium Ranunculaceae Embryo Testa (seed coat) Radicle Tobacco Nicotiana Solanaceae Seed structure: Thin micropylar endosperm (cap) lettuce Lactuca Asteraceae Brassicaceae: Lepidium sativum (garden cress), Arabidopsis thaliana

9 1. Endosperm in mature seeds: Evolution, roles, diversity Mechanical restraint, e.g. inhibition of GA-induced endosperm weakening Prevention of inhibitor leakage, e.g. abscisic acid (ABA) Interference with water uptake or gas exchange, e.g. O 2 (sugar beet pericarp)* Gibberellin (GA) - Abscisic acid (ABA) antagonism Ethylene - ABA antagonism Linkies et al. (2009) *Sugarbeet: Hermann et al. (2007) Journal of Experimental Botany 58: Ethylene-ABA, tissue-specific transcriptome: Linkies, et al. (2009) Plant Cell 21:

10 1. Endosperm in mature seeds: Evolution, roles, diversity Mechanical restraint, e.g. inhibition of GA-induced endosperm weakening Prevention of inhibitor leakage, e.g. abscisic acid (ABA) Interference with water uptake or gas exchange, e.g. O 2 (sugar beet pericarp)* Seed biotechnologies and enhancements improve seed quality: Seed priming, seed coating/pelleting (artificial envelopes),... Seed treatments: fungi-, insect-, nematicides, plant hormones *Sugarbeet: Hermann et al. (2007) Journal of Experimental Botany 58: Ethylene-ABA, tissue-specific transcriptome: Linkies, et al. (2009) Plant Cell 21:

11 1. Endosperm in mature seeds: Evolution, roles, diversity SEST2009-5th International Symposium on "Seed, Transplant and Stand Establishment of Horticultural Crops.", Sept./Oct. 2009, Murcia - Almeria, Spain - Foto: Gerhard Leubner

12 1. Endosperm in mature seeds: Evolution, roles, diversity Mechanical restraint, e.g. inhibition of GA-induced endosperm weakening Prevention of inhibitor leakage, e.g. abscisic acid (ABA) Interference with water uptake or gas exchange, e.g. O 2 (sugar beet pericarp)* Gibberellin (GA) - Abscisic acid (ABA) antagonism Ethylene - ABA antagonism Linkies et al. (2009) *Sugarbeet: Hermann et al. (2007) Journal of Experimental Botany 58: Ethylene-ABA, tissue-specific transcriptome: Linkies, et al. (2009) Plant Cell 21:

13 1. Endosperm in mature seeds: Evolution, roles, diversity Testa rupture Endosperm rupture Seedling establish. Developmental switch (ABA) Linkies, Müller, Morris,..., Finch-Savage, Leubner-Metzger (2009) Plant Cell 21: Tansley Review: Finch-Savage, Leubner-Metzger (2006) New Phytologist 171:

14 1. Endosperm in mature seeds: Evolution, roles, diversity Testa rupture Endosperm rupture Seedling establish. Developmental switch (ABA) Hormonal antagonisms on endosperm rupture: Gibberellins (GA) - ABA Ethylene - ABA Brassinosteroids (BR) - ABA Linkies, Müller, Morris,..., Finch-Savage, Leubner-Metzger (2009) Plant Cell 21: Tansley Review: Finch-Savage, Leubner-Metzger (2006) New Phytologist 171:

15 1. Endosperm in mature seeds: Evolution, roles, diversity Testa rupture Endosperm rupture Seedling establish. Tansley Review: Holdsworth, Bentsink, Soppe (2008) New Phytologist 179: 33-54

16 2. Seed biomechanics: Hormones and endosperm weakening Müller, Heß, Leubner-Metzger (2007) Chapter 30, pp in: Adkins, Ashmore, Navie (Eds.), Seeds: Biology, Development and Ecology. CAB International, Wallingford, UK.

17 2. Seed biomechanics: Hormones and endosperm weakening Lepidium sativum (garde cress) Seed biomechanics ('puncture-force')

18 2. Seed biomechanics: Hormones and endosperm weakening Lepidium sativum (garden cress) Müller et al. (2006) Plant Cell Physiol 47: Linkies et al. (2009) Plant Cell 21: Graeber et al. (2010) Plant Mol Biol 73: Seed biomechanics ('puncture-force')

19 2. Seed biomechanics: Hormones and endosperm weakening ABA inhibits and GA promotes endosperm weakening Linkies, Müller, Morris,..., Finch-Savage, Leubner-Metzger (2009) Plant Cell 21: Morris, Linkies,..., Leubner-Metzger, Finch-Savage (2011) Plant Physiol Preview (in press)

20 2. Seed biomechanics: Hormones and endosperm weakening combined with tissue-specific transcriptome analysis RNA from specific Lepidium seed tissues ±ABA: 1) Radicle (Rad) 2) Endosperm cap (Cap) 3) Non-micropylar endosperm (NonE) CON: without hormones ABA: with ABA added Physiologically defined times (cap weakening) Cross-species arrays Arabidopsis-CATMA in collaboration with Bill Finch-Savage (Warwick HRI, UK) Linkies, Müller, Morris,..., Finch-Savage, Leubner-Metzger (2009) Plant Cell 21: Morris, Linkies,..., Leubner-Metzger, Finch-Savage (2011) Plant Physiol Preview (in press)

21 2. Seed biomechanics: Hormones and endosperm weakening combined with tissue-specific transcriptome analysis RNA from specific Lepidium seed tissues ±ABA: 1) Radicle (Rad) 2) Endosperm cap (Cap) 3) Non-micropylar endosperm (NonE) CON: without hormones ABA: with ABA added Physiologically defined times (cap weakening) Cross-species arrays Arabidopsis-CATMA in collaboration with Bill Finch-Savage (Warwick HRI, UK) Linkies, Müller, Morris,..., Finch-Savage, Leubner-Metzger (2009) Plant Cell 21: Morris, Linkies,..., Leubner-Metzger, Finch-Savage (2011) Plant Physiol Preview (in press)

22 3. Comparative biology: Brassicaceae endosperm weakening Ethylene promotes cap weakening and counteracts ABA Tissue-specific crossspecies microarrays Ethylene promotes endosperm rupture of Arabidopsis and Lepidium sativum Ethylene promotes endosperm cap weakening and counteracts the ABA-inhibition by interference with ABA-signaling Ethylene production by the Brassicaceae ACO2 orthologs are important for endosperm cap weakening and rupture; evolutionary conserved Ethylene-ABA, tissue-specific transcriptome: Linkies, et al. (2009) Plant Cell 21:

23 3. Comparative biology: Brassicaceae endosperm weakening Ethylene promotes cap weakening and counteracts ABA Tissue-specific crossspecies microarrays Ethylene promotes endosperm rupture of Arabidopsis and Lepidium sativum Ethylene promotes endosperm cap weakening and counteracts the ABA-inhibition by interference with ABA-signaling Ethylene production by the Brassicaceae ACO2 orthologs are important for endosperm cap weakening and rupture; evolutionary conserved Cultivar comparison of endosperm weakening: Graeber et al. (2010) Plant Mol Biol 73: 67-87

24 4. vseed: Seed biomechanics and mathematical modelling Lepidium sativum (garden cress) Biomechanics to determine endosperm tissue properties by using the punctureforce technique: The micropylar endosperm is a visco-elastic tissue/material. Movie directed by Dr. Sebastian Busch (group Leubner)

25 4. vseed: Seed biomechanics and mathematical modelling Lepidium sativum (garden cress) Biomechanics to determine endosperm tissue properties by using the punctureforce technique: The micropylar endosperm is a visco-elastic tissue/material. Movie directed by Dr. Sebastian Busch (group Leubner)

26 4. vseed: Seed biomechanics and mathematical modelling Improving the puncture-force technique by glueing the endosperm caps into a perforated metal plate and placing it on a slit-holder. Dr. Sebastian Busch (Freiburg) Modelling the mechanical properties Elastic / shear moduli Dr. Simon Pearce (Nottingham)

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28 4. vseed: Seed biomechanics and mathematical modelling Embryo Streckungswachstum Arabidopsis thaliana Sliwinska, Bassel, Bewley (2009) Journal of Experimental Botany 60: Lepidium sativum (garden cress) Embryo elongation: Cell elongation by cell wall loosening. Immunohistochemistry pectin, cell-wall remodelling proteins, reactive oxygen species (ROS)? Karin Weitbrecht (group Leubner) Arabidopsis thaliana embryo elongation zone: George Bassel (group Holdsworth, Nottingham)

29 5. vseed: Cross-species comparison transcriptome networks Lepidium: Karin Weitbrecht (Freiburg) Arabidopsis: Bas Dekkers (Utrecht) Normalisation: Simon Pearce (Nottingham)

30 5. vseed: Cross-species comparison transcriptome networks Generate condition dependant unweighted co-expression network similar to the SeedNet results of George Bassel Dormancy Germination Genes promoting germination Genes promoting dormancy Unpublished results of George Bassel and Mike Holdsworth et al. (2011), based on 138 arrays

31 6. Future possibilities for systems biology data integration ONDEX website for information:

32 PD Dr. Gerhard Leubner Computer Modelling of Seed Germination: The 'virtual SEED' European Network Project (vseed) Modelling John King, Nottingham Andy Wood Simon Pearce Anthony Hampstead Biophysics Gerhard Leubner, Freiburg Sebastian Busch Karin Weitbrecht Nicola Everitt, Nottingham Informatics Alex Marshall, Nottingham Cell wall biology Paul Knox, Kieran Lee, Leeds Transcriptomics Leonie Bentsink, Utrecht Bas Dekkers Marieke van Bolderen-Veldkamp Gerhard Leubner, Freiburg Karin Weitbrecht George Bassel, Mike Holdsworth, Nottingham Main PI vseed: Mike Holdsworth, Nottingham

33 PD Dr. Gerhard Leubner Dr. Ada Linkies (Postdoc DFG, weakening) Antje Vögele (PhD DFG, weakening) Katrin Biermann (Diplom, weakening) Dr. Krystyna Oracz (Postdoc AvH) Magdalena Jura (PhD DFG, pectin) Claudia Scheler (Diplom, pectin) Dr. Sebastian Busch (Postdoc, vseed) Karin Weitbrecht (PhD vseed) Johannes Lörcher (Staatsexamen) Kai Gräber (PhD DFG, seed dormancy) Maren Siegrist (Staatsexamen, dormancy) Dr. Annette Büttner-Mainik (Postdoc, sugarbeet) Collab. Dr. U. Fischer, KWS Saat AG, Einbeck Prof. Klaus Mummenhoff, Osnabrück Prof. Bill Finch-Savage, Warwick (UK) Prof. Mike Holdsworth et al., Nottingham (UK)