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AGROPOLIS
LES DOSSIERS
Expertise of the Agropolis scientific community
Genetic
Genetic
resources
resources
Genomics
Genomics
&
&
Plant
Plant
biotechnology
biotechnology
Number 1 – May 2001Agropolis,
International complex for research and higher education
in agriculture
This scientific complex, with the vocation of an international agricultural
Agropolis groups research and
higher education institutions
university, forms a huge potential of scientific and technical expertise:
in Montpellier and the
3,000 researchers, teachers and technicians in more than 200 research
Languedoc-Roussillon region,
in partnership with foreign
units in Montpellier and the region and 600 scientists working in
and international
60 countries.
institutions, regional
authorities and business,
aiming at the
Relaying on its centres of expertise, Agropolis addresses the major
economic and social
scientific, technological and economic challenges of agricultural
development of
Mediterranean and development:
tropical regions.
• Biodiversity management and utilisation of genetic resources,
• Integrated approach of agricultural systems and rural development,
• Sustainable management of natural resources and food security,
• Agrifood processing in relation with human nutrition issues and food
safety.Genetic
resources
Consumer demands for food
Genomics
security and better quality in
agribusiness practices and in the
agrifood industry can be met
&
through the creation of new
Vegetal
varieties adapted to
environmentally friendly
biotechnology
production systems that are
sparing in their exploitation of
natural resources. In producing
“Genetic resources: towards better understanding, Page 4
such varieties, research scientists
conservation and use” Serge Hamon
now have at their disposal a wide
range of tools allied to increasingly
detailed knowledge of plant
“Genomics applied to agronomic traits” Page 8
functioning. The possibilities of
Jean-Christophe Glaszmann
varietal improvement have never
been greater.
“Genomics and plant development” Page 12
At Agropolis, over 400 people,
Michel Delseny
some 300 of whom are research
scientists, are involved in the study
of genetic resources, genomics
“The Montpellier Languedoc-Roussillon Page 16
and plant biotechnology.
Génopole” Michel Delseny
Agropolis is a benchmark in plant
genomics research in Europe,
“Adaptation of plants to stress Page 18
particularly in studies of factors
that limit the production of
environments” Claude Grignon
Mediterranean and tropical
plants. The participants in this
“Biology of the development of cultivated Page 22
work are researchers from the
perennial plants” Françoise Dosba
various member organizations
that constitute Agropolis: Agro.M,
Cirad, CNRS, INRA, IRD,
“Creation of drought-resistant plants?” Page 26
the University of Montpellier and
François Tardieu
the University of Perpignan.
This dossier presents the major
“Plant-parasite interactions: prospects for Page 29
lines of research conducted at
integrated protection” Jean-Loup Notteghem
Agropolis, and describes projects
that make full use of the skills
and know-how of its scientists. “Dissemination of innovations: from research Page 32
to applications” Jacques Meunier
“Education and training at Agropolis” Page 36
André Charrier
summaryGenetic resources:
towards better
understanding,
conservation and use
uccessful development of
Agronomic research must
needed to improve resistance to
new, higher-yield and
diseases, tolerance of drought
continue to produce new
S
better-quality varieties in a
and of poor-quality soils, to
varieties if we are to meet the
more environmentally friendly
accelerate growth, increase yields,
demands of sustainable
agribusiness sector will follow
improve nutritional quality, and
agriculture which is both
from sustainable and responsible
so forth.
exploitation of biodiversity, and
environmentally friendly and
from understanding how this
Effective and reasoned exploitation
able to ensure food security for
biodiversity can be conserved for
of the genetic diversity of cultivated
a world population that will
future generations. Biodiversity in
and wild relatives calls for
top 8,000 million by the year
agriculture can be equated with
extensive knowledge and for
2020. Intensification of
genetic resources of the wild and
effective tools for the transfer of
cultivated plant species that
agricultural production seen
traits of agronomic value. In its
together constitute a pool of
work on the genetic resources of
during the second half of the
agronomically valuable genes
tropical and Mediterranean
20th century has reduced both
the number and the genetic
diversity of the species used by
Conserving
man, resulting in increased
vulnerability of crops to recalcitrant seeds
diseases and pests.
at subpolar
Team and co-ordinator
temperatures
The "Diversity and Genome of
The genetic resources of many plants cannot be
Cultivated Plants" research group
conserved under the conditions conventionally
(UMR DGPC) includes 50 researchers
used in gene libraries (storage of dehydrated
from Agro.M, Cirad, INRA, IRD and the
University of Montpellier
seeds in cold rooms). Either the seeds of these
plants do not tolerate the dehydration and/or
Co-ordinator : Serge Hamon, IRD
cold (coffee trees, for example), or they
serge.hamon@mpl.ird.fr
propagate vegetatively (vines).
fax : +33(0)4 67 41 62 22
Cryoconservation, i.e. storage of living plant
Coffee beans
material at very low temperature (-196°C), is
conserved at –196°C
the only method available for the long-term
conservation of the diversity of these species.The DGPC
research group aims to develop methods of cryoconservation
routinely applicable in conservation centres and to study the
underlying biophysical and physiological mechanisms.
Contact : Stéphane Dussert, stephane.dussert@mpl.ird.fr
4
Agropolis - May 2001
Stéphane Dussert, © IRDBetter quality sunflower oils
found in other oils. It is naturally rich in linoleic acid and
vitamin E, whose antioxidant properties protect against
ageing and stress, lacks linolenic acid (thus allowing safe
high-temperature use), and contains phytosterols, which are
known to counter so-called bad cholesterol.The DGPC
research group aims to make better use of these characteristics
of sunflower oil by investigating wild forms of Helianthus
annuus as novel resources for improvement, and by creating
new varieties.The objectives are:
- to produce oils as rich as possible in linoleic or oleic acid to
be used in mixes in response to demand;
- to increase the vitamin E content so that consumers can
reach the recommended daily intake by consuming small
Using wild relatives to improve oil quality
amounts of oil (a portion of vinaigrette on salad, for instance);
Sunflower oil is much coveted by consumers and industrialists
- to increase the quantity and quality of phytosterols.
alike for its nutritional quality and several characteristics not Contact : André Bervillé, berville@ensam.inra.fr
plants, the Diversity and Genome More recent research on genetic valuable trait can be identified
of Cultivated Plants (DGPC)
diversity has adopted a functional using molecular tools and labelling
research group has a twofold aim:
approach designed to elucidate techniques. The same tools can
to make use of plant diversity for
the mechanisms that control and then be transformed into efficient
variety improvement and
characterize biodiversity and to screening and selection techniques.
conservation.
explore plant genomics. With
improvements in molecular By linking a particular agronomic
From plant diversity
biology tools and the use of plant feature to one or more molecular
models, we can now work with markers, effective selection
to gene mapping
the genes that govern agronomic becomes feasible. It can be ensured
Until the early 1990s, research on
characteristics. These tools reveal that a hybrid between a cultivated
genetic diversity employed a
the diversity of genes (alleles), plant and a wild relatives has
descriptive approach which paid
localize them and “shed light” on recovered the gene or genes that
particular attention to the
their expression in various genetic control the expression of the
"evolution" and "history" of plant
or environmental contexts. desired agronomic feature from a
resources. Researchers collected
very early, plantlet stage. This
numerous plant species and
Agronomic characteristics, which circumvents the need for field
varieties and organized them in
are of paramount importance in tests or experiments under
collections. This approach yielded
breeding, are sometimes difficult controlled conditions, as in
extensive information on the
to assess and of complex genetic studies of disease resistance,
species complexes that cultivated
determinism. The chromosomal which are difficult, costly and
plants form with their wild
regions containing the gene(s) time-consuming.•••
relatives, on their subgroupings,
involved in the expression of a
and on gene flow.
5
André Bervillié, © INRA
Agropolis - May 2001Genetic resources: towards better understanding, conservation and use
Conserving
Using coloured
genetic resources
chromosomes to
If we are to meet the foreseeable
identify species origin and unexpected demands of the
agriculture of tomorrow, it is vital
to conserve the most diversified
Genome structure can be investigated using molecular
resources possible. Over the last
cytogenetics. Fluorescent In Situ Hybridization (FISH) locates
three decades this goal has led to
precise sequences which will be fluorescently labelled on the
the creation of ex situ collections, in
chromosomes. Genomic In Situ Hybridization (GISH)
which diversity is conserved outside
differentiates the chromosomes of parental species in
the natural environment, generally
interspecific hybrids.
as seeds kept in cold storage, but
These techniques are particularly useful in cultivated plants
also as cultivated plants (notably in
with many chromosomes (polyploid)
the case of perennials). The
and/or in interspecific hybrids, like sugar
management and utilization of
cane, banana, coffee, citrus or cotton.
base collections are simplified
The finer techniques of hybridization of
using core collections, in which the
Bacterial Artificial Chromosomes
diversity of a collection is represented
(BACs) to chromosomes and to uncoiled
by a small number of plants.
DNA complement physical mapping and
in particular positional cloning of genes
These methods of conservation
of agronomic interest.
Fluorescence is used to
have proved highly valuable but do
Contact :Angélique D’Hont,
screen chromosomes in
have some drawbacks, as they:
angelique.dhont@cirad.fr
hybrids
- "freeze" diversity,
- are ill-suited to species with
unorthodox seeds,
- are subject to climatic or parasitic
hazards.
Such methods do not allow the
conserved material to evolve in
parallel with its environment, and
so after 20 or 30 years the conserved
Detective work
plants may no longer be able to
survive the new environmental
in identifying vine varieties
stresses. Furthermore, some plants,
notably tropical, poorly tolerate
The vine is a highly diversified species, with 5,000 to 6,000
low-temperature storage. Lastly,
vine varieties listed worldwide.The INRA at Vassal houses the
stored seeds gradually lose their
largest vine collection in the world, with some 2,300 identified
germinative power and must be
vine varieties and a thousand undergoing identification. INRA
regenerated regularly, which is
researchers have begun the analysis of the genetic diversity of
costly and labour-intensive.
this collection using molecular markers (microsatellites and
chloroplast markers).The main purpose of these analyses is
J.-P. Bruno- © INRA-Domaine de vassal
the characterization and management of the genetic resources
of the vine.The goal is the genetic fingerprinting of all these
vine varieties. Preliminary results have demonstrated the utility
of these genetic fingerprints:
- as an aid to identification: the analysis of the DNA extracted
from leaves, wood, roots, or rafle (peduncles/pedicels) allows
unambiguous identification of unknown samples,
- in the analysis of the origin of current vine varieties: it has
been shown that prestigious vine varieties such as
Chardonnay, Gamay and Aligoté resulted from seeds
obtained by a natural cross between the vine varieties
Pinot and Gouais.
Contact : Patrice This, this@ensam.inra.fr
Vine variety:
securing identification
6
Agropolis - May 2001
Angélique D’Hont, © Cirad-CABoosting rubber production
through resistance to a fungus
In Latin America, industrial and local plantations of the hevea regarding the genetic origin of hevea's resistance to leaf
are decimated by the South American leaf blight vector blight.We now know that:
Microcyclus ulei. Over half a century of work has failed to - the genetic determinism of resistance to leaf blight, whether
produce high-latex-yield varieties resistant to leaf blight.As a partial or total, is complex and multigenic (controlled by
result, Latin America, the original home of hevea, now only several genes);
accounts for 1% of - 8 QTL of resistance have been identified on 7 chromosomes;
- 1 QTL with a major effect is common to all hevea varieties
natural rubber production
and to the two types of resistance, partial and total.
worldwide.
This work has yielded findings vital to strategies and to the
To unravel the genetic
development of new tools for the improvement breeding of
determinism of resistance
variety resistance to Microcyclus ulei.
identified in Amazonian
Contact : Marc Seguin, seguin@cirad.fr
genetic resources,
researchers at Cirad have
used genome mapping to
analyze Quantitative Trait
Loci (QTL) or
chromosomal regions
implicated in resistance.
The results have disproved
previous hypotheses
- product quality, as in seedless
Meeting
grape varieties, the "in the cup"
the demands
aroma of coffee varieties, and
sunflower oils (stability of the
of tomorrow
oleic acid content);
Helping Brazil to come back
- sources of resistance to diseases
into the rubber business Through their research into
caused caused by viruses (e.g.
genetic resources, the scientists
Solutions to these drawbacks are
rice yellow mottle virus) and
of Agro-Montpellier, Cirad, INRA,
to be found through two
fungi (e.g. powdery mildew of the
IRD and the University of
alternative approaches pursued
vine or fusarium in the oil palm),
Montpellier are anticipating the
by the DGPC research group:
but also by animal parasites (e.g.
future needs of the whole agrifood
- In situ conservation, the
nematodes in rice, banana and
chain, from producer to consumer,
conservation of plants in their
Solanaceae or certain vectors of
while paying particular attention
natural environment, conserves
serious viral diseases in vines).
to tropical species and the special
diversity but above all maintains
This search for sources of disease
requirements and demands of
the plants' capacity to evolve and
resistance, together with studies
agriculture in southern countries.
adapt. Plants conserved in situ
of plant-pathogen interactions,
Increasing attention is being paid
continue dynamically to "create"
leads to the identification of the
to the study of "diversity of
diversity because they are subject
most durable resistances;
expression", with a view to better
to environmental constraints
- assessment of the risks associated
understanding of the genetic
(diseases, pests…) and can
with gene flow (genetic pollution,
determinants of the diversity and
interact and exchange genetic
diffusion of transgenes) occurring
of gene function.
material with other plants;
between new varieties and
Through its development of more
- Cryoconservation, i.e. the
neighbouring plants.
effective research tools, the DGPC
storage of material at ultralow
research group has mainly
temperature, generally that of
focused on three major types of
liquid nitrogen (-196°C), is the
application of plant genomics:
only technique that ensures
inexpensive, long-term
conservation of recalcitrant
seeds. It is also applicable to the
conservation of the buds of
plants that propagate vegetatively.
7
Denis Lespinasse,© Cirad-CP
Agropolis - May 2001Genomics applied
to agronomic
Genetic improvement is founded
traits
on better understanding of the
characteristics and functioning
of individual plants and on a enomics offers various ways of to the development of a whole range
acquiring knowledge on of new methods and improved
finer perception of the diversity
G
cultivated plants and of precision of existing methods.
present in the genetic resources
improving them:
- molecular physiology, which uses
of the cultivated species. The
Mapping and
functional genomics to identify
various technologies of
agronomically valuable traits, sequencing of
genomics should make a
- genetic mixing, which enables the
genomes
creation of new varieties based on
major contribution to the
better genome mapping of factors
• Genetic mapping uses labelling
characterization of genes and
that govern the agronomic
with molecular markers to map the
their functions.
characteristics.
genetic factors responsible for certain
Genomics is applied to:
agronomic traits of interest (such as
- general agronomic characteristics,
resistance to disease or a criterion of
Team and co-ordinator
which can be studied in model plants
the technological quality of the plant).
The "Genomics applied to such as rice (model plant for
Offspring are generated by controlled
monocotyledons),
agronomic traits" research group
crosses and then analyzed, using
- specific agronomic traits, which
(UMR GACA) comprises 13
molecular markers and agronomic
should be studied in the different
researchers from Agro.M, Cirad assessment in the field. This molecular
species of agronomic value, as done
and INRA. characterization yields a detailed
for twenty or so Mediterranean and
Co-ordinator: Jean-Christophe genetic map of the genome of the
tropical plants.
Glaszmann, Cirad, species. Fine mapping, based on the
jean-christophe.glaszmann@cirad.fr, analysis of more offspring then locates
Genomics is based on recent progress these genetic factors precisely
fax: +33 (0)4 67 61 56 05
in molecular biology, which has led enough to allow physical mapping.
Cirad-Flhor
A BAC library for the study of the structure
of banana plant chromosomes
The banana is a giant herbaceous forms are diploid, 2n=2x=22.There are six main genomic
plant that may grow to between groups:AA,AAA,AB,AAB,ABB,ABBB. In addition to the
1.5 and 8 metres in height.The contribution (different proportions) of genomes A and B,
fruit of cultivated banana (cultivars) there are also translocations, exchanges and inversions in
are the only ones to be eaten. each of the two genomes, although their frequency is
Wild banana with seeds to
They are seedless, whereas the unknown.The availability of large fragments of DNA combined
improve crop varieties
fruits of wild banana plants contain with in situ hybridization to chromosomes (FISH, Fluorescent
seeds about 5 mm in diameter.The cultivars are divided into In Situ Hybridization) should lead to characterization of
two subgroups: sweet bananas (or dessert bananas) and variations in genome structure in the banana plant.A BAC
cooking bananas, among which plantains are the most (Bacterial Artificial Chromosome) library constructed from
important. the cultivar Calcutta 4 (AA) is used for this purpose.This
The cultivars, of interspecific origin, are classified according research will clarify the relative structure of banana cultivars
to their ploidy level (number of chromosomes) and the and the impact of translocations on their diversity, and open
relative contribution of the species Musa acuminata (genome up new ways to improvement.
A) and Musa balbisiana (genome B) to the characteristics of Contact: Pierre Lagoda, pierre.lagoda@cirad.fr
the clone considered.All the wild acuminata and balbisiana
8
Agropolis - May 2001Quality of cotton fibre
Cotton fibre is the natural fibre most used by the textile
industry. It has a unicellular structure which develops from
epidermal cells of the seed integument.We currently have
few molecular data that would enable a correlation to be
made between gene expression and the technological quality
of the fibres (length, strength, resistance to stretching…). It is
now possible to identify which genes account for the different
qualities of fibres in diverse mutants, varieties and species of
cotton plant. For this, patterns of expression of cDNA
(complementary DNA) and of Expressed Sequence Tags
(ESTs) during cotton fibre development are investigated.This
indicates which genes are involved in this agronomic trait
and, in each case, identifies the favourable alleles. It will thus
be possible to locate important genes whose expression
determines in fine intrinsic fibre quality, and possibly to assign
a biological function to these genes.The candidate genes thus
What genes are
identified are of agronomic interest and can be genetically
controlling technological
tested in the analysis of Quantitative Trait Loci involved in
quality in cotton
the fibre technological quality.
(fibre length, strength,
Contact: Marc Giband, marc.giband@cirad.fr
resistance…) ?
All this presupposes access to genetic typically applied to positional cloning
resources, land for field trials, (see page 11 “Synteny and parallel
laboratory facilities, and a capacity chromosome walking in the Poaceae”)
to raise offspring in confinement. of genes of agronomic interest. It also
serves to recover the complete version
• Structural genomics reveals the of genes detected by means of their
physical organization of the genome transcribed sequences, or Expressed
in the form of chromosomes bearing Sequence Tags (ESTs);
various types of sequences which - systematic sequencing of the genome
contain genes of interest. gives access to all the genes of a plant,
- physical mapping of the genome i.e. between 20,000 and 50,000. Large
constructs a replica of a whole genome industrial groups and laboratory
in the form of large DNA fragments networks generate this type of
that are cloned (inside bacteria in the information using model plants like
case of Bacterial Artificial Chromosome Arabidopsis and rice. The Languedoc-
clones) and ordered with respect to Roussillon laboratories have
one other. This mapping translates a participated in the setting up of such
genetic map – which locates the an initiative in France for the
genomic regions implicated in the chromosome 12 of rice (see page 16
expression of particular traits – into "The Montpellier and Languedoc-
DNA fragments that contain the Roussillon Génopole ").
•••
genes governing these traits. It is
9
J.-L. Chanselme, © Cirad-CA
Bernard Hau, © Cirad-CA
Agropolis - May 2001Genomics applied to agronomic traits
Identifying gene function
using rice mutants
The rice genome contains about 30,000 genes, half of which mutant carrying the
have an as yet undetermined role.The function of these altered sequence
genes can be found by analysing of a large population of (reverse genetics).
plants in which a mutagen has been randomly inserted into This will enable
each gene. Mutagens are short DNA sequences of different isolation of the rice
types that are used as tools to map and isolate genes genes involved in
("molecular labels" so to speak). plant morphogenesis
In the framework of the national plant genomics initiative (architecture,
Génoplante (see page 16), a team of researchers from flowering,
Cirad-INRA-IRD-CNRS / University of Perpignan based at embryogenesis…)
Montpellier has created a collection of rice insertion mutants and in the tolerance
large enough (100,000) so that each gene has a good of biotic stress
A reporter (blue) gene reveals gene
probability of being interrupted at least once by an insertional (diseases and pests)
expression in vessels of a rice flower
mutagen, here the T-DNA from Agrobacterium tumefaciens. and abiotic stress
The collection of mutants will be progressively screened (drought, salinity,
under various constraints in a controlled environment mineral deficiency
(confinement greenhouse, phytotrons) so as to identify plants or toxicity). Molecular mapping of these genes will shed light
of altered morphology, physiology or tolerance of environmental on the genetic control of quantitative traits and will greatly
constraints, and subsequently to isolate the affected genes facilitate varietal improvement in rice and other cereals
that govern the characteristics in question (forward genetics). (wheat, barley, maize, sorghum…) .
The genome sequences adjacent to the T-DNA insertion sites Contact: Emmanuel Guiderdoni,
in each mutant will be entered in a database.They will then emmanuel.guiderdoni@cirad.fr
be used to study the function of any gene with a known
sequence, by searching for and then evaluating the relevant
Characterizing
- partial sequencing of expressed its expression in the plant;
genes (Expressed Sequence Tags or - the fine evaluation of transformed
gene function
ESTs) allows the characterization of material to elucidate all facets of the
genome expression patterns. The function of a gene, by means of cellular
• Functional genomics aims to
analysis of RNA extracted from certain and molecular biology, and physiology.
characterize the expression of the
organs of cultivated plants, under
genome and its integration in the
given conditions and at a given These technologies, applied to some
major metabolic functions.
moment, yields an image of all the model plants and to a range of more
- insertional mutagenesis (see above
genes expressed under these complex cultivated plants, can build
"Identifying gene function using rice
conditions. Among these genes are bridges between genomes. Genetic
mutants ") creates mutants by
some of agronomic value that it information can be transferred
randomly inserting in the genome a
would useful to clone. Depending on between several species because of
DNA fragment that can be mapped.
the characteristics of the sequences the conservation throughout evolution
When this fragment is integrated in a
or of the expression patterns, some of of certain elements of the general
gene, thus generating a mutant, it
these ESTs can be attributed a genome organization, like the
alters the gene's function, thereby
hypothetical function, thus making similarity in gene distribution between
modifying the trait of interest. The
them candidate genes. This is now chromosomes (conservation of
mutated gene is located thanks to the
under way using model plants and synteny, see next page "Synteny and
inserted fragment, and its function is
will be extended to the major crops. parallel chromosome walking in the
identified using the affected trait.
The precise functions of the candidate Poaceae") or the colinearity between
This technique has been developed
genes, identified through genomic homologous chromosomes.
for different model plants
approaches, are characterized in two Genomics gives an impetus which
(Arabidopsis, Medicago truncatula,
stages: unites research teams formerly
for example). The Montpellier
- genetic transformation to test the specialized in different cultivated
research teams are studying rice as a
effect of a gene or of a candidate plants.
representative of the grass family
sequence on the phenotype of a
(Poaceae);
plant, through its insertion in the
genome and/or the modification of
10
Agropolis - May 2001Studies are under way to investigate proteins of importance
in the value of wheats, notably the thioredoxin system.
Wheat genes, proteins
The thioredoxin system is used to improve the
and quality
breadmaking quality of wheat varieties deemed
unsuitable for breadmaking
Research on durum wheat and bread wheat is intended to
The proteins in flour are responsible for the viscoelastic
improve the quality of cereal-based products (pasta, bread,
properties of dough.The reserve proteins (gliadins and
biscuits…) and to develop new tools for breeding, such as
glutenins) are the major constituents of the gluten obtained
molecular markers. Proteins involved in a given characteristic
after kneading dough under a fine stream of water.
are identified and characterized biochemically, thus yielding
Depending on the rheological properties of gluten, the bread
data for the isolation of the relevant genes.These genes are
will be more or less developed after fermentation.Although
then investigated (regulation, structure), mapped and/or used
numerous chemical bonds are involved, disulphide bonds are
as markers in breeding.
believed to play an important part in the elasticity of the
In the national Génoplante programme, a genomic approach is
dough.The NADP-dependent thioredoxin system (an enzymatic
currently being developed: 100,000 ESTs (Expressed Sequence
system) is able to reduce the disulphide bridges of the reserve
Tags) will be
proteins but also of other small proteins especially rich in
Fréderic de Lamotte, © UBBMC-INRA
produced from
disulphide bridges.This generates free –SH groups which can
different libraries
then be reoxidized by creating inter-protein bonds, thus
of cDNA
facilitating the network development and contributing to
(complementary)
dough elasticity.The controlled addition of the different
from mRNAs
components of this thioredoxin system therefore allows to
(messenger)
improve the breadmaking quality of varieties deemed to be
extracted from
unsuitable for breadmaking.
ripening seeds.The
Biochemical and molecular studies of the thioredoxin system
goal is to identify
have yielded several isoforms and their relevant cDNAs.The
all the seed proteins
proteins encoded by these cDNAs are produced in
that play a part in
heterologous hosts so as to study their structures and
the wheat quality
functions.
and also to use
Contact: Philippe Joudrier, joudrier@inra.ensam.fr
these ESTs for
genetic mapping in
Studying proteins involved in
order to define
wheat quality to develop new
Quantitative Trait Loci
breeding tools
(QTL) usable in selection.
Canne à Sucre
BAC
marqueur Riz
Synteny and parallel
BAC
chromosome walking in Séquences
microsynténie?
répétées ( )
the Poaceae
gène cible
The grass family (Poaceae) is remarkable for the conservation
Polyploïdie
of the basic structure of their genome: conservation of synteny
Rice as a short cut for chromosome walking in other large genome species of
the Poaceae using BAC libraries
(distribution of genes between chromosomes) and of colinearity
between homologous chromosomes.This conservation is seen
despite great genome diversity stemming from the frequency
been constructed for the main species such as rice, sorghum,
of anonymous repeated sequences (of undetermined function)
sugar cane or wheat.The next step is genomic analysis of
and the ploidy level (number of copies of the basic
characteristics such as resistance to diseases, grain quality,
chromosomes in the cells).This parallelism allows interspecific
plant architecture and drought tolerance.
transposition of information and creation of common analytical
Contact: J.-C. Glaszmann,
and biological resources.The model species is rice, which
jean christophe.glaszmann@cirad.fr
among the Poaceae has the simplest genome, which is now
being sequenced. Libraries of large fragments of DNA,
constituted in Bacterial Artificial Chromosomes (BACs), have
11
microcolinéarité?
J.C. Glaszmann, © Cirad-Amis
Agropolis - May 2001Genomics and
plant development
From its creation, the and researchers who are analyzing
Genomics and molecular
University of Perpignan developmental processes and
genetics are now providing
D
laboratory has been studying dissecting basic cellular and
great insights into how a seed
plant development using molecular biochemical mechanisms.
analysis. By the early 1980s, this
forms and acquires its
approach had laid the groundwork
longevity and germination The early stages of
for the application of genomic
vigour, how protein production
technologies. The laboratory has thus
plant development
played a pioneering role in France in
is controlled by the ribosome,
Our work centres on embryogenesis,
the launch of projects on Arabidopsis
and how the potential of
seed formation and maturation,
thaliana, a species which remains the
oxidoreduction controls the topics of vital interest to the seed
principal research model because of
industry and the agricultural sector.
a number of advantages: its genome
cell cycle, growth and
Our first aim is to identify the role
has been sequenced, there are
environmental adaptation
and function of genes involved in
numerous mutants for use in
of plants. early embryogenesis and embryo
dissecting metabolic pathways,
formation. Secondly, our plan is to
development programmes, responses
determine the role and regulation of
to environmental stimuli and basic
Team and co-ordinator
proteins involved in seed maturation.
cellular mechanisms, and it is
This research leads to various
accessible to forward and reverse
The “Genome and Development of
technological developments: search for
genetic approaches.
Plants” research team (UMR GDP)
promoter genes, conditional control of
comprises 17 researchers from
gene expression, manipulation of
Our laboratory brings together
CNRS and the University of
reserve lipid or protein contents.
•••
experts in most aspects of genomics
Perpignan.
(continued on page 14)
Co-ordinator: Michel Delseny,
University of Perpignan,
delseny@univ-perp.fr,
fax: +33 (0)4 68 66 22 24, website:
http://syrah.univ-perp.fr/lgdp,
Biosynthesis of the ribosome
The ribosome is a cellular organelle that biosynthesizes proteins
and is therefore largely responsible for the productivity of the
plant cell. It is composed of ribosomal RNA and 80 different
proteins.To date, our work has focused on analysis of the
maturation of precursors of ribosomal RNAs.We have
characterized ribonucleoprotein complexes involved in
precursor maturation, and purified and microsequenced
the proteins, thus allowing cloning the relevant genes.
We have shown that some of these proteins bind to the
promoter of several genes of ribosomal proteins,
suggesting the existence of an integrated regulation of
their synthesis. Using the Arabidopsis genome data, we are
systematically identifying genes encoding ribosomal
proteins, genes of proteins involved in ribonucleoprotein
Observation of fibrillarin
complexes, and genes of snoRNA (small nucleolar RNA)
through a linkage with
a green fluorescence
responsible for the modification of ribosomal RNA.
reporter in transgenic
Contact: Manuel Echeverria, manuel@univ-perp.fr
onion cells.
12
Agropolis - May 2001
Fredy Barneche,© Univ de PerpignanRole of thioredoxins in the plant cell
Thioredoxins are enzymes that can break disulphide cell processes? What are the targets of the different
bridges in proteins, thus regulating their conformation thioredoxins? Which functional domains of thioredoxins
and hence their activity. The first gene of plant account for their specificity? We have made
cytosolic thioredoxin was isolated in our substantial progress in seeking answers to
laboratory by differential screening of the these questions. We have shown that
relevant cDNA (complementary DNA) different thioredoxins are specialized
from messenger RNAs expressed in sulphate uptake, cell cycle control,
very early in the dedifferentiation of the response to oxidative stress or
tobacco protoplasts.The activity of a pathogens. Several insertion mutants
second gene of tobacco thioredoxin have been obtained,
Structure of
was demonstrated on resumption but none has revealed
cytosolic thioredoxin in
of cell division when the tobacco Arabidopsis thaliana a clear phenotype.
protoplasts were cultured. This This suggests that
showed that these proteins are the alteration of one gene could
involved in the regulation of the cell possibly be compensated by the
cycle.The discovery of multiple copies expression of another, or by the
of thioredoxin genes in the genome of expression of genes of another redoxins
Arabidopsis prompted a variety of questions. family, such as the glutaredoxins.
J.M. Lancellin,© Univ.
de Perpignan
What part does each gene play in the various Contact:Yves Meyer, ymeyer@univ-perp.fr
Alain Got,© Univ. de Perpignan
Studying model plants
Two model plants representing of all the plant genes, and to identify the elements which
the two large divisions in the control their expression. Gene function can also be investigated
higher plants (monocotyledons through the creation of mutants (by random insertion of a
and dicotyledons) were chosen fragment of DNA in the genes) and the observation of the
for the systematic study of characteristics altered by the mutation.The Perpignan group
plant genome structure and has participated in all these projects since 1992.
function. The expertise and know-how acquired in studying Arabidopsis
For dicotyledons, the model are now being applied to study the structure and expression
plant is Arabidopsis thaliana, of the rice genome, the model plant for monocotyledons.
which genome sequencing The complete sequence of the rice genome should be available
was completed at the end of by 2003. By putting the clones of large DNA fragments (used
2000.The expression profile for sequencing) in order, we have been able to supply the
Arabidopsis thaliana, model
of the genes has also been National Sequencing Centre with the starting points for the
plant for dicots
studied using Expressed sequencing of the chromosome 12. Libraries of cDNA are
Sequence Tags (ESTs) from cDNA (complementary DNA) being prepared for the study of gene expression and structure,
libraries. Each EST identifies a gene which is expressed at a while a systematic analysis of insertion mutants is under way
given moment in the life of the plant. However, ESTs are to determine the function of the genes.This work is being
available for only half of the genes of the Arabidopsis, and done on the cultivar chosen by all the partners in the
functions can be suggested for just 60% or so of some international sequencing project.
25,000 genes. Bioinformatic analysis of Arabidopsis genome (see page 10 "Identifying gene function using rice mutants ")
structure will enable us to map and determine the structure Contact: Richard Cooke, cooke@univ-perp.fr
13
Agropolis - May 2001Genomics and Plant Development
Genetic
Using genetics to clarify
determinism of
the mechanisms of
basic biochemical
embryogenesis
processes
We are also seeking to clarify how
Embryogenesis of flowering plants occurs in three stages:
mechanisms such as the formation
early embryogenesis during which the embryo forms,
and rupture of protein disulphide
seed maturation, with synthesis and accumulation of reserve
bridges contribute to cell cycle
proteins, lipids and carbohydrates, and desiccation, when
control and to responses to plant
the seed loses much of its water and enters dormancy.These
oxidative stress. Our group is therefore
systematically analyzing redoxin
three stages are studied by the GDP research group.
genes, studying their regulation, and
Early embryogenesis: this is studied by the genetic analysis of
seeking the proteins targeted by
"embryogenesis mutants" in Arabidopsis called embryo-defective
thioredoxins.
mutants (emb).The INRA collection of T-DNA insertion
mutants is screened to identify plants that have aborted seeds
Finally, we are analysing a basic cell
in their fruit.These seeds have not been able to complete
process: the biosynthesis of ribosome
and the coordination of the synthesis
their formation because an essential gene (EMB gene) has
of its different constituents, ribosomal
been altered.This altered EMB gene is identified and studied
RNAs and ribosomal proteins. Using
using the T-DNA inserted tag. Six or so EMB genes essential for
biochemical techniques, we have
the first divisions of the embryo cells have been characterized.
identified regulatory proteins of the
Seed maturation: having identified the principal reserve
maturation of the precursor of
proteins of Arabidopsis seeds, we are now interested in the
ribosomal RNAs. Now that the genome
of Arabidopsis is entirely sequenced,
genes encoding enzymes of lipid biosynthesis.We are focusing
our ambition is to understand how
mainly on rapeseed, notably the genes encoding elongases
the different elements are integrated
and acyltransferases which contribute to the formation of
and coregulated and how functional
triglycerides.
redundancy is managed, doubtless
Desiccation: LEA (Late Embryogenesis Abundant) proteins
by creating an heterogeneity of
are synthesized in large quantities during desiccation of the
ribosomes between different
physiological stages.
seed. One of their roles seems to be the maintenance of a
survival environment for the cells.We inventoried the LEA
proteins, and then investigated one of
them, the Em1 protein. Using the Em1
gene as a tool, we isolated the ABI5 gene,
an activator of the expression of the LEA
genes.We are now investigating how
AB15 interacts with other regulators of
LEA proteins.
Contacts: Martine Devic, University of
Perpignan, devic@univ-perp.fr and
Michel Delseny, University of
Perpignan, delseny@univ-perp.fr
Jocelyne Guilleminot, © Univ. de Perpignan
The reporter gene reveals a
gene expressed in the seed
development
14
Agropolis - May 2001Rice yellow mottle virus interactions
and natural resistance
Rice yellow mottle virus
(RYMV) has spread
considerably over the last 20
years, following intensification
of irrigated rice growing in
Africa.The only possible
solution to control this
pathogen is the development
of varietal resistance. Since its
discovery, research has focused
RYMV seen on the virus itself (structure,
through infectious cycle, serological and molecular variability) and on
Constantly evolving
A- electron
natural resistances that could be used in breeding. In its study
1
microscopy
of the infectious cycle, ILTAB has described the different
research activities
B- cryomicroscopy
stages and characteristics of viral movement in the plant.
2
and image
Our group's main thrust in genome Cryomicroscopy and crystallography have been used to
reconstruction
analysis has been related to
determine the high-resolution three-dimensional structure of
C- cristallography
Arabidopsis, with participation in the
the virus.Taken together, these data underpin the interpretation
programme designed to obtain
of the molecular interactions between the viral envelope
Expressed Sequence Tags (ESTs) and
protein and the host proteins, and their consequences for
in genome sequencing. We now
the variability of viral pathogenicity. In collaboration with
concentrate our efforts on functional
3
WARDA in Côte d’Ivoire, we have studied different natural
analysis, with an extensive study of
sources of resistance to this virus in the two rice species
mutants, and on the analysis of the
4
grown in Africa . Mapping and genetic labelling have led to
genome structure and organization
(presence of large duplications, locate these resistance genes (or QTLs) on the rice
multigene families, annotation…).
chromosomes.
We are currently using the genome
Positional cloning of these resistance genes and the study of
sequencing experience acquired with
their functions is now a realistic goal using genomic tools. In
Arabidopsis to initiate new genomic
collaboration with WARDA, these genes of natural resistance
projects on rice, cassava and other
are now transferred by marker-assisted selection. Cloning of
species, in collaboration with
these genes will allow the assessment of diversity in rice
research teams at regional level in the
collections, the characterization of other host-virus
framework of the Montpellier-
interactions such as tolerance, and laboratory simulation of
Languedoc-Roussillon Génopole (see
next page), or at Génoplante and how these resistance genes may be bypassed, in order to
foreign institutions level.
ensure a sustainable resistance after deployment across large
areas. Lastly, as rice is a model plant for the cereal functional
genomics, rice-RYMV molecular interactions probably also
constitute a model for the exploration of host-virus
interactions in other cereals.
This work on the rice yellow mottle virus is a prime example
of the multidisciplinary research conducted by several
Montpellier teams in concert with international colleagues. It
both added considerably to fundamental understanding and
yielded practical applications usable in rural development.
(1) ILTAB: International Laboratory for Tropical Agriculture Biotechnology, USA.
(2) Collaboration with ILTAB and the Scripps Research Institute.
(3) WARDA:West African Rice Development Association
(4) Oryza sativa and Oryza glaberrima
Contact:Alain Ghesquière, alain.ghesquiere@mpl.ird.fr
15
© IRD/ILTAB/scripps
Agropolis - May 2001The Montpellier
Languedoc-Roussillon
Génopole
United we stand, divided we fall
The Génopoles were created in France so as to share access to
complex and cutting-edge equipment with various genomics research
teams working within the same region.This pooling of strengths and Génopole: shared
resources is expected to boost national and European genomics and equipments for
post-genomics studies.
research in
genomics
The Montpellier Languedoc-Roussillon Génopole embraces forty or
so laboratories working on plant, microbial, animal or human genomics.
It was one of the first networks of its type in France, and from the
outset was strongly focused on plant genomics.
Apart from making research tools available, the Génopole is also
designed to generate new information in genomics and to promote
the creation of biotechnology start-up companies with high added value.
Joint input from the
Various investments have allowed acquisition of:
public and private
- robots, DNA sequencers,
- information technology computing capacity,
sectors to enhance
- equipment for the production and reading of DNA chips,
- complementing device for the analysis of proteins by mass
performance: the
spectrometry, and
- adequate greenhouses for transgenic plants.
Génoplante programme
Several technologies are already implemented, such as:
Génoplante is a national programme involving partners from
- genomic robotics,
- medium-scale sequencing (ca.5 Mbp/year), the public (Cirad, CNRS, INRA and IRD) and private (Aventis
- transcriptome analysis,
Crop Science, Biogemma and Bioplante) sectors. Génoplante is
- proteome analysis,
more focused on crops of major economic importance than
- bioinformatics,
the regional Montpellier Languedoc-Roussillon Génopole. Its
- structural biology.
aim is to provide France with a global, coherent and competitive
structure for the study of plant genomes and its potential
We are also in the process of setting up other techniques (plant
applications.The objectives are to stimulate research and
genotyping, analysis of transgenic mice, analysis of protein-protein and
protein-nucleic acid interactions). creativity in genomics and to develop quality seeds that meet
the consumers and farmers demands.
Several major plant genome sequencing projects are under way,
The research projects range in scope from genetic resources to
principally using ESTs (Expressed Sequence Tags) with tropical species
genomic analysis of plant species.The main plants studied are
(rice, oil palm, cassava), one fungus and an alga. Some regions of
Arabidopsis and rice, as model plants, and major species grown
interest in the rice genome are also sequenced. Several BAC (Bacterial
in Europe: maize, rapeseed, wheat….The Languedoc-Roussillon
Artificial Chromosome) libraries are under construction. Functional
laboratories are deeply committed to this research, and actively
analysis relates above all to mutants of Arabidopsis and rice, but the
production of ESTs from various genomes will boost transcriptome participate in this programme, especially through their research
analysis programmes. Proteomic studies are also being developed.
activities on rice.
Contact: Michel Delseny, University of Perpignan,
Contact: Michel Delseny,
delseny@univ-perp.fr
delseny@univ-perp.fr
Rice: model plant
for monocots
16
Agropolis - May 2001
Michel Dukhan-IRD Sémiha Cebti, ©AgropolisThe experience of a new Sequencing the Arabidopsis
form of partnership: the thaliana genome:
Agropolis platform mouse-ear cress is not
what we thought …
The Agropolis research platform on plant genomics and
biotechnology promotes a collaborative research effort by
Size of the genome
French researchers, scientists from international agricultural
Species
(base pairs)
research centres, and research scientists from countries of
the South, in the European context of highly equipped
8
Mouse-ear cress 1.0 x 10
infrastructures, expertise and know-how.This platform
8
Rice 4.2 x 10
9
supports the cutting-edge research activities specifically
Tomato 1.0 x 10
9
needed to strengthen the studies required for the agricultural
Maize 2.5 x 10
10
development in the South. Wheat 1.6 x 10
Agropolis benefits from an especially favourable context since
Montpellier and its region already participate in two large-scale
The Montpellier-Languedoc-Roussillon Génopole and Michel
projects in genomics and plant biotechnology: Génopole and
Delseny's team (see precedent pages) have contributed to the
Génoplante.
international Arabidopsis thaliana genome sequencing project,
This multi-organizational platform concept encourages the
and especially to the sequencing of one of the five chromosomes
sharing of human resources and facilities dedicated to a global
of the species. Mouse-ear cress (Arabidopsis thaliana) was chosen
objective and a common goal. It synergizes the research
as a model plant because it has a number of experimental
efforts of national organizations and international agricultural
advantages – it is small, grows rapidly, has a short reproductive
research centers in the South, and highly equipped European
cycle, and above has a small genome. It was initially believed
institutions.Tested today on plant biotechnology, this concept
that mouse-ear cress had a small genome essentially because its
might be extended in the future to other research fields, in
genes are present as single copies, unlike species with a larger
line with the wishes of several national and international
genome (see table). However, sequencing has in fact shown that
partners.
over 70% of mouse-ear cress genes are duplicated (figure), and
Contact:Yves SAVIDAN,Agropolis, savidan@agropolis.fr
there are less than 15,000 different genes among the 26,000
sequenced.The next step is to identify the function of each
gene and of the protein it encodes. Sequencing is just one step,
but it opens up unprecedented possibilities, notably for the
study of species diversity and its use in crop improvement.
17
Map of duplicated region in the Arabidopsis thaliana genome
Guillaume Blanc-Univ.de Perpignan
Agropolis - May 2001Adaptation of
plants to stress
environments
he Biology and Molecular coherent molecular physiology
Environmental constraints
Physiology of Plants (B&PMP) approach, ranging from identification
linked to climate and soil
T research group aims to identify of a gene to discovery of its function
quality are the principal
the genetic and molecular bases of in the plant, including the molecular
plant adaptation to factors such as function of the encoded protein, and
hindrance to plant production
salinity, water availability, excess of the site and conditions of its
worldwide. Plant species and
toxic metals, and deficiency in expression (see page 21, "Genes…
varieties vary enormously in
inorganic nutrients. The B&PMP for which proteins?"). We use:
work places the group at the heart of - various systems for heterologous
their tolerance of these
national and European research in expression of plant genes (yeast,
constraints. In most cases,
plant molecular physiology. batrachian oöcytes, insect and
each plant has a panoply of
mammal cell cultures);
- reverse genetics (genetic
variants to its genetic
A global approach:
transformation of plants with reporter
programmes. Subjected to
genes, over- and underexpressors,
from gene to protein
each type of stress, the plant is
dissection of promoters and collections
of disrupted mutants);
The strategic positioning of the
able to select alternatives
- physiological techniques (flows of
B&PMP research group is defined by
within this set of genetic
isotopic tracers, in vivo
four keywords: molecular genetics,
programmes whose expression
electrophysiology, spectroscopic
molecular physiology, integrated
analyses of in vitro transport in
biology, and functional genomics. In
enhances adaptation to the
reconstituted systems, pressurized
our research we employ the molecular
new conditions. This ability to
microprobes for water transport, etc.)
genetics discipline-tool, i.e. the cloning
use environmental signals to
of genes and the study of their
expression. This work is designed to
drive genome expression is a
shed light on the physiological
speciality of the plant kingdom,
mechanisms looking at them from a
and is known as phenotypic
molecular viewpoint (see next page
"Cloning of the first transporter gene").
plasticity.
The discipline-object is molecular
Team and co-ordinator
physiology. The different research
The “Biology and Molecular Physiology
groups complete their molecular
of Plants” research group
studies by using biochemistry,
(UMR B&PMP) comprises almost 40 biophysics and physiology to find out
researchers from Agro.M, CNRS, INRA the gene function. Many of the
and the University of Montpellier II. mechanisms go beyond the cellular
Co-ordinator: Claude Grignon,Agro.M, level and reach the scale of the whole
grignon@ensam.inra.fr plant. Our group follows an integrated
biology approach, using molecular
fax: +33 (0)4 67 52 57 37
physiology, and through collaborations
with ecophysiologists teams and soil
scientists specialized in the study of
plant-environment interactions.
The B&PMP research group has at its
disposal a set of tools allowing a
18
Agropolis - May 2001Cloning of the first transporter gene of
the plant iron-siderophore complex
of this essential element.This causes the yellowing of leaves
called iron chlorosis.Whereas the roots of dicotyledons
reduce the ferric iron to ferrous iron and then absorb the
latter, the roots of grasses (Poaceae) use another mechanism:
they secrete molecules (siderophores) able to complex the
ferric iron in solution, and absorb the whole complex.This
process, which ensures that ferric irons is available for the
membrane transporters, allows grasses (Poaceae) to resist
iron chlorosis effectively. In maize, the YS1 mutation prevents
absorption of the iron-siderophore complex, resulting in
chlorotic zones on the leaves. Genetic analysis of a collection
of maize mutants created by insertion of a transposon has
allowed identification of homozygous individuals in which the
chlorotic phenotype is due to the transposon.The exploration
of genomic sequences near the transposon led to identification
of the YS1 gene, which encodes a polypeptide with a structure
In a rapeseed field, only one sorgho plant
similar to that of an ion transporter.This protein's ability to
escapes chlorosis
transport the iron-siderophore complex has been verified by
complementation of a mutant yeast strain unable to absorb
Molecular physiology is largely based on forward genetics iron.The YS1 gene of maize restores the yeast ability to
(from phenotype to gene) and reverse genetics (from gene to develop in an iron-poor environment, but only if the iron is
phenotype).This strategy is illustrated by the recent cloning supplied with the siderophore.The YS1 gene is expressed in
in maize of the first transporter gene of the iron-siderophore the roots and leaves and is induced by iron deficiency, thus
complex. explaining why iron-deficient plants have an increased capacity
Iron requirements of plants are quite high, but the insolubility to transport the iron-siderophore complex.
of the dominant ferric form in many soils limits the availability Contact: Jean-François Briat, briat@ensam.inra.fr
interactions of the mutated gene with deeply involved in the Montpellier
Strong commitment
its cellular environment. Several of the Génopole and Génoplante national
B&PMP group's research programmes programme, with fifteen functional
to national initiatives
are based on these principles, including: genomics projects, most of which
- a national proteomics permanent concern the model species Arabidopsis
in genomics
workshop; thaliana (see page 16). We are now
- various transcriptome approaches applying the know-how acquired in
Unlike molecular genetics, genomics is (DNA membranes, SAGE Serial these programmes to target species,
global as it focuses on the whole Analysis of Gene Expression); such as vine and maize.
•••
genome. The B&PMP research group is and all teams participate in the
a major national player in functional systematic use of the available
plant genomics. The genomics collections of Arabidopsis insertion
approaches facilitate understanding of mutants.
physiological complexity, revealing, for
instance, the major physiological Functional genomics reveals the
functions brought into play during molecular determinants of the
development or in response to particular physiological functions, thereby
environmental situations. When opening up possibilities for the
applied to the comparison of mutants, practical application of biological
such approaches shed light on the knowledge. The research group is
19
J.-F. Briat, © UMR B&PMP
Agropolis - May 2001Adaptation of plants to stress environments
A propitious scientific
Arabidopsis root-leaf
environment:
dialogue for better
the Institut des
mineral nutrition
Productions Végétales
The molecular physiology approach is illustrated by the study of
The research objectives and
signals that inform the roots of the nutritional requirements of the experimental strategies of the B&PMP
research group position it at the heart
aboveground parts of the plant. In this example, an Arabidopsis plant
of three Montpellier research groups
is deficient in nitrogen because half of its root system is placed in a
whose complementary activities range
nitrogen-free environment.The other roots, placed in an environment
from the analysis of genetic resources
containing nitrate, are adequately supplied with nitrogen.
to the ecophysiology of plant
Nonetheless, they receive signals indicating deficiency from the
development. The Institut des
aboveground plant structures, and this triggers expression of a gene
Productions Végétales merges these
encoding a specific nitrate transporter.This gene induction is visualized
three groups, i.e. B&PMP, LEPSE
by hybridization of messenger RNAs in the roots, using a pertinent
(Ecophysiology of Plants under
probe. Measurements of the uptake of nitrate labelled with the Environmental Stresses, see page 26),
15
and BDPPC (Biology of Development
isotope N show that the roots' nitrate uptake capacity increases in
of Cultivated Perennial Plants, see
parallel. So, even though they are not deficient in nitrogen, the roots
page 22). Their presence on the same
adapt their molecular machinery and functioning to the increased
campus constitutes a unique
nitrogen requirements of the aboveground parts: they respond to
opportunity in France to bridge the
signals whose identification is critical.We can search for the molecular
gap between the genetic, molecular
components of such signals indicating nutritional requirements
and cellular approaches and the global
through functional dissection of the promoters of marker genes of
expression in the whole plant in its
this response.
environment.
Contact:Alain Gojon, gojon@ensam.inra.fr
J.-B. Thibaut, © UMR B&PMP
S.Munoz – P.Tillard, © UMR B&PMP
Plant roots are
grown with (left) or
without (right)
nitrates. As answer
to a deficiency in
the upper part of
the plant, a nitrate
transporter gene is
overexpressed in
the root
Electrophysiology
20
Agropolis - May 2001The proteomics platform
P.Doumas, M.Rossignol, V.Santoni, N.Sommerer©UMR B&PMP
The proteomics platform environmental constraints, and developing new methodologies
of the B&PMP research for the analysis of membrane proteomes.
group (see page 16 “The These technologies can be applied, for instance, to the adaptive
Montpellier Languedoc- changes in root morphogenesis induced by mineral deficiencies.
Roussillon Génopole”) is Global genomic approaches are used to analyze the changes in
oriented towards Arabidopsis gene expression induced by phosphate deficiency.
high-throughput functional Transcriptome analysis uses medium- and high-density DNA
analysis of proteomes: arrays and proteome analysis employs MALDI-TOF technology.
- 2D mapping and These methods are coupled to image analysis of the dynamics of
construction of databases, root development.This programme is conducted in collaboration
analysis of gene expression with the Ecophysiology of Plants under Environmental Stresses
profiles; research group (see p. 26).The objectives are:
- robotized identification - identification of the main physiological functions contributing
of proteins using to adaptive morphogenesis, by identification of groups of
peptide-mass maps recruited genes;
(MALDI-TOF MS), - screening for candidate genes involved in the regulation of
Upper left: 2D electrophoresis gel of
sequencing (ESI MS/MS, adaptive responses;
Arabidopsis thaliana root proteins.
sequencer). - separation of general and specific pathways of the response to
Upper right: bio-informatic analysis
of the root protein content during
The B&PMP research applied stress (e.g. general response to stress vs. specific response
establishment of phosphate
group is constructing to phosphate deficiency).
deficiency. Bottom: mass spectrum
reference databases, Contact: Michel Rossignol, rossignol@ensam.inra.fr
of a polypeptide digestion in 2D
analysing post-translational
electrophoresis (MaldiTof)
modifications, identifying
responses to
Genes… J.-B. Thibaut, © UMR B&PMP
for which proteins?
In molecular physiology, the first step after cloning of a gene is
the identification of the molecular function of the gene product.
This is achieved through biochemical and/or physiological
approaches which are generally based on the expression of the
gene in a heterologous system. For example, the encoded
protein may be produced in the bacterium Escherichia coli or in
a yeast. In the case of proteins with a role as ion and water
transporters, expression in Xenopus (tropical toad) oöcyte
allows direct measurement of the function of these channels.
Xenopus oöcyte, like the COS cells of cercopithecus or the Sf9
cells of lepidoptera, also constitute a system of expression
compatible with patch-clamp techniques used in
electrophysiological characterization of ion channels.This
combination of molecular and physiological tools not only
allows identification of the function of the gene product, but
can also be used to dissect structure-function relations, using
site-directed mutagenesis.
Contact: Hervé Sentenac, sentenac@ensam.inra.fr
Heterologous expression system
21
Agropolis - May 2001Biology of the
development of
cultivated perennial
plants
he biology of plant development
Perennial plants are subject to
Development
embraces knowledge of all the
environmental changes and to
T molecular, cellular and
and optimized
competition in cultivated
structural processes leading from the
exploitation of trees
zygote to the reproductively viable
populations, and adapt to
adult plant (embryogenesis, juvenile
these changes through more or
The primary goal of the "Biology of
and adult development phases).
Development of Cultivated Perennial
less marked alterations in
In cultivated perennial species,
Plants" (BDPPC) research group is to
account should be taken of specific
development. These alterations
enhance understanding of the
features linked to the perenniality of
may be accelerated through
development of ligneous plants using
crops, the length of the juvenile
temperate and tropical species, in
genetic improvement.
phase, the process of lignification,
order to master their functioning,
and establishment of a perennial
their genetic usefulness, and their
plant architecture.
Team and co-ordinator
agronomic utilization.•••
The “Biology of Development of
Cultivated Perennial Plants” research
group (UMR BDPPC) comprises 33
researchers from Agro.M, Cirad,
INRA, IRD and the University of
Thousands of rubber
Montpellier II.
Co-ordinator: Françoise Dosba,
trees born in
dosba@ensam.inra.fr,
fax: +33 (0)4 99 61 26 16
the laboratory
Website:
http://www.ensam.inra.fr/arbo/arbo34.htm
Hevea is an exclusive source of natural rubber.The homogeneity
and productivity of hevea plantations are reduced not only by
the genetic heterogeneity of seed stocks but also by the
physiological ageing of the stocks of selected genotypes.
Somatic embryogenesis is used for the rapid and reliable
multiplication of these genotypes.The rejuvenation of plant
material and the cloning of the whole tree should enhance
vigour and increase the homogeneity of plantations.
Different lines of "embryogenic calli" (cells kept proliferating in
a suitable culture medium) from the PB 260 genotype were
used in the experimental production of 20,000 vitroplants
between 1996 and 2000.The process is now being adapted to
other selected genotypes. Since 1992, field trials have been
conducted regularly at five sites (Africa,Asia, Latin America) to
measure the growth, production and evaluate other agronomic
characteristics of this new plantation material.
Contact: Ludovic Lardet, ludovic.lardet@cirad.fr
22
Agropolis - May 2001Hevea vitroclone in field test
(Côte d’Ivoire), clone PB 260,
3 years old
M.-P. Carron, © Cirad-CPBiology of the development of cultivated perennial plants
The scientific goals of the research
group are as follows:
- to extend to cultivated perennial
Genes that enable trees
plants the tools of structural and
functional genomics developed with
to fix nitrogen
other plants, notably Arabidopsis
thaliana and forest species,
- to develop the technologies needed
Filao is a tropical tree from Oceania which belongs to the
for study of biological mechanisms
Casuarinaceae. Because of its low nutritional requirements
and breeding (genetic manipulations
and remarkable tolerance of drought, the filao plays an
and somatic embryogenesis),
important role in countries of the South in the production of
- to use modelling methodologies to
wood and biomass, the protection of soil against all types of understand the temporal and spatial
relations between the development
erosion, and the restoration of the fertility of degraded
and life cycle of perennial plants and
zones. Filao lives in nitrogen-fixing symbiosis with a
the underlying genetic and molecular
nitrogen-fixing microorganism called Frankia.The actinorhizal
mechanisms.
nodules or symbiotic roots created by this symbiosis
resemble modified lateral roots.The research undertaken at
IRD aims to understand the molecular dialogue between the
plant and the microorganism during differentiation and
functioning of the symbiotic roots.The filao genes mediating
symbiotic rhizogenesis – the formation of these modified
roots – are identified and characterized by means of molecular
physiology and cell biology. Genetic transformation of filao is
also used to characterize its genes.The resulting findings will
clarify the mechanisms underpinning the transformation of a
Didier Bogusz, © IRD
lateral root into a symbiotic root.They will also suggest how
to improve the conditions of symbiotic rhizogenesis in filao.
The identification and characterization of the symbiotic genes
of filao will allow us to produce new symbioses that are
more efficient or better adapted to environmental stresses.
Contact: Didier Bogusz, didier.bogusz@mpl.ird.fr
Filao symbiotic genes are studied
to improve symbiosis efficiency
24
Agropolis - May 2001Trees architecture
From gene
and fruit quality
to architecture
The architectural analysis of
This research is currently being
pursued at three complementary plants, developed in the 1960s in
structural levels:
intertropical forest, is being applied
- molecular: identification of the
to temperate fruit-bearing species
genes involved in the different phases
by the "Architecture and
of development of perennial plants
Functioning of Fruit-bearing
and to investigate the regulation of
Species" research group of the
their expression, use these genes to
understand the architecture of these INRA and Agro.M at Montpellier.
species with a view to improvement,
This involves observation of the
description of the mechanisms
tree, which is considered globally
modulating genome expression.
and in its temporal context.This
- cellular: development of in vitro
analysis allows to reconstitute the
regeneration systems to study
history of the tree's development
morphogenetic responses to
environmental changes; identification from morphological markers.
of the important stages of growth and
The main goals of this work are the
role of growth regulators; genetic
study and analysis of the rules
transformation adapted to perennial
governing early stages of production,
plants.
and its sustainability of trees of a
- whole plant: root and branch
given species.
development and architecture in
relation to genotype and
This work leads to propose
environmental conditions, relations
adaptive management practices
between architectural features and
based on in-depth knowledge of the rules governing varietal
the genetic mechanisms underlying
Comparison of
the expression and regulation of the tree architecture growth and fructification.Against an economic background of
genes concerned. for two apple tree
overproduction, the production of quality fruits is of
of the Fuji variety
particular interest today. Knowledge of the positioning of fruits
The perennial species used in these that have been
in the foliage and the characteristics of the supporting wood
studies are:
managed
will enhance understanding of fruit quality.This approach takes
- temperate species: apple tree (see differently (free
into account management practices, notably tree shaping and
right "Architecture of trees and quality growth left,
of fruits") and vine, and for more “solaxe” growth thinning out the fruits.This multidisciplinary approach brings
specific topics, apricot tree, olive tree right).
together morphologists, physiologists, ecophysiologists,
and pear tree;
Consequence for
agronomists and plant biotechnologists from INRA.
- tropical species: oil palm, fruit size
Casuarina (see left "Genes that allow distribution.
The BDPPC research group's primary goal is to study the
trees to fix nitrogen"), coconut palm,
genetic determinism of the principal architectural
coffee and banana, and for more
components. We plan to make genetic improvements on the
specific topics, hevea (see page 22
basis of enhanced understanding of the mechanisms underpinning
"Thousands of rubber trees born in
the architecture and functioning of plants of economic or
the laboratory"), cacao and
environmental value. Using the apple tree, we shall identify and
Eucalyptus.
manipulate the genes involved in the different development
stages and in their regulation, notably those involved in
morphogenesis of caules or roots.This will involve the use of
genetic transformation systems. In the longer term, it will be
necessary to integrate into breeding schemes
morphological characteristics governing yield and to
allow selected material to evolve towards more integrated
culture systems that require less input and are less
environmentally costly.
Contact: Evelyne Costes, costes@ensam.inra.fr
25
Evelyne Coste, © INRA
Agropolis - May 2001Creation of
drought-resistant
plants?
gricultural production is clearly
The search for better
Tolerance of drought:
contingent on a minimum
adaptation of plants to water
A
water supply: in plants,
a multifactorial
deficit is vital for agricultural
photosynthesis and growth are only
determinism
possible if there is transpiration.
production in the decades
Carbon dioxide enters leaves through
ahead. Headway can be made
Research on drought tolerance consists
microscopic pores, the stomata,
in optimizing the photosynthesis,
through the use of
through which water is transpired in
growth and development of plants so
large quantities (up to three times the
biotechnology and modelling
as to maximize production for a
plant's weight a day in summer). If
of plant gene regulation.
given water supply. The strategy for
the plant cannot take up this amount
improvement cannot be the same as
of water, it must slow its transpiration
that followed for other traits, such as
by closing the stomata and reducing
Team and co-ordinator
resistance to a disease or to a herbicide,
leaf growth. This avoids dehydration
which depends on the transfer of one
The“Laboratory of Ecophysiology of
but also reduces photosynthesis. The
or a few genes. This is because:
Plants under Environmental Stresses”
"water for carbon dioxide" trade off is
the climate varies year on year and
research group comprises 13
inevitable, regardless of any genetic
according to location, and so a
researchers from Agro.M and INRA.
progress.
genotype resistant to one drought
Co-ordinator: François T ardieu,
scenario will not necessarily be
tardieu@ensam.inra.fr,
resistant to another. A purely
fax: +33 (0)4 67 52 44 43
experimental
Drought and rate
of leaf growth
F.Tardieu, © INRA
Natural genetic variability in the response of foliage
growth rate to water deficit in the air and soil
A model has been established which predicts the responses of
leaf growth rate to soil water status, air humidity, and the
temperature of the meristem.This model has been tested both
in the laboratory and in the field, by relating the environmental
conditions to the measured growth rate (photograph).We are
now evaluating the genetic variability of the responses to each
set of environmental conditions for 100 recombinant lines of
maize.This will enable us to relate gene alleles to each
environmental response.
Contact: Bertrand Muller, muller@ensam.inra.fr
26
Agropolis - May 2001Predicting the effects
of transgenesis
Modelling the effect of a genetic transformation on
transpiration and the water status of plants subject to
water shortage
F. Tardieu et T. Simonneau, © INRA
Nicotiana plumbaginifolia plants
have been transformed at a
gene involved in the synthesis
of abscissic acid (ABA).The
resulting enzyme-deficient
plants lose all capacity to
close their stomata. Partially
enzyme-deficient plants were
subjected to different water
deficits or were grafted onto
wild relatives or fed artificial
ABA.All behaviours of the
transformants under all the
conditions tested can be
predicted by means of a single
model (see picture), which
varies only in the rate of
synthesis of ABA.
Contact:Thierry Simonneau,
simonneau@ensam.inra.fr
evaluation of a genotype would Exploration of the natural genetic
require dozens of years, which is variability in the responses of
hardly feasible for practical and
growth and development to water
economic reasons. deficit in the soil and air (maize,
the search for an optimum is more Arabidopsis thaliana, Dactylis). The
difficult than the search for a combination of development models,
qualitative characteristic, and involves micrometeorological measurements
the farmer's strategy. When choosing and genetic analysis (search for
a genotype, the farmer may seek to Quantitative Trait Loci) allows
maximize the potential yield, thereby individual identification of the alleles
running a high risk of total loss of characteristic of the response to
yield, or to maximize protection temperature, atmospheric humidity,
against risks and therefore settle for a and water deficit in the soil
lower potential yield. (collaboration with the INRA genetics
groups at Moulon and Versailles).
The LEPSE (Laboratory for Similar research is exploring
Ecophysiology of Plants under genotypic variability in the capacity
Environmental Stresses) seeks to of Dactylis to survive severe water
construct and evaluate genotypes shortage. •••
exhibiting contrasting responses to
several water deficit scenarios, from a
weak response (maintenance of
photosynthesis, growth and
transpiration: maximized potential
yield at the price of a higher risk) to a
strong response (better protection,
lower risk, reduced potential yield).
To achieve this, we combine modelling
with screening for genes of interest. A
four-pronged approach is used:
27
Agropolis - May 2001Creation of drought-resistant plants?
Analysis of the expression of genes
associated with adaptations in
plants subject to known
environmental conditions (maize,
Arabidopsis, Dactylis)
Gene expression analysis can now be
done in the field or laboratory, thanks
to advances in micrometeorological
Virtual plants in
measurements. In collaboration with
the B&BMP research group (see page
simulating resistance
18), we assess mRNA (cDNA
microarrays) and proteins (Western
to stress
blots, analysis of activity) to establish
Modelling the architecture of sunflower and Arabidopsis
correspondences between gene
thaliana subjected to environmental constraints
expression and a quantitative variable
in different environmental scenarios
(for example, expression of a cell
Computer modelling is essential in simulating the long-term
cycle gene and the rate of cell division).
effects on plant behaviour of stress and/or an allelic variation.A
programme is under way to represent in real time the adaptive
Systematic assessment of the
responses of sunflower and Arabidopsis genotypes to transient
effects of a gene manipulation on
variations in environmental conditions. In Arabidopsis, several
the genotype's responses to
ecotypes have been systematically compared for the architecture environmental conditions
model parameters.
Because the plant is a regulated system,
Contacts: Jérémie Lecoeur, lecoeur@ensam.inra.fr, Hervé
several variables characterizing the
Rey, rey@cirad.fr
phenotype are functionally related.
Modelling reduces the apparent
complexity of the responses to the
essential characteristics of each
genotype. The main test consisted in
the manipulation of a gene involved
in the synthesis of one hormone that
controls transpiration and growth in
plants subject to water shortage.
Modelling of the behaviour of a
given genotype in a large number of
pedoclimatic scenarios (Arabidopsis,
sunflower)
The microclimatic characteristics
and genotypic traits are fed into a
computer in order to calculate water
uptake, biomass production, etc. This
operation has a low marginal cost,
Three-dimensional computer
therefore it is possible to simulate a
representations of
large number of scenarios and
Arabidopsis thaliana
calculate the risks associated with a
genotype. This work is in its early
stages, and as yet we cannot establish
a correspondence between one gene
and a simulation of yield. However, it
is already possible to establish this
correspondence for the simplest
functions, such as transpiration or the
rate of foliage growth (in collaboration
with the Cirad-INRA-AMAP unit).
28
Agropolis - May 2001
© H. Rey, Cirad-AMAP et J. Lecoeur, INRAPlant-parasite
interactions
prospects for integrated pest management
he Biology and Genetics of allow progress in:
Ever-increasing consumer
Plant-Parasite Interactions for - population genetics,
demands for quality food and
T
Integrated Control (BGPI) - genetics of interactions,
preservation of the
research group is developing novel
- mathematical modelling of
approaches to integrated pest
population fluctuations. •••
environment mean that
management through improved
solutions must be found to the
combinations of biocontrol methods.
new constraints on agriculture.
We aim to enhance understanding
of plant-parasite interactions in
It is crucial to develop
terms of the underlying mechanisms
methods that limit the use of
and at the population level. Basic
phytosanitary treatments, and
research on suitable models are
yielding approaches and tools that
to encourage use of alternative
approaches such as varietal
resistance to diseases and
J.-L. Notteghem, © INRA
pests. These research activities
should be paralleled by
The Rice-Magnaporthe
development of
grisea pathosystem as
decision-making aids.
a research model
Team and co-ordinator
Rice blast caused by Magnaporthe grisea is the most important
Blast damage
The “Biology and Genetics of Plant-
fungal disease of rice, and greatly limits production, particularly
evaluation in a
Parasite Interactions for Integrated
rice trial, with a
in Latin America.The resistance of a new variety is in general
Protection” research group (UMR
resistant variety
quickly overcome by the pathogen, and the cost of fungicides is
BGPI) comprises 25 researchers from
(center row) and
prohibitive for most rice growers.
Agro.M, Cirad and INRA.
susceptible
Rice blast is a research model for numerous international
Co-ordinator: Jean-Loup Notteghem,
varieties (side
notteghem@ensam.inra.fr
research teams.A large collection of isolates has been assembled
rows)
fax: +33 (0)4 67 54 59 77
and is used in studies of M. grisea population structures and
their evolution.This work has been conducted at different
levels: worldwide, European, Chinese and fertile populations of
Asia.
The mechanisms of interaction have also been studied. New
resistance and virulence genes have been mapped. In a
collaboration with an Aventis-CNRS (National Centre for
Scientific Research) research group, one of the avirulence genes
has been cloned, and others are now being studied.The cloning
of a resistance gene is currently under way. Genomics is now
being used to identify and clone genes involved in the defence
mechanisms of rice.
Contact: Didier Tharreau, tharreau@cirad.fr
29
Agropolis - May 2001Red leaf mottle
in sugarcane
induced by the
Peanut Clump
Virus (PCV)
30
Agropolis - May 2001
P. Baudin, © Cirad-CAOur group is pursuing three lines
of research:
Narrow-leaved ragwort-
• In studying the mechanisms of
rust interactions to
interaction, we use gene mapping
and cloning to analyze the
develop biological control
pathogenicity of the agents that
cause plant diseases, as well as the
methods
disease resistance of plants. Our
study of the genomics of the defence
Senecio inaequidens, the narrow-leaved ragwort, an exotic
reactions of rice is based on the plant
weed which invades natural areas and crops, such as the vine
materials produced by the teams of
in Languedoc-Roussillon, is expanding throughout Europe. the Montpellier Génopole
(see page 16).
This species is sensitive to a rust fungus from Australia,
Puccinia lagenophorae, which reached France
• The study of the factors of viral
some thirty years ago.We are studying the
epidemics transmitted by insects is
epidemiology, population dynamics, and genetic
based on a space-time study of the
structure of narrow-leaved ragwort, and the
epidemics and an analysis of the
ragwort's interaction with the rust fungus, with
major factors: vector biology, vection,
a view to establishing whether the rust fungus diversity of viral populations, host
resistance, geographical
could be used as a biocontrol agent.This
fragmentation of cultivated regions,
Damage caused
project strengthens ongoing collaborations of the BGPI
insect control methods. This work is
by Puccinia
research group with associate members of Agropolis and
being done in close collaboration
1
lagenephorae
with local laboratories of Australian (CSIRO ) and American
with farmers and technical institutes
2 (rust) on
(EBCL-USDA-ARS ) organizations specialized in biocontrol
specializing in this field.
narrow-leaved
(1) CSIRO: Commonwealth Scientific and Industrial Research Organization
ragwort
(2) EBCL: European Biological Control Laboratory - USDA-ARS: United States Department of Agriculture -
Agricultural Research Services • The study of the population
genetics of phytoparasitic fungi,
Contact: Jacques Maillet,Agro-Montpellier,
bacteria and nematodes, and of
maillet@ensam.inra.fr
their interactions with resistant
cultivars has been boosted by recent
developments, such as the use of
molecular tools to characterize
pathogen populations and their
mechanisms of genetic evolution.
Plant-pathogen interactions are
Diagnosing viral diseases
investigated in terms of the effect of
host resistance on pathogen
The diagnosis of viral diseases is a major priority which calls for
population structures, pathogenicity,
aetiology and pathogen characterization. Cirad is developing tests for
and plant resistance.
the serological or molecular detection of a large number of
Applications of the research projects
microorganisms that attack cultures of banana, sugar cane, cacao,
include diagnosis of plant diseases
vegetable crops, palm trees including coconut palms. New detection
and expertise on the sustainability
methods are constantly reviewed to guarantee the quality of Cirad's
and optimal management of
phytosanitary testing in international quarantine services for sugar
resistance. Characterized resistances
1
cane and the indexing of banana (VIC-INIBAP ), taking into account
are used by the plant geneticists and
the risk of emergence of new viral strains, or even
breeders. Methods are proposed to
limit vector transmission of viral
new pathogens.Through these studies we hope to
infection.
develop diagnostic kits for onsite use by our
partners.
(1) VIC-INIBAP:Virus Indexing Center of the International Network for the Improvement
of Banana and Plantain
Peanut Clump
Contact : Michel Peterschmitt,Cirad,
Virus (PCV)
michel.peterschmitt@cirad.fr
infecting sugar
cane
31
M. Chatenet, © Cirad-CA
Jacques Maillet, © Agro.M
Agropolis - May 2001Dissemination
of innovations
From research to applications
Improved seeds and plants are
Facilitating the
then doubled to restore fertility. For
the traditional and most
instance, a cross between such pure
creation of new
lines is currently used to produce
favoured way of transferring
varieties hybrids of tropical or temperate rice.
genetic advances to producers.
Plant biotechnologies have
The creation of a new variety is • Somatic fusions and hybridizations
time-consuming and costly. The exchange of genetic material
greatly accelerated and
Numerous techniques now improve between different varieties during
enhanced this transfer. The
the performance of traditional reproduction is an important source
research groups of the
methods, and some of these are of variability, but some species
presented below. hybridize poorly and are therefore
Languedoc-Roussillon region
difficult to improve by classical
participate actively in the
• Haploid methods methods. Somatic fusions and
development of these new
The use of pure lines is often hybridizations enable mixing in the
necessary when the goal of the laboratory of the genetic and
technologies. They have
breeding programmes is to create cytoplasmic structures of plants by
fine-tuned methods and
hybrids. Traditional methods need fusing protoplasts, thereby increasing
processes that are available
eight to ten years, whereas haploid the genetic diversity of certain
methods (haploid-diploidization) species. At Agropolis, this technique
from Agropolis, and some of
rapidly yield hybrid varieties by is used with citrus fruits.
these have been transferred to
generating pure lines in a single
the private sector and the
generation. Plants with only half of • Marker-assisted selection
the genetic make-up are produced by To ensure that a cultivated hybrid has
countries of the South.
growing reproductive cells – ovules or recovered the gene or genes
pollen – whose genetic make-up is controlling the agronomic trait of
Marc Lartaud (© Cirad-Amis, Biotrop)
RITA, an apparatus which
facilitates in vitro culture
In vitro culture allows routine immersion recipient).This two-compartment apparatus makes
preparation of thousands of use of the advantages of the liquid medium but does not suffer
"certified copies" of a plant from its drawbacks, since the plant material is only briefly in contact
a simple tissue fragment from with the liquid. Rita is easy to use because of its design and size
the mother plant.This is achieved and is currently being utilized to micropropagate a large number
through the use of complex of plants, notably selected hybrids of Coffea arabica.
The RITA device with
mixtures of mineral salts, sugars, Contact: Marc Berthouly, Cirad, marc.berthouly@cirad.fr,
coffee vitroclone
amino acids, vitamins, and UMR BDPPC (see page 22)
growth regulators. Although a liquid medium is considered Website: http://www.cirad.fr/produits/rita/fr/accueil.htm
ideal for the mass production of vitroplants, there are frequent
problems of hyperhydricity and of physiological disorder
(asphyxia) caused by the presence of residues in the medium.
It has long been known that temporary immersion reduces
these problems. From 1988, the Biotrop laboratory of Cirad
has worked on the use of this technique and the development
of a simple, easy-to-use apparatus: Rita (automated temporary
32
Agropolis - May 2001Vitropic: a laboratory for production of
vitroplants of tropical species in
Languedoc-Roussillon
Vitropic S.A., a subsidiary of Cirad, is
interest, difficult and often
time-consuming field tests were
a laboratory at St Mathieu de
traditionally necessary. Molecular
Tréviers near Montpellier which
genetics can now be used to identify
produces vitroplants (plants obtained
and locate genes and to follow them
by in vitro culture). It was set up in
during crossing and selection
1986 and now has an annual turnover
through their association with
molecular markers. This technique of 1 million US$, 15 employees, and
allows concentration of the most
produces two to three million
valuable traits and avoids their loss
vitroplants a year, especially of
during these operations. This process
banana, which are sent mainly to the
was first applied to simple
West Indies and Africa.Vitropic is a
characteristics, and is now increasingly
leader in these foreign markets and
used for quantitative traits, which are
more difficult to handle. its planlets production site is one of
the more important in the world for
• Direct transfer of genes by transgenesis
banana.
The transfer of an agronomic trait to
An example of how
a hybrid is particularly lengthy and
biotechnology improves
difficult by natural means, but it is
production
now possible to transfer the gene
The production of vitroplants does
controlling the relevant characteristic
directly into the cultivated plant by
not involve genetic transformation
means of transgenesis.
techniques but rather tissue culture.
The first applications of this method
Plants selected for their agronomic traits are multiplied rapidly
Use of banana
are much debated in Europe, yet at
vitroclones in test tubes.The miniature banana plantlets produced under
this early stage much remains to be
increases
the protected laboratory conditions are disease-free and are
discovered. Among the varieties
production with
selected, increasing use is made of shipped from Montpellier to the production zones.Their
less pesticides
transfer of a valuable trait to a plant
utilization as planting material enhances production, since
of the same or a similar species. •••
vitroplants give greater yields with less use of pesticide when
grown in soil free of nematodes (soil parasites). In the case of
banana, vitroplants help promoting a more environmentally-
friendly agriculture.
The need for constant innovation
To increase its know-how and to improve and diversify its
products,Vitropic must innovate constantly and invest in
research and development.Agropolis, and in particular Cirad,
provide Vitropic with a favourable environment and expert
scientific and technical partners in the pursuit of its goals.
Vitropic operates mostly in the Languedoc-Roussillon region,
but is also developing collaborations with numerous partners
from countries of the South.
Contact: François Cote, Cirad, francois.cote@cirad.fr
33
Yvan Matthieu, © Vitropic S.A.
Agropolis - May 2001Multiplying the most interesting
palm tree in large numbers to fix
useful agronomical
characteristicsensuring large-scale production of true copies of reproduction
of the most valuable plants. Large-scale multiplication and
In vitro culture to
regeneration using somatic embryogenesis have been developed
produce true copies
since the early 1980s in collaboration between IRD and Cirad,
and have been transferred to the main producing countries
of oil palm
(Côte d’Ivoire, Malaysia, Indonesia) for pilot testing. Several
hundred thousand oil palm plantlets regenerated in vitro have
The oil palm is the major source of vegetable fat in the humid been planted, and various clones have been identified, leading to
intertropical zone.With an annual output of ca. 20 millions
a 20 to 30% yield increase, thus underscoring the value of this
tons, it accounts for 20% of world oilseed production. approach.We have also noted the existence of sterile, off-types
Conventional techniques of vegetative propagation (cuttings, or variants, resulting from regeneration.This phenomenon is
shoots, grafts) do not exist for this plant with its obligate known as somaclonal variation and is now being studied in
cross-pollination and seed-only propagation.The mode of depth in tandem with research teams from Great Britain and
reproduction and the time needed for genetic improvement
Malaysia, using molecular approaches based on cutting-edge
lead to substantial heterogeneity in the plants grown from techniques available at Agropolis, notably through the
selected seeds available to growers. Because of this, the most Montpellier Génopole (see page 16).
useful agronomic traits can only be fi xed by means of control- Contact:Yves Duval, Cirad-IRD, yves.duval@mpl.ird.fr,
led artificial vegetative propagation using cell biology techniques UMR BDPPC (see page 22)
• Somatic embryogenesis growth of in vitro cultures. Other
Multiplication
This form of vegetative propagation equipment has been developed in
techniques
yields a large number of plantlets collaboration with small- and
genetically identical to the mother medium-sized local companies, such
In vitro culture of plants in a sterile plant that gave the explants. It can be as confinement greenhouses and
nutrient medium is a longstanding
used to reproduce millions of identical culture rooms, several of which have
and widespread technique in
copies of a plant from a fragment of been built in Africa and Asia.
microcutting and micrografting.
leaf or stem. This is a highly promising Agropolis member institutions
Other techniques are being improved,
technique as it allows enormous possess considerable know-how in
including: multiplication rates. It is also usable this area, particularly regarding in
in transgenic systems. It is especially vitro cultures, which have a wide
• Embryo rescue
useful when the plant does not
range of potential applications.
Similar but poorly compatible species
naturally propagate vegetatively (oil Co-ordinator: Jacques Meunier, Cirad,
may sometimes be crossed, but the
palm, coconut palm...). Despite jacques.meunier@cirad.fr
resulting embryo is often unviable or certain technical difficulties, hundreds
does not develop beyond a certain
of thousands of palm trees, hevea
stage. Yet this type of cross would
trees, cotton plants and banana
improve cultivated varieties. Embryo
plantlets have been produced by this
rescue allows the production of
procedure at Montpellier.
hybrids from the first cells of a cross
between "incompatible" species.
Appropriate and officially approved
Embryos can be rescued at an early
new equipment for all these
stage, soon after fertilization,
techniques is needed, and has been
cultivated and thus saved. This
invented or adapted by the research
technique has been used with citrus teams at Agropolis. An example is
fruits and rice.
RITA (see page 32 "Rita, an apparatus
which facilitates in vitro culture"),
which was designed to improve the
35
Yves Duval, © IRD
Agropolis - May 2001Education and training
at Agropolis
Agropolis is one of the major French and European training pole
in agriculture, agribusiness and rural development. The
Universities of Montpellier II and of Perpignan, as well as Agro of
Montpellier (Agro.M), offer numerous courses in plant genomics,
genetic resources and biotechnology.
Degree courses
Level Degree Courses Institute Director
Biology:
Under-
Bac + 3 BSc Cell biology and applied plant UM II Yves Sauvaires
graduate
physiology
Post- Cell biology and physiology:
MSc UM II Francine Casse
graduate Applied plant physiology
Conservation of biodiversity:
Agro.M André Charrier
genetic diversity of organisms
Bac + 4
The impact of biotechnologies
Post- Special
on the seed and breeding Agro.M Dominique This
graduate modules
sectors
Regulating agriculture: example Jean-Loup
Agro.M
of integrated pest management Notteghem
Genetics, genomics and
DESS UM II Michel Lebrun
professionally
advanced plant biotechnology
oriented
Bac + 5
postgraduate
Plant production engineering: INA-PG /
degrees
DAA André Charrier
seeds and plants Agro.M / INH
Plant genetic resources and J.-L. Notteghem
UM II / Agro.M
biological interactions Isabelle Oliviéri
DEA (bac+5) Michel Lebrun
Bac + 5 Doctoral Plant development UM II / UP /
Michel Delseny
à 8 studies and adaptation Agro.M
Doctorat (bac+8) Claude Grignon
Bernard Delay
Evolution and ecology UM II / Agro.M
Jacques Maillet
Abbreviations
Agro.M: National Agronomy School at Montpellier
DAA: Degree in Advanced Agronomy
DEA: Degree of Higher Studies
DESS: Degree of Specialized Higher Studies
DEUG: Degree of General University Studies
INA-PG: National Agronomic Institute – Paris Grignon
INH: National Institute of Horticulture (Angers)
UM II: University of Montpellier II
36
UP: University of Perpignan
Agropolis - May 2001The evolving French
higher-education system
The reform of the French higher education
French system International system
system begun in late 1998 is intended to
harmonize teaching and training within the
Baccalauréat End of high school
European area; it emphasizes on three main
degrees: Licence (BSc level), Master (MSc
level) and Doctorat (PhD level). Postgraduate
Bac+1 years
DEUG
students have to choose between a short term
+2 years
BSc curriculum, professionally oriented or
research oriented doctoral studies.
Licence +3 years
Maîtrise +4 years
MSc
DESS DEA +5 years
+6 years
Doctorat +7 years PhD
+8 years
Alain Rival, © IRD-Cirad-CP
Continuing education
Customized training
Agropolis can organize specific educational events tailored to
collective and individual requirements, such as seminars, laboratory
work, on-field training, training of trainers, and so forth.
Depending on demand and content, these courses will take place
in or outside Montpellier.
For further information on personalized training, see our website:
http://www.agropolis.fr/formation/servicesfc.html
Please note that modules from doctoral studies and
professionally oriented degree can be followed in continuing
education.
" Introduction to molecular biology ", one-week course
open to students with the baccalaureate plus two years of
higher-education training. Site:Agro.M campus.
Director: Philippe Joudrier, joudrier@ensam.inra.fr
Training in molecular biology at Montpellier
37
Agropolis - May 2001Graduate school Welcoming foreign
"Integrative Biology" students and trainees
The Graduate School (GS) embraces all lecture and practical Agropolis provides information and guidance for foreign students
courses that lead to the PhD degree.This course begins in the and trainees on:
year of the DEA (baccalauréat+5) and continues with additional - how to obtain a resident or student permit,
training involving seminars, scientific conferences and training - finding accommodation,
modules for the three years of thesis preparation.These modules - applying for housing benefit,
have the twofold purpose of improving the students' scientific - campus facilities and restaurants, public transport, cultural
training and preparing them for their professional career. activities…
The Graduate School “Integrative Biology” at the University of For certain specialized courses,Agropolis also offers a
Montpellier II focuses on the integration in the biological personalized set of services for foreign students. Depending on
processes and the interactions of biological systems, with a view the course chosen, an introductory period may comprise:
to conservation of biodiversity, protection of the environment, - French courses,
sustainable development and agriculture and the progress in - laboratory training,
biotechnology.The school's six scientific priorities are: - additional required courses defined with the training advisor,
- personal tutoring.
• Biodiversity, mechanisms of evolution, genetic resources.
• Genomics: structure and organization of the genome, gene
function and regulation, functional genomics.
J.-L. Porreye, © Agro.M
• Host-parasite interactions and symbiotic hosts.
• Ecology of populations, communities and ecosystems; global
changes.
• Physiology and ecophysiology of relations between plants and
the biotic and abiotic environment.
• Mathematics and information technology applied to biological
systems and processes.
The Graduate School “Integrative Biology” offers seven courses
leading to a DEA degree, with an annual intake of 75-80 students.
Some 60 graduates begin the PhD course every year, and there
are almost 200 PhD students in all.The PhD students work in
Training in a vine collection (Agro.M)
some thirty research groups in universities (UM II / Agro.M) and
research institutes (Cirad, CNRS, INRA, IRD at Montpellier).
Some figures…
Three doctoral courses are more specifically oriented towards
- Number of thesis completed in plant biotechnologies, genomics
plant biotechnologies, genomics and genetic resources:
and genetic resources: 20-25 per year.
- Student population: 75 PhD students, 30 DEA, 15 DESS, 15
- DEA " Plant Genetic Resources and Biological Interactions"
DAA, i.e. a total of 135 students on various postgraduate courses.
- DEA "Development and Adaptation of Plants"
- DEA "Evolution and Ecology".
Contact
- DEA and Graduate School “Integrative Biology”:
André Charrier,Agro.M, acharrie@ensam.inra.fr
fax: +33 (0) 4 67 04 54 15
- Continuing education and services to foreign students
and trainees: http://www.agropolis.fr, heading "training",
agropolis@agropolis.fr,
fax: +33 (0)4 67 04 75 99
38
Agropolis - May 2001This publication was supported
by the French government and
the Languedoc-Roussillon
regional authority
Agropolis member organizations
involved in genetic resources,
genomics, and biotechnology
research:
AGRO Montpellier (Ecole Nationale
Supérieure Agronomique de Montpellier)
2, Place Pierre Viala
F-34060 Montpellier Cedex 1
Tél : +33 (0)4.99.61.22.00
http : //www.ensam.inra.fr
CIRAD (Centre de coopération internationale
en recherche agronomique pour le
développement)
Avenue Agropolis
F-34398 Montpellier Cedex 5
Tél : +33 (0) 4 67 61 58 00
http : //www.cirad.fr
CNRS (Centre National de la
Recherche Scientifique)
Route de Mende
F-34293 Montpellier Cedex 5
Tél.: +33 (0)4 67 61 34 34
http://www.dr13.cnrs.fr/
INRA (Institut National de la
Recherche Agronomique)
2, Place Pierre Viala
F-34060 Montpellier Cedex 1
Tél : +33 (0) 4 99 61 22 00
http : //www.ensam.inra.fr
IRD (Institut de Recherche pour le
Développement)
911, avenue Agropolis - BP 5045
F-34032 Montpellier Cedex 1
Tél : +33 (0) 4 67 41 61 00
http : //www.mpl.orstom.fr
Université Montpellier II (UM II) Institut de recherche
pour le développement
Place Eugène Bataillon
F-34095 Montpellier Cedex 5
Tél : +33 (0) 4 67 14 30 30
http : //www.univ-montp.fr
Université de Perpignan
52, Avenue de Villeneuve
F-66860 Perpignan Cedex
Tél : +33 (0) 4 68 66 20 00
http : //www.univ-perp.fr
Director in chief :
Michel de Nucé de Lamothe
Technical editors : Véronique Molénat,
Yves Savidan
Scientific coordinator :
André Charrier
Participed to this issue :
Marc Berthouly, André Bervillé, Didier Bogusz,
Fabien Boulier, Jean-François Briat, Richard Cooke,
Evelyne Coste, François Cote, Michel Delseny,
Martine Devic, Angélique D’Hont, Françoise
Dosba, Stéphane Dussert, Yves Duval, Manuel
Echeverria, Alain Ghesquière, Marc Giband, Jean-
Christophe Glaszmann, Alain Gojon, Claude
Grignon, Serge Hamon, Emmanuel Guiderdoni,
Philippe Joudrier, Pierre Lagoda, Ludovic Lardet,
Jérémie Lecoeur, Jacques Maillet, Jacques Meunier,
Yves Meyer, Bertrand Muller, Jean-Loup
Notteghem, Michel Peterschmitt, Jean-Claude Prot,
Hervé Rey, Michel Rossignol, Marc Seguin, Hervé
Sentenac, Thierry Simonneau, François Tardieu,
Didier Tharreau, Patrice This.
Translation : David Marsh
Corrections : M.-C. Kohler , Yves Savidan
Photo acknowledgements : Bernard Marin,
Danièle Cavanna, Sémiha Cebti,
Jean-Pierre Grouzis, Thierry Lacombe,
Marc Lartaud,
Production :
Design Publicis Méditerranée
Impression : IMP’ACT imprimerieAGROPOLIS
Avenue Agropolis
F-34394 Montpellier Cedex 5
France
Phone : +33 (0)4 67 04 75 75 - Fax : +33 (0)4 67 04 75 99
e-mail : agropolis@agropolis.fr
http://www.agropolis.fr