Plant Biotechnology :

an urgency

Prof. Em. Marc Van Montagu

Chairman I.P.B.O.
Institute Plant Biotechnology for Developing Countries
Website : http://www.ipbo.ugent.be
http://www.psb.ugent.be
E-mail : mamon@psb.ugent.be
 21st Century

Knowledge based economy

build on
the molecular foundations of life sciences
 Worldwide effort

• Capacity building in Plant Sciences

• Awareness of the global environmental
damage due to the increasing population
growth
• Explain the complementarity between
scientific and traditional knowledge
 Capacity building in Plant
Biotechnology includes
• capacity building for participation in needed
R&D
• knowledge on international regulations
regarding GMOs
• how to run tests and trials
• how to plan a R&D project
• how to get acquainted with IPR regulations
• how to teach their best scientists to do
business deals
 Capacity building

• Public sector as major stakeholder

• Private initiative for applying research
results
• Private and public partnership
 To order this book go to:
www.plantbiotech.jbpub.com

Jones and Bartlett Publishers, Inc.

Potentials of Agriculture Biotechnology

• Food and Feed production

• Food processing Industry
• Forestry
• New materials (bulk products)
• Molecular Pharming
• Environment
 Seed Industry for Less Developed Countries

Promoting a vibrant sector seed industry, with

access to value enhancing technologies can
help ensure food production, stimulate rural
economy and become the driving force for
developing an agriculture based industry.
Certain domesticated tomato fruits (left) are dramatically larger
than their wild counterparts (right). Liu et al. (Cornell
University, Ithaca, NY) provide evidence that much of this size
difference is attributable to a heterochronically regulated,
negative fruit growth regulator (fw2.2) that affects cell division
patterns in the tomato fruit (copy-righted by Kent Loeffler)

Plant Physiology, May 2003, Vol. 132, pp. 292-299)

 From applied to fundamental
QTL genes in plants
Species Trait Gene - Function
Tomato Fruit Size OFRX – regulatory (?)
Sugar Content Lin5 – Apoplastic invertase
Fruit shape Ovate - unknown
Rice Flowering time Se1- Transcription factor
CK2 – protein kinase
Hd3a - unknown
Maize Apical dominance Tb1 – Transcription factor
Arabidopsis Flowering time CRY2 - Cytochrome

Source: Morgane & Salamini Curr Opinion in Biotechnology 2003

Plant Genome Initiatives
 Important observations from the
Arabidopsis and rice genome sequencing

• Average gene size: Arabidopsis 2,4 Kb in rice 4,5 Kb

in humans 73 Kb
• Number of genes Arabidopsis: 28.000 (30% new)
• Number of genes Rice: 45 to 55.000
(yeast :6.000, Drosophila : 14.000 C.elegans :
19.000)
• Number of transcription factors : 1800
(yeast : 200, Drosophila :700 , C.elegans : 450 )
• High conservation of genes through evolution
• Limited use of alternative splicing (2.000)
 Populus as a model tree
• Fast growth
• Vegetative propagation
• Inter-specific hybridisation
• 3-generation breeding pedigrees
• Genetic transformation
• Small genome: 550Mb; 19 chr
• Genome sequenced (first tree)
• Economically relevant woody
crop
– Pulp and paper
– Timber
– Board, ….
 OSTREOCOCCUS tauri
(Prasinophyceae)
• Smallest micro alga (1-2 µ)
• 1 chloroplast mitochondria 1 nucleus
• 12.6 Mb 19/20 chromosomes
• 29 contigs
• Few duplicated genes
• Functions grouped
• « abnormal » chromosome

(annotation Pierre Rouzé)

 Mining Biological Data

• Biological processes are not always

completely understood. Need for
bidirectional algorithms and use of
reiterative processes
• Improved annotation of splice sites and
branchpoints
• 100 x faster alignment (Field Programmable
Gate Array)
 Large scale gene duplication in
dicots and monocots

Wheat Barley Rice Corn

chromosome
2 genome duplications
duplication ?
dicots monocots

Split dicots - monocots

1 genome duplication ?
(Yves Van de Peer)
 Functional Genomics
DNA microarrays

• Cutting Edge Transcriptome Analysis

N. Eckhardt – Plant Cell (2004), 16: 2249-2251
• Pleiotropy of a mutation
Antje Rhode – Arabidopsis PAL
• Pseudocaspases (Arabidopsis)
Frank Van Breuseghem
 microRNAs in plants
C. elegans A. thaliana

adapted from David Bartel

 Validated miRNA targets in Arabidopsis
Arabidopsis miRNA Oryza Targets Reference
homologs
156/157 yes Squamosa-promoter biding ptn Kasschau et al., 2003

159a/b/c/jaw yes MYB ptn, TCP ptn Palstnik et al., 2003

Kasschau et al., 2003
162 yes Dicer-like ptn Xie et al., 2003

164 yes NAC domain ptn Kasschau et al., 2003

165/166 yes HD-Zip transcription factor Tang et al., 2003

Emery et al., 2003

167 yes Auxin response factor Kasschau et al., 2003

270/171 yes GRAS-domain ptn Llave et al., 2002

172a/b yes AP2 and AP2-like ptn Kasschau et al., 2003

Adapted from Malloy & Vaucheret, Curr Opin Plant Biol 7: 120 (2004)
 Computational Identification of Plant miRNAs

Based in a
comparative
Genome approach
Based on ac
of intergenic
sequences between omparativegenomics
Arabidopsis approach of
thaliana and Oryza intergenic sequences
sativa between
A. thaliana and
Pierre Rouzé et al., in preparation
O. sativa
 Plant miRNAs finder
• Amongst 91 candidates, 58 have at least one
potential Arabidopsis messenger RNA target
• 56% are transcription factors controlling
developmental process, e.g. in flower and leaf,
and auxin-dependant processes
• Other targets are novel & cover a range of
important functions, such as ubiquitination-
dependant auxin signaling, sulfur assimilation …
 RNA silencing: History
introduction of transgenes in plants

to provide plants with new or altered traits

example: DFR in Petunia

high DFR mRNA specific reduction of the
steady-state level DFR mRNA steady-state level

WT-phenotype cosuppression-phenotype

Van der Krol et al., 1990

1990 Post-transcriptional gene silencing (PTGS)

 RNA Silencing

• Caenorhabditis elegans
Meister, G. and Tuschl, T. (2004) Nature 431, 371-378

• Plants
Baulcombe, D. (2004) Nature 431, 356-363

• Mammals
Hannon, G.J., and Rossi J.J. (2004) Nature 431, 371-378
 Transitive silencing: principle

X: silencing inducer
(dsRNA)
homology
between X and Y

Y: primary target
homology
between Y and Z

Z: secondary target

Transitive silencing occurs in plants and nematodes …

UNIVERSITEIT
Garcia-Peres, Van Hout and Depicker, Plant J. 39:594 (2004)
GENT
 Transitive silencing in grafting experiments?

Pnos-npt-3’ocs P35S gus c.s. 3’nos

graft junction
Z
?
Pss-bar-3’g7 P35S gus c.s. 3’chs
Y

P35S nptII c.s. 3’chs 3’chs nptII c.s. P35S

X

Activity of gus in ZZ scions

ZZ/XXYY  silenced
ZZ/X_YY  silenced
Grafts:
ZZ/XXY_  silenced
ZZ/X_Y_  non silenced
Garcia-Peres, Van Hout and Depicker, Plant J. 39:594 (2004)
 Genome Dynamics

Cracking chromatin code

Non coding DNA

Chemical modifications of DNA and histones
Changes in the structure of chromatin

All of these are subject to “manipulation”

resulting in altered phenotypes
 Secondary Metabolites
Evolved:
• To interact with some specific protein folds
• NOT to interact with the majority of the protein folds

The number of protein fold is low (700)

They are highly conserved in evolution
 Metabolite Display
• Improved tools of analytical organic chemistry (CE-MS;
GC-MS; LC-MS, FT-MS, 800 MHz NMR) allow the
establishment of a profile of all metabolites present in a
specific plant tissue.
• A variety of till now unidentified biochemical pathways can
now be understood.
• Genes encoding the biosynthetic enzymes can then be
identified more easily.
• The production of secundary and intermediar metabolites in
crop plants can consequently be envisaged.
Yun Bing (Chinese 1473)
Chinese Opium Poppy
Possibilities to produce plant-derived
biomolecules
 Wild or cultivated plants

 Chemical synthesis

 Plant cell and tissue cultures

 Research approach

Technology platform – Tools for metabolic

engineering

 To enhance production of known plant-

based compounds in cell cultures

 To produce novel compounds in plant

cell cultures

 To build the biosynthetic pathway in

easy to culture plants (tobacco)
cDNA-AFLP transcript profiling

 Transcriptome analysis in medicinal plants

 lack of extensive gene sequence data banks
 use of EST database mining or microarray analysis
difficult/limited

 Alternative technology = cDNA-AFLP based

transcript profiling
 no prior sequence information required
 provides quantitative expression profiles
 genome-wide coverage
 allows the identification of novel genes
 allows to distinguish between isoforms
 Transcript Profiling in BY-2

+ MeJA
Harvest
samples
Terpenoid indole alkaloids

 Catharanthus roseus produces

vinblastine & vinchristine
 Use: Hodgkin's disease,
acute leukemia, breast cancer
 Content in plants: In leaves ~
0.0003 % (500 kg plant
material is needed to obtain
1 g vincristine)
 Price: ~13 000 € / g
 Economic Value of the Biodiversity

• Must be demonstrated before we can

convince governments to protect the
biodiversity
• Major hurdles are the new international
legislations
Plants for the Future

Environment
• Less polluting agriculture
• Agriculture on marginal lands
• Preservation of water supply
• Cleaning up of polluted soils
(phytoremediation)
 Major Public Concerns
Safety Issues
• Human and Animal Health
• No adverse effect reported with the approved GM-crops
• Environmental
• Already a long list of beneficial effects
• No alarming scenario was confirmed
• Long term ecological effects can be lower than those of
traditional agriculture
 Actions

• Improve science education and awareness of the

importance of science in decision making.
• But move from “educating the public” to engaging
with the public.
• Discuss new products with consumer organisations.
• Explain the consequences of not using GM plants.
21st Century Plants will be GM-Plants