AGROPOLIS LES DOSSIERS Expertise of the Agropolis scientific community

GeneticGenetic resourcesresources GenomicsGenomics PlantPlant& biotechnologybiotechnology

Number 1 – May 2001 Agropolis, International complex for research and higher education in agriculture

Agropolis groups research and This scientific complex, with the vocation of an international agricultural higher education institutions university, forms a huge potential of scientific and technical expertise: in Montpellier and the Languedoc-Roussillon region, 3,000 researchers, teachers and technicians in more than 200 research 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 development of scientific, technological and economic challenges of agricultural 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. scientists, are involvedinthestudy range oftoolsalliedtoincreasingly Agropolis isabenchmark inplant that constituteAgropolis: Agro.M, the University ofMontpellier and now haveattheirdisposalawide such varieties, research scientists Agropolis, projects anddescribes varietal improvementvarietal havenever agribusiness practicesagribusiness andinthe particularly instudiesoffactors particularly functioning. The possibilitiesof some 300ofwhomare research natural resources. In producing This dossierpresents themajor and know-how ofitsscientists. various memberorganizationsvarious plants. inthis The participants sparing intheirexploitationof sparing lines ofresearch conductedat work are researchers from the that makefulluseoftheskills of geneticresources, genomics At Agropolis, over 400people, genomics research inEurope, agrifood industry canbemet industry agrifood security andbetterqualityin security Consumer demandsforfood the University ofPerpignan. production systemsthatare through thecreation ofnew detailed knowledge ofplant Mediterranean andtropical that limittheproduction of and plantbiotechnology. environmentally friendly environmentally friendly Cirad, CNRS,INRA,IRD, varieties adaptedto varieties been greater. integrated protection” prospects for “Plant-parasite interactions: Jean-Christophe Glaszmann appliedto agronomic traits”“Genomics conservation anduse” towards betterunderstanding, resources: “Genetic André Charrier andtraining“Education atAgropolis” to applications from research ofinnovations: “Dissemination François Tardieu “Creation of drought-resistant plants?” perennial plants” ofthedevelopment ofcultivated “Biology environments” “Adaptation ofplantstostress Génopole” Montpellier Languedoc-Roussillon “The Michel Delseny andplantdevelopment”“Genomics biotechnology Genomics resources Michel Delseny Genetic Vegetal ” & Claude Grignon Jacques Meunier Françoise Dosba Serge Hamon Jean-Loup Notteghem Page 36 Page 32 Page 29 Page 26 Page 22 Page 18 Page 16 Page 12 Page summary8 Page 4 Page 4 Agropolis - May 2001 rmAr.,Crd NA IRDandthe INRA, Cirad, from Agro.M, able toensure foodsecurityfor 20th century hasreduced20th century both (UMR DGPC)includes50researchers diversity ofthespeciesusedby environmentally friendlyand Team andco-ordinator varieties ifweare tomeetthe oodntr:SreHmn IRD Serge Hamon, Co-ordinator : agricultural production seen a world populationthatwill during thesecondhalfof top 8,000millionby theyear Cultivated Plants"research group the numberandgenetic a,resulting inincreased man, The "Diversity andGenomeof Agronomic research must [email protected] agriculture whichisboth a +33(0)467416222 fax : continue toproduce new University ofMontpellier demands ofsustainable vulnerability ofcrops to 00 Intensification of 2020. diseases andpests. conservation anduse Genetic resources:

Stéphane Dussert, © IRD S agronomically valuable genes together constituteapoolof cultivated plantspeciesthat genetic resources ofthewildand agriculture canbeequatedwith future generations. Biodiversity in for biodiversity canbeconserved from understandinghow this exploitation ofbiodiversity, and from sustainableandresponsible sectorwillfollowagribusiness more environmentally friendly understanding, better-quality ina varieties new, higher-yield and uccessful developmentof towards better conserved at–196°C Coffee beans otc tpaeDset stephane StéphaneDussert, Contact : underlying biophysical andphysiological mechanisms. routinely centres andtostudythe applicable inconservation research group aimstodevelop methodsofcryoconservation conservation of the diversity of these species.The DGPC ofthediversity ofthesespecies.The conservation the only methodavailable for thelong-term is low temperaturematerial atvery (-196°C), storageoflivingplant i.e. Cryoconservation, propagate vegetatively (vines). orthey for example), cold (coffee trees, plants donottoleratethedehydration and/or Eithertheseedsofthese seeds incoldrooms). used ingenelibraries(storageofdehydrated undertheconditionsconventionallyconserved The geneticresources ofmany plantscannotbe temperatures subpolar at recalcitrantseeds Conserving improve quality, nutritional tropical andMediterranean work onthegeneticresources of traits ofagronomic value. In its effective toolsforthetransfer of extensive knowledge andfor and wildrelatives callsfor of thegeneticdiversitycultivated Effective andreasoned exploitation accelerate growth, increase and ofpoor-quality soils, to diseases, tolerance ofdrought needed toimprove resistance to so forth. so forth. .dusser [email protected] yields, and d.fr varieties andorganizedvarieties themin numerous plantspeciesand resources. Researchers collected of plant "evolution" and"history" attentiontothe particular approach whichpaid descriptive genetic diversityemployed a and ongeneflow. relatives, ontheir subgroupings, withtheirwild plants form species complexesthatcultivated onthe extensive information collections. This approach yielded Until thee to genemapping From plantdiversity conservation. improvementvariety and to makeuseofplantdiversityfor research group hasatwofoldaim: of Cultivated Plants (DGPC) plants, theDiversity andGenome alike for itsnutritional qualityandseveral characteristicsnot Sunflower oilismuch coveted by consumersandindustrialists quality Better arly 1990s, research on Using wildrelatives toimprove oilquality sunflower oils sunflower involved intheexpression ofa regions containingthegene(s) chromosomal The determinism. to assessandofcomplexgenetic breeding, are sometimesdifficult are ofparamount in importance Agronomic characteristics, which or environmental contexts. their expression genetic invarious localize themand “shed light” on the diversityofgenes(alleles), characteristics. These toolsreveal the genesthatgovern agronomic models, we cannow work with biology toolsandtheuseofplant improvements inmolecular explore plantgenomics. With characterize biodiversityandto the mechanismsthatcontrol and approach designedtoelucidate diversity hasadoptedafunctional More recent research ongenetic

André Bervillié, © INRA new varieties.The objectives are: new varieties.The otc nr evlé ber André Bervillé, Contact : - toincrease thequantityandqualityofphytosterols. for instance); ofvinaigretteamounts ofoil(aportion onsalad, reach therecommended daily intake by consumingsmall - toincrease thevitaminEcontentso thatconsumerscan be usedinmixes inresponse todemand; - toproduce oilsasrichpossibleinlinoleicor oleicacidto annuu of sunflower oilby investigating wildforms of research group aimstomake betteruseofthese characteristics DGPC known tocounter so-calledbadcholesterol.The whichare andcontainsphytosterols, high-temperature use), lackslinolenicacid(thusallowing safe ageing andstress, whoseantioxidant properties protect against vitamin E, Itisnaturally richinlinoleicacidand found inotheroils. snvlrsucsfripoeet andby creating s asnovel resources for improvement, time-consuming which are difficult,costlyand studies ofdiseaseresistance, controlled conditions, asin under tests orexperiments circumvents theneedforfield early,very plantletstage. This desired agronomic feature from a control theexpression ofthe recovered thegeneorgenesthat plant andawildrelatives has between acultivatedthat ahybrid becomes feasible. It canbeensured markers, effectiveselection feature tooneormore molecular By agronomic linkingaparticular screening andselectiontechniques. then betransformed intoefficient techniques. The sametoolscan using moleculartoolsandlabelling valuable trait canbeidentified [email protected] .••• Helianthus

5 Agropolis - May 2001 screen chromosomesscreen in Fluorescence isusedto

6 Agropolis - May 2001 in identifying vine varieties vine identifying in researchers have beguntheanalysis ofthegeneticdiversity of vine varieties. Preliminary results Preliminary have demonstratedtheutility vine varieties. sa i oietfcto:theanalysis oftheDNAextracted - asanaidtoidentification: the characterizationandmanagementofgeneticresources ags iecleto ntewrd with some2,300identified largest vinecollectionintheworld, yoeeis Fluorescent InSituHybridization(FISH)locates cytogenetics. precise sequenceswhichwillbefluorescently labelledonthe vine varieties listed worldwide.The INRAat vine varietieslistedworldwide.The Vassal housesthe rmlae,wo,ros or roots, wood, from leaves, vine varietiesandathousandundergoing identification. of the vine.The goal isthegeneticfingerprintingofallthese of thevine.The nteaayi fteoii fcretvn aite:ithas - intheanalysis oftheorigincurrent vinevarieties: chloroplast markers).The mainpurposeoftheseanalyses is chloroplast markers).The this collectionusingmolecularmarkers (microsatellites and These techniquesare usefulincultivatedplants particularly h iei ihydvriidseis with5,000to6,000 The vineisahighly diversified species, Genetic resources: Genome structure canbeinvestigated usingmolecular hybrids obtained by anaturalcross between thevinevarieties differentiates thechromosomes ofparental speciesin hoooe.GenomicInSituHybridization(GISH) chromosomes. identify species origin species identify hrony Gamay and Chardonnay, Aligoté resulted from seeds been shown thatprestigious vinevarietiessuchas unambiguous identificationofunknown samples, otc arc hs [email protected] Patrice This, Contact : Angélique D’Hont, © Cirad-CA (BACs) tochromosomes andtouncoiled DNA complementphysical mapping and n/ri neseii yrd,like sugar and/or ininterspecifichybrids, The finertechniquesofhybridization of in particular positionalcloningofgenes in particular chromosomesto ae aaa ofe citrusorcotton. coffee, banana, cane, with many chromosomes (polyploid) Detective workDetective Using colouredUsing Bacterial Artificial Chromosomes Bacterial Artificial towards better rafle Contact :Angélique D’Hont, Contact :Angélique of thesegeneticfingerprints: ang (peduncles/pedicels) allows elique of agronomic interest. interspecific hybrids. Pinot andGouais. [email protected] understanding, INRA .P rn-©INRA-Domainedevassal J.-P. Bruno-© securing identification Vine variety: conservation anduse using base collectionsare simplified management andutilizationof the caseofperennials). The also ascultivated plants(notablyin parallel withitsenvironment, and toevolvein material conserved Such methodsdonotallow the hazards. - are subjecttoclimaticorparasitic unorthodox seeds, - are ill-suitedtospecieswith - "freeze" diversity, have somedrawbacks, asthey: have proved highlyvaluable butdo These methodsofconservation by asmallnumberofplants. diversity ofacollectionisrepresented as seedskeptincoldstorage, the natural environment, generally outside which diversityisconserved the creation of three decadesthisgoalhasledto resources possible. Overthelast themostdiversified to conserve agriculture oftomorrow, itisvital and unexpecteddemandsofthe If we are tomeettheforeseeable genetic resources Conserving costly andlabour-intensive. regenerated regularly, whichis powergerminative andmustbe stored seedsgradually losetheir low-temperature storage. Lastly, notably tropical, poorlytolerate stresses. Furthermore, someplants, thenewenvironmental survive plants maynolongerbeableto so after20or30years theconserved core collections ex situcollections , in whichthe but , in through resistance to a fungus a throughresistanceto rubberproductionBoosting - by theDGPCresearch group: approaches pursued alternative to befoundthrough two Solutions tothesedrawbacks are now only theoriginalhomeofhevea, Latin America, result, a produce high-latex-yieldvarietiesresistant toleafblight.As ulei. Microcyclus are decimatedby theSouth American leafblightvector industrial andlocalplantationsofthehevea In Latin America, plants thatpropagate vegetatively. ofthebuds conservation seeds. It isalsoapplicabletothe ofrecalcitrantconservation inexpensive, long-term only techniquethatensures liquid nitrogen (-196°C), isthe temperature, generally thatof storage atultralow ofmaterial - withotherplants; material interact andexchange genetic (diseases, pests…)andcan to environmental constraints diversity becausetheyare subject continue dynamicallyto"create" insitu adapt. Plants conserved the plants'capacitytoevolveand diversity butabove allmaintains natural environment, conserves ofplantsintheir conservation Helping Brazil tocomeback In situconservation Cryoconservation into therubberbusiness Over half a century ofworkOver hasfailedto halfacentury , i.e. the , the

Denis Lespinasse,© Cirad-CP previous hypotheses The results have disproved implicated inresistance. chromosomal regions Loci (QTL)or analyze Quantitative Trait used genomemapping to researchers atCiradhave genetic resources, identified in Amazonian determinism ofresistance To unravel thegenetic worldwide. natural rubberproduction accounts for 1% of application ofplantgenomics: focused onthree majortypesof research group hasmainly effective research tools, theDGPC Through itsdevelopmentofmore of genefunction. ofthediversityand determinants understanding ofthegenetic expression", withaviewtobetter to thestudyof"diversity Increasing attentionisbeingpaid agriculture countries. insouthern requirements anddemandsof to tropical speciesandthespecial attention while payingparticular chain, from producer toconsumer, future needsofthewholeagrifood Montpellier are anticipatingthe IRD andtheUniversity of of Agro-Montpellier, Cirad, INRA, genetic resources, thescientists Through theirresearch into of tomorrow the demands Meeting otc acSgi,[email protected] Marc Seguin, Contact : variety resistance to development ofnew toolsfor theimprovement breeding of This work hasyieldedfindingsvitaltostrategiesandthe andtotal. partial and tothetwo typesofresistance, - 1QTLwithamajoreffect iscommontoallhevea varieties - 8QTLofresistance have beenidentifiedon7chromosomes; several genes); iscomplexandmultigenic (controlled by ortotal, partial whether - thegeneticdeterminismofresistance toleafblight, blight.We now know that: regarding thegeneticoriginofhevea's resistance toleaf Microcyclus ulei. Microcyclus - oleic acidcontent); sunflower oils(stabilityofthe aroma ofcoffeevarieties, and grape varieties, the"incup" - neighbouring plants.neighbouring between and newvarieties diffusion oftransgenes) occurring with geneflow (geneticpollution, - most durable resistances; leads totheidentificationof of plant-pathogeninteractions, resistance, togetherwithstudies This search forsources ofdisease viralserious diseasesinvines). Solanaceae nematodes inrice, bananaand but alsoby animalparasites (e.g. intheoilpalm), vine orfusarium fungi (e.g. powdery mildewofthe yellowrice and mottlevirus) caused by (e.g. viruses assessment of the risks associated assessment oftherisks sources ofresistance todiseases product quality or certain vectorsof or certain , asinseedless

7 Agropolis - May 2001 Genomics applied to agronomic

Genetic improvement is founded on better understanding of the traits characteristics and functioning of individual plants and on a enomics offers various ways of to the development of a whole range finer perception of the diversity acquiring knowledge on of new methods and improved G cultivated plants and of precision of existing methods. present in the genetic resources improving them: of the cultivated species. The - molecular physiology, which uses Mapping and various technologies of functional genomics to identify agronomically valuable traits, sequencing of genomics should make a - genetic mixing, which enables the major contribution to the creation of new varieties based on genomes characterization of genes and better genome mapping of factors • Genetic mapping uses labelling 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 Team and co-ordinator - general agronomic characteristics, resistance to disease or a criterion of 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 agronomic traits" research group monocotyledons), crosses and then analyzed, using (UMR GACA) comprises 13 - specific agronomic traits, which molecular markers and agronomic researchers from Agro.M, Cirad should be studied in the different assessment in the field. This molecular and INRA. species of agronomic value, as done characterization yields a detailed Co-ordinator: Jean-Christophe for twenty or so Mediterranean and genetic map of the genome of the Glaszmann, Cirad, tropical plants. species. Fine mapping, based on the [email protected], analysis of more offspring then locates fax: +33 (0)4 67 61 56 05 Genomics is based on recent progress these genetic factors precisely 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 Wild banana with seeds to are the only ones to be eaten. each of the two genomes, although their frequency is improve crop varieties They are seedless, whereas the unknown.The availability of large fragments of DNA combined 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, [email protected] the clone considered.All the wild acuminata and balbisiana Agropolis - May 2001 - May Agropolis 8 controlling technological fbelnt,strength, (fibre length, DNA fragments genes governing thesetraits. It is expression of genomic regions implicatedinthe genetic map–whichlocates the one other. This mappingtranslates a clones) andordered withrespect to Chromosomecase ofBacterial Artificial that are inthe cloned(insidebacteria oflarge DNAfragmentsin theform areplicaconstructs ofawholegenome • to raise inconfinement. offspring facilities,laboratory andacapacity resources, landforfield trials, All thispresupposes accesstogenetic - contain genesofinterest. typesofsequenceswhich various ofchromosomes bearing in theform physical organization ofthegenome physical mappingofthegenome Structural genomics quality incotton What genesare resistance…) ? particular traitsparticular –into that containthe reveals the industrial groups andlaboratory industrial of genesagronomic interest. It also chromosome walkinginthePoaceae - Sequence Tags(ESTs); transcribed sequences, orExpressed of genesdetectedby means oftheir torecoverserves thecompleteversion (see page11 “ typically appliedtopositionalcloning Roussillon Génopole " (seepage16 chromosome 12of rice an initiativeinFrance forthe inthesettingupofsuch participated Roussillon laboratories have Arabidopsis usingmodelplantslike information networks generate thistypeof i.e. between 20,000and50,000. gives accesstoallthegenesofaplant, The Montpellier andLanguedoc- systematic sequencingofthegenome and rice. The Languedoc- Synteny andparallel

J.-L. Chanselme, © Cirad-CA Bernard Hau, © Cirad-CA "). the fibre technological quality. tested intheanalysis ofQuantitative Trait Lociinvolved in identified are ofagronomic interest andcan begenetically candidategenes thus a biologicalfunctiontothesegenes.The andpossibly toassign determines infineintrinsicfibre quality, genes whoseexpression be possibletolocateimportant Itwillthus identifiesthefavourable alleles. ineachcase, and, indicates whichgenesare involved inthisagronomic trait (ESTs) duringcottonfibre development are investigated.This DNA)andofExpressed Sequence (complementary Tags patternsofexpression ofcDNA For this, cotton plant. varietiesandspeciesof qualities offibres indiverse mutants, now possibletoidentifywhichgenesaccountfor thedifferent Itis resistance tostretching…). strength, of thefibres (length, made between geneexpression andthetechnologicalquality few moleculardatathatwould enableacorrelation tobe epidermal cellsoftheseedintegument.We currently have Ithasaunicellularstructure whichdevelops from industry. Cotton fibre isthenaturalfibre mostusedby thetextile otc:Mr iad mar Marc Giband, Contact: Quality of cotton fibrecotton of Quality ••• Large ”) c [email protected]

9 Agropolis - May 2001 Genomics 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 probability of being interrupted at least once by an insertional (diseases and pests) A reporter (blue) gene reveals gene mutagen, here the T-DNA from Agrobacterium tumefaciens. and abiotic stress expression in vessels of a rice flower 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 [email protected] 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; gene function genes (Expressed Sequence Tags or - the fine evaluation of transformed ESTs) allows the characterization of material to elucidate all facets of the • Functional genomics aims to genome expression patterns. The function of a gene, by means of cellular characterize the expression of the analysis of RNA extracted from certain and molecular biology, and physiology. genome and its integration in the organs of cultivated plants, under major metabolic functions. given conditions and at a given These technologies, applied to some - insertional mutagenesis (see above moment, yields an image of all the model plants and to a range of more "Identifying gene function using rice genes expressed under these complex cultivated plants, can build mutants ") creates mutants by conditions. Among these genes are bridges between genomes. Genetic randomly inserting in the genome a some of agronomic value that it information can be transferred DNA fragment that can be mapped. would useful to clone. Depending on between several species because of When this fragment is integrated in a the characteristics of the sequences the conservation throughout evolution gene, thus generating a mutant, it or of the expression patterns, some of of certain elements of the general alters the gene's function, thereby these ESTs can be attributed a genome organization, like the modifying the trait of interest. The hypothetical function, thus making similarity in gene distribution between mutated gene is located thanks to the them candidate genes. This is now chromosomes (conservation of inserted fragment, and its function is under way using model plants and synteny, see next page "Synteny and identified using the affected trait. will be extended to the major crops. parallel chromosome walking in the This technique has been developed The precise functions of the candidate Poaceae") or the colinearity between for different model plants genes, identified through genomic homologous chromosomes. (Arabidopsis, Medicago truncatula, approaches, are characterized in two Genomics gives an impetus which for example). The Montpellier stages: unites research teams formerly research teams are studying rice as a - genetic transformation to test the specialized in different cultivated representative of the grass family effect of a gene or of a candidate plants. (Poaceae); sequence on the phenotype of a plant, through its insertion in the genome and/or the modification of Agropolis - May 2001 - May Agropolis 10 Studies are under way to investigate proteins of importance Wheat genes, proteins in the value of wheats, notably the thioredoxin system. 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 Fréderic de Lamotte, © UBBMC-INRA proteins but also of other small proteins especially rich in 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, [email protected] 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 Synteny and parallel marqueur Riz BAC Séquences chromosome walking in microsynténie? the Poaceae répétées () microcolinéarité?

gène cible J.C. Glaszmann, © Cirad-Amis

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 (distribution of genes between chromosomes) and of colinearity the Poaceae using BAC libraries 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 [email protected] 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 Agropolis - May 2001 - May Agropolis 11 Genomics and plant development

Genomics and molecular From its creation, the and researchers who are analyzing genetics are now providing University of Perpignan developmental processes and D laboratory has been studying dissecting basic cellular and great insights into how a seed plant development using molecular biochemical mechanisms. forms and acquires its analysis. By the early 1980s, this approach had laid the groundwork longevity and germination for the application of genomic The early stages of vigour, how protein production technologies. The laboratory has thus plant development is controlled by the ribosome, played a pioneering role in France in the launch of projects on Arabidopsis Our work centres on embryogenesis, and how the potential of thaliana, a species which remains the seed formation and maturation, oxidoreduction controls the principal research model because of topics of vital interest to the seed cell cycle, growth and a number of advantages: its genome industry and the agricultural sector. has been sequenced, there are Our first aim is to identify the role environmental adaptation numerous mutants for use in and function of genes involved in of plants. dissecting metabolic pathways, early embryogenesis and embryo development programmes, responses formation. Secondly, our plan is to to environmental stimuli and basic determine the role and regulation of Team and co-ordinator cellular mechanisms, and it is proteins involved in seed maturation. The “Genome and Development of accessible to forward and reverse This research leads to various Plants” research team (UMR GDP) genetic approaches. technological developments: search for comprises 17 researchers from promoter genes, conditional control of CNRS and the University of Our laboratory brings together gene expression, manipulation of Perpignan. experts in most aspects of genomics reserve lipid or protein contents. ••• Co-ordinator: Michel Delseny, (continued on page 14) University of Perpignan, [email protected], 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 Fredy Barneche,© Univ de Perpignan their synthesis. Using the Arabidopsis genome data, we are systematically identifying genes encoding ribosomal Observation of fibrillarin proteins, genes of proteins involved in ribonucleoprotein through a linkage with complexes, and genes of snoRNA (small nucleolar RNA) a green fluorescence responsible for the modification of ribosomal RNA. reporter in transgenic Contact: Manuel Echeverria, [email protected] onion cells. Agropolis - May 2001 - May Agropolis 12 rbdpi hlaa model Arabidopsis thaliana, What part doeseachgeneplayWhat part inthevarious Arabidopsis of thioredoxin genesinthegenomeof ofmultiple discovery copies cycle.The involved intheregulation ofthecell showed thattheseproteins are This protoplasts were cultured. of celldivisionwhenthetobacco was demonstratedonresumption second geneoftobaccothioredoxin activityofa tobacco protoplasts.The early inthededifferentiationvery of from messengerRNAsexpressed relevant DNA) cDNA(complementary by differentiallaboratory screening ofthe cytosolic thioredoxin wasisolatedinour Thefirstgeneofplant and hencetheiractivity. thusregulating theirconformation bridges inproteins, Thioredoxins are enzymesthatcanbreak disulphide available for only halfofthegenes ESTsare However, given momentinthelife oftheplant. EachESTidentifiesagenewhichisexpressed ata libraries. Sequence Tags DNA) (ESTs)from cDNA(complementary structure willenableustomap anddeterminethestructure Bioinformatic analysis of 25,000 genes. functions canbesuggestedfor just60%orsoofsome prompted avarietyofquestions. plant fordicots li o, Univ. dePerpignan Alain Got,© Role of thioredoxinsof Role studied usingExpressed of thegeneshasalsobeen expression profile 2000.The was completedattheendof which genomesequencing plant is For function. plant genomestructure and for thesystematicstudyof and dicotyledons)were chosen higher plants(monocotyledons the two large divisionsinthe Two modelplantsrepresenting Studying dicotyledons Arabidopsis Arabidopsis thaliana Arabidopsis genome themodel , and , model plants model , thioredoxins? Which functionaldomainsofthioredoxins cell processes? What are thetargetsofdifferent otc:RcadCoe cook Richard Cooke, Contact: ( international sequencingproject. inthe done onthecultivarchosenby allthepartners work isbeing to determinethefunctionofgenes.This mutants isunderwaywhile asystematicanalysis ofinsertion being prepared for thestudyofgeneexpression andstructure, LibrariesofcDNAare sequencing ofthechromosome 12. pointsforNational SequencingCentre the withthestarting we have beenabletosupplyfor the sequencing)inorder, ByputtingtheclonesoflargeDNAfragments(used by 2003. The completesequenceofthericegenomeshouldbeavailable themodelplantfor of thericegenome, are now beingapplied tostudythestructure andexpression andknow-how acquiredThe expertise instudying inalltheseprojectshas participated since1992. Perpignan groupcharacteristics altered by the mutation.The ofthe fragment ofDNAinthegenes)andobservation through thecreation ofa ofmutants (by randominsertion Genefunctioncanalsobeinvestigated control theirexpression. andtoidentifytheelementswhich of alltheplantgenes, account for theirspecificity? We have made de Perpignan Univ. J.M. Lancellin,© see page 10 in the plant cell plant the in substantial progress inseekinganswers to hs usin.We have shown that these questions. otc:vsMyr yme Contact:Yves Meyer, cytosolic thioredoxin in different thioredoxins are specialized " Arabidopsis thaliana nslht pae cellcyclecontrol, in sulphateuptake, Identifying gene function using rice mutantsIdentifying gene functionusingrice the response tooxidative stress or aiy suchastheglutaredoxins. family, expression ofgenesanotherredoxins xrsino nte,orby the expression ofanother, Structure of possibly becompensatedby the ahgn.Several mutants insertion pathogens. the alterationofonegenecould e@univ-perp y er@univ-perp This suggeststhat a clearphenotype. but nonehasrevealed have beenobtained, monocotyledons. .fr Arabidopsis .fr ") 13 Agropolis - May 2001 14 Agropolis - May 2001 genes encodingenzymesoflipidbiosynthesis.We are focusing mutants isscreened toidentifyplantsthathave seeds aborted Early embryogenesis eea ol we isolatedthe gene asatool, otcs atn ei,University of Devic, Martine Contacts: the seedlosesmuch ofitswaterandentersdormancy.These seed maturation using the Sixorso T-DNA tag. inserted an activatoroftheexpression ofthe Desiccation: been altered.This altered been altered.This the first divisions of the embryo cellshavethe firstdivisionsofembryo beencharacterized. AB15 are synthesized inlargequantitiesduringdesiccationofthe " survival environmentsurvival for thecells.We inventoried theLEA ed Oneoftheirroles seemstobethemaintenanceofa seed. proteins of Seed maturation: Genomics and embryogenesis mutants embryogenesis rtis iisadcroyrts and lipidsandcarbohydrates, proteins, hm h m rti.Usingthe theEm1protein. them, and acyltransferases whichcontributetotheformation of anyo aeed notably thegenesencodingelongases mainly onrapeseed, their formation becauseanessentialgene( rtis andtheninvestigated oneof proteins, Using genetics to clarify to genetics Using Embryogenesis offloweringEmbryogenesis plantsoccursinthree stages: in their fruit.These seedshave notbeenabletocomplete in theirfruit.These epga,de Perpignan, early embryogenesis genes.We are now investigating how mutants (emb).The INRAcollectionof mutants (emb).The T-DNA insertion epga,delsen Perpignan, interacts withotherregulators of three stagesare studiedby theGDPresearch group. ihlDley University of Michel Delseny, Arabidopsis LEA (Late Embryogenesis LEA (LateEmbryogenesis Abundant) proteins the mechanisms of mechanisms the vic@univ-perp withsynthesisandaccumulation ofreserve , thisisstudiedby thegeneticanalysis of : Plant Development having identifiedtheprincipalreserve " in y@univ-perp embryogenesis ed,we are now interested inthe seeds, EMB LEA proteins. Arabidopsis during which the embryo forms, during whichtheembryo The reporter gene revealsa ABI5 gene expressed inthe seed gene isidentifiedandstudied .fr gene, Em1 and LEA .fr called embryo-defective EMB desiccation genes essentialfor development EMB triglycerides. gene) has when , oeyeGilmnt Univ. dePerpignan Jocelyne Guilleminot,© physiological stages. between differentribosomes by creating anheterogeneity of redundancy ismanaged,doubtless and coregulated andhow functional the different elementsare integrated our ambitionistounderstandhow of RNAs.ribosomal Now thatthegenome maturation oftheprecursor of identified regulatory proteins ofthe biochemical techniques, we have proteins.RNAs andribosomal Using of itsdifferent constituents, ribosomal and thecoordination ofthesynthesis process: thebiosynthesisofribosome Finally, we are analysingabasiccell thioredoxins. seeking theproteins targeted by genes, studyingtheirregulation, and systematically analyzingredoxin oxidative stress. Our group istherefore control andtoresponses toplant tocellcycle contribute bridges and rupture ofprotein disulphide mechanisms suchastheformation We are how alsoseekingtoclarify processes basic biochemical of determinism Genetic Arabidopsis is entirely sequenced, foreign institutionslevel. next page),oratGénoplanteand Languedoc-Roussillon Génopole(see framework oftheMontpellier- research teamsatregional levelinthe species, incollaboration with projects onrice, cassava andother Arabidopsis acquiredsequencing experience with We are currently usingthegenome multigene families, annotation…). (presence oflarge duplications, genome structure andorganization mutants, andontheanalysisof analysis, withanextensivestudyof concentrate onfunctional ourefforts in genomesequencing. We now Expressed Sequence Tags (ESTs) and programme designedtoobtain Arabidopsis analysis hasbeenrelated to Our ingenome group's mainthrust research Constantly evolving , with participation inthe , withparticipation to initiatenewgenomic activities

© IRD/ILTAB/scripps and naturalresistanceand virusinteractionsmottle yellow Rice B- cryomicroscopy C- cristallogr reconstruction microscopy RYMV seen and image A- electron through aphy Cryomicroscopy andcrystallography stages andcharacteristicsofviralmovement intheplant. grown in Africa sources ofresistance tothisvirusinthetwo ricespecies WARDA Incollaborationwith the variabilityofviralpathogenicity. andtheirconsequencesfor protein andthehostproteins, of themolecularinteractionsbetween theviralenvelope thesedataunderpintheinterpretation the virus.Taken together, otc:li hsuèe alain.ghesquier Ghesquière, Contact:Alain glaberrima sativaandOryza (4) Oryza (3) WARDA:West RiceDevelopment African Association (2) Collaboration withILTAB Institute. Research andtheScripps for InternationalLaboratory (1) ILTAB: Tropical USA. Biotechnology, Agriculture fteifciu yl,ILTAB of theinfectious cycle, Initsstudy natural resistances thatcouldbeusedinbreeding. serological andmolecularvariability)on infectious cycle, determine thehigh-resolution three-dimensional structure of yielded practicalapplications usableinruraldevelopment. both added considerably tofundamentalunderstandingand It withinternationalcolleagues. Montpellier teamsinconcert researchof themultidisciplinary conductedby several This work onthericeyellow mottlevirusisaprimeexample interactions inothercereals. constitute amodelfor theexplorationofhost-virus rice-RYMV molecularinteractionsprobably also genomics, asriceisamodelplantfor thecereal functional Lastly, areas. ensure asustainableresistance afterdeployment across large inorder to how theseresistance genesmay bebypassed, simulation of andlaboratory interactions suchastolerance, thecharacterizationofotherhost-virus collections, these geneswillallow theassessmentofdiversity inrice Cloningof are now transferred by marker-assisted selection. collaboration with thesegenesofnaturalresistance WARDA, In their functionsisnow arealistic goal using genomic tools. Positional cloningoftheseresistance genesandthestudyof chromosomes. locate theseresistance genes(orQTLs)ontherice 3 nCt ’vie we have studieddifferent natural in Côted’Ivoire, 4 Mapping andgeneticlabellinghave ledto . 1 has describedthedifferent on thevirusitself(structure, research hasfocused discovery, Sinceits of varietalresistance. pathogen isthedevelopment solution tocontrol this only possible Africa.The of irrigated rice growing in following intensification years, considerably over thelast20 (RYMV) hasspread Rice yellow mottlevirus 2 have beenusedto [email protected] d.fr 15 Agropolis - May 2001 16 Agropolis - May 2001 delsen University ofPerpignan, MichelDelseny, Contact: analysis relates above alltomutants of Functional Chromosome)Artificial librariesare underconstruction. Several BAC (Bacterial interest inthericegenomeare alsosequenced. Someregions of onefungusandanalga. cassava), oilpalm, (rice, principally usingESTs(Expressed Sequence Tags) with tropical species Several majorplantgenomesequencingprojects are underway, protein-nucleic acidinteractions). analysis ofprotein-protein and analysis oftransgenicmice, genotyping, We are alsointheprocess ofsettingupothertechniques(plant - structuralbiology. - bioinformatics, - proteome analysis, - transcriptomeanalysis, - medium-scalesequencing(ca.5Mbp/year), - genomicrobotics, suchas: Several technologiesare already implemented, - adequategreenhouses for transgenicplants. and spectrometry, - complementingdevice for theanalysis ofproteins by mass - equipmentfor theproduction andreading ofDNAchips, computingcapacity,- information technology DNAsequencers, - robots, Various investments have allowed acquisitionof: companieswithhighadded value. the creation start-up ofbiotechnology designed togeneratenew information ingenomicsandtopromote theGénopoleisalso fromApart makingresearch toolsavailable, outset wasstrongly focused onplantgenomics. andfrom the It wasoneofthefirstnetworks ofitstype in France, animalorhumangenomics. microbial, so laboratoriesworking onplant, or The MontpellierLanguedoc-RoussillonGénopoleembracesforty post-genomics studies. resources isexpectedtoboostnationalandEuropean genomicsand poolingofstrengths and teams working withinthesameregion.This complex andcutting-edgeequipmentwithvariousgenomicsresearch The Génopoleswere created inFrancesoastoshare accessto nlssporme.Proteomic studiesare alsobeing developed. analysis programmes. production ofESTsfrom variousgenomes willboosttranscriptome y@univ-perp Languedoc-Roussillon .fr United we stand,divided we fall Arabidopsis The Montpellier ie modelplant Rice: n ie butthe and rice, for monocots

Michel Dukhan-IRD Sémiha Cebti, ©Agropolis Génoplante programmeGénoplante the performance: enhance to sectors private and public fromthe input Joint atcpt nti rgam,especially through theirresearch inthisprogramme, participate andactively laboratories are deeply committedtothisresearch, Languedoc-Roussillon wheat….The rapeseed, maize, in Europe: Arabidopsis mainplantsstudiedare genomic analysis ofplantspecies.The The research projects rangeinscopefrom geneticresources to the consumersandfarmersdemands. creativity ingenomicsandtodevelop qualityseedsthatmeet objectives are tostimulate researchapplications.The and structure for thestudyofplant genomesanditspotential coherent andcompetitive aim istoprovide Francewithaglobal, Its the regional MontpellierLanguedoc-RoussillonGénopole. more focused oncrops than ofmajoreconomicimportance Génoplanteis BiogemmaandBioplante)sectors. Crop Science, INRAandIRD)private(Aventis CNRS, the public(Cirad, Génoplante Génopole n ie smdlpat,andmajorspeciesgrown asmodelplants, and rice, is anationalprogramme involving from partners activities onrice. delsen MichelDelseny, Contact: y@univ-perp genomics research in equipments for Génopole: .fr shared Guillaume Blanc-Univ.de Perpignan otc:vsSVDNArpls sa Contact:Yves SAVIDAN,Agropolis, partners. line withthewishesofseveral nationalandinternational in might beextendedinthefuture tootherresearch fields, thisconcept institutions.Tested today onplantbiotechnology, andhighly equippedEuropean research centersintheSouth, ofnationalorganizationsandinternationalagricultural efforts Itsynergizestheresearch objective andacommongoal. sharing ofhumanresources andfacilitiesdedicatedtoaglobal This multi-organizational platform conceptencouragesthe Génoplante. Génopoleand projects ingenomicsandplantbiotechnology: Montpellier anditsregion already intwo participate large-scale Agropolis benefitsfrom anespecially favourable contextsince development intheSouth. needed tostrengthen thestudiesrequired for theagricultural thecutting-edgeresearchsupports activitiesspecifically platform andknow-how.This expertise infrastructures, intheEuropean contextofhighly equipped the South, andresearch scientistsfrom countriesof research centres, scientistsfrom internationalagricultural French researchers, promotesbiotechnology acollaborative research by effort The Agropolis research platform onplantgenomicsand Agropolisplatform the partnership: of form new a of experience The Map ofduplicated region intheArabidopsis thalianagenome vidan@a gr opolis.fr os-a rs 1.0x10 Mouse-ear cress study ofspeciesdiversity anditsuseincrop improvement. notably for the but itopensupunprecedented possibilities, Sequencingisjustonestep, gene andoftheprotein itencodes. nextstepistoidentifythefunctionofeach sequenced.The there are lessthan15,000different genesamong the 26,000 1.6x10 and over 2.5x10 70%ofmouse-earcress genesare duplicated(figure), sequencinghasinfactshown that However, genome (seetable). 4.2x10 1.0x10 unlike specieswithalarger genes are present assinglecopies, that mouse-earcress hadasmallgenomeessentially becauseits Itwasinitially believed andabove hasasmallgenome. cycle, reproductive hasashort grows rapidly, advantages –itissmall, as amodelplantbecauseithasnumber ofexperimental Mouse-earcress of thespecies. and especially to the sequencingofonefive chromosomes international Delseny's team(seeprecedent pages)have contributedtothe The Montpellier-Languedoc-Roussillon GénopoleandMichel Wheat Maize Tomato Rice Species … thought we what not cressis mouse-ear thaliana the Sequencing Arabidopsis thaliana genome: (Arabidopsis thaliana) genome sequencingproject, Size ofthegenome Arabidopsis (base pairs) was chosen 10 9 9 8 8 17 Agropolis - May 2001 18 Agropolis - May 2001 speciality oftheplantkingdom, The andMolecularPhysiology“Biology hindrance toplantproduction eerhr rmAr.,CR,INRA researchers from CNRS, Agro.M, oodntr ClaudeGrignon,Agro.M, Co-ordinator: programmes whoseexpression e odtos Thisabilityto new conditions. ahtp fsrs,theplantis each typeofstress, (UMR B&PMP)comprisesalmost40 Team andco-ordinator olwd.Plant speciesand worldwide. and theUniversity ofMontpellierII. use environmental signalsto drive genomeexpression isa varieties vary enormouslyin varieties vary and isknown asphenotypic each planthasapanoplyof enhances adaptationtothe Environmental constraints rgams Subjected to programmes. osrit.In mostcases, constraints. linked toclimateandsoil of Plants”research group able toselectalternatives a:+33(0)46752 5737 fax: quality are theprincipal within thissetofgenetic [email protected] their tolerance ofthese variants toitsgenetic plasticity. level andreach thescaleofwhole mechanisms gobeyond thecellular the genefunction.Many ofthe biophysics andphysiologytofindout studies by usingbiochemistry, groups completetheirmolecular physiology The discipline-objectis " molecular viewpoint(seenextpage mechanisms lookingatthemfrom a shed lightonthephysiological expression. This work isdesignedto of genesandthestudytheir genetics our research we employ the biology, andfunctionalgenomics. In molecular physiology, integrated four keywords: moleculargenetics, B&PMP research group isdefinedby The strategic positioningofthe from geneto protein A globalapproach: plant molecularphysiology. national andEuropean research in work of placesthegroup attheheart inorganic nutrients. The B&PMP toxic metals, anddeficiencyin salinity, wateravailability, excess of plant adaptationtofactorssuchas the geneticandmolecularbasesof disposal asetoftoolsallowing a The B&PMPresearch group hasatits plant-environment interactions. scientists specialized inthestudyof with ecophysiologiststeamsandsoil physiology, andthrough collaborations biology plant. Our group follows an T Cloning ofthefirsttransporter gene research group aimstoidentify Physiology ofPlants (B&PMP) he Biology and Molecular plants tostress approach, usingmolecular discipline-tool, i.e. thecloning environments Adaptation of . The different researchdifferent . The molecular molecular integrated "). genes, over- andunderexpressors, transformation ofplantswithreporter - mammal cellcultures); batrachian oöcytes, insectand expression - various for whichproteins?" expression (seepage21, the siteandconditionsofits function oftheencodedprotein, and in theplant,includingmolecular of agenetodiscovery ofitsfunction approach, ranging from identification coherent molecular physiology microprobes forwatertransport, etc.) reconstituted systems, pressurized analyses ofinvitro transport in electrophysiology, spectroscopic isotopic tracers, invivo - mutants); of disrupted dissection ofpromoters andcollections reverse genetics physiological techniques systems forheterologous of plantgenes(yeast, (genetic ). Weuse: "Genes… "Genes… (flows of such approaches shed lightonthe ofmutants,applied tothecomparison environmental situations. When development orinresponse toparticular functions brought into playduring instance, themajorphysiological physiological complexity, revealing, for approaches facilitateunderstandingof plant genomics. a majornationalplayer in genome. The B&PMPresearch group is global asitfocusesonthewhole Unlike moleculargenetics, genomicsis in genomics to nationalinitiatives Strong commitment of thedominantferric form inmany soilslimitstheavailability buttheinsolubility Iron requirements ofplantsare quitehigh, complex. gene oftheiron-siderophorein maizeofthefirsttransporter isillustratedby therecent strategy cloning phenotype).This (from phenotypetogene) andreverse genetics(from geneto Molecular physiology islargely basedonforward genetics iron-siderophoreplant the complex of transportergene first the of Cloning escapes chlorosis onlyonesorghoplant In arapeseed field, The genomics functional collections of systematic useoftheavailable inthe and allteamsparticipate Expression);Analysis ofGene (DNA membranes, SAGE Serial transcriptome approaches- various workshop; - anationalproteomics permanent are basedontheseprinciples, including: knowledge. The research group is practical application ofbiological opening uppossibilitiesforthe physiological functions, thereby of the molecular determinants Functional genomicsreveals the mutants. B&PMP group's research programmes its cellularenvironment. Several ofthe interactions ofthemutatedgenewith Arabidopsis

J.-F. Briat, © UMR B&PMP of the of genomicsequencesnearthetransposonledtoidentification exploration chlorotic phenotypeis duetothetransposon.The theroots ofgrasses( latter, reduce theferric iron toferrous iron andthenabsorbthe therootscalled iron ofdicotyledons chlorosis.Whereas causestheyellowing ofleavesof thisessentialelement.This otc:Ja-rnosBit [email protected] Jean-François Briat, Contact: theiron-siderophoreto transport complex. explaining why iron-deficient plantshave anincreased capacity thus the roots andleaves andisinducedby iron deficiency, supplied withthesiderophore.The butonly iftheiron is develop inaniron-poor environment, iron.The complementation ofamutant yeast strainunabletoabsorb theiron-siderophoretransport complexhasbeenverified by protein'ssimilar tothatofaniontransporter.This abilityto allowed identificationofhomozygous individuals inwhichthe of maizemutants created ofatransposonhas by insertion Geneticanalysis ofacollection chlorotic zonesontheleaves. resulting in absorption oftheiron-siderophore complex, the Inmaize, iron chlorosis effectively. allows grasses( membrane transporters, whichensures thatferric irons isavailable for the process, andabsorbthewholecomplex.This ferric iron insolution, they secrete molecules(siderophores) abletocomplexthe insertion YS1 YS1 ee whichencodesapolypeptide withastructure gene, gene ofmaizerestores theyeast abilityto such asvineandmaize. these programmes totarget species, applying theknow-how acquired in thaliana themodelspecies concern genomics projects, mostof which programme, withfifteenfunctional Génopole andGénoplantenational deeply involvedintheMontpellier Poaceae (see page16). We are now ) useanothermechanism: YS1 YS1 gene isexpressed in Poaceae mutation prevents ••• ) toresist Arabidopsis 19 Agropolis - May 2001 20 Agropolis - May 2001 .uo .ilr,©UMRB&PMP S.Munoz ÐP.Tillard, © signals whoseidentificationiscritical.We cansearch for themolecular bvgon ln tutrs andthistriggersexpression ofagene aboveground plantstructures, aall o vntog hyaentdfceti irgn theroots even thoughthey are notdeficientinnitrogen, So, parallel. isotope irgnfe niomn.h te ot,placedinanenvironment nitrogen-free otherroots, environment.The encoding aspecificnitratetransporter.This geneinductionisvisualized bvgon at ftepat nti xml,an Inthisexample, aboveground oftheplant. parts is deficientinnitrogen becausehalfofitsroot systemisplacedina yhbiiaino esne Nsi h ot,usingapertinent by hybridization ofmessengerRNAs intheroots, through functionaldissectionofthepromoters ofmarker genesof signals thatinform theroots ofthenutritional requirements ofthe irgnrqieet fteaoerudprs they respond to nitrogen requirements oftheaboveground parts: adapt their molecular machinery andfunctioningtotheincreasedadapt theirmolecularmachinery The molecularphysiology approach isillustratedby thestudyof Adaptation of oehls,they receive signalsindicatingdeficiencyfrom the Nonetheless, rb.Measurements oftheuptake ofnitratelabelledwiththe probe. components ofsuchsignalsindicatingnutritional requirements 15 N show thattheroots' nitrateuptake capacity increases in otiigntae are adequately suppliedwithnitrogen. containing nitrate, Arabidopsis dialogue for better for dialogue otc:li oo,[email protected] Gojon, Contact:Alain mineralnutrition plants tostress root-leaf environments Arabidopsis this response. plant the root overexpressed in transpor nitrate a the plant, the upperpart of to adeficiencyin Asanswer nitrates. without (right) grown with (left)or Plant roots are ter geneis environment. expression inthewholeplantits and cellularapproaches andtheglobal gap between thegenetic,molecular inFranceopportunity the tobridge campus constitutesaunique page 22). Their presence onthesame of Cultivated Perennial Plants, see and BDPPC(Biology ofDevelopment Environmental Stresses, seepage26), (Ecophysiology ofPlants under three groups, i.e. B&PMP, LEPSE Productions Végétales merges these des Institut development. The to theecophysiologyofplant from theanalysisofgeneticresources activitiesrange whose complementary of three Montpellier research groups research group positionitattheheart strategiesexperimental oftheB&PMP The research objectivesand Productions Végétales the Institut des environment: A propitious scientific Electrophysiology J.-B. Thibaut, © UMR B&PMP UMR © J.-B. Thibaut, The 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; Upper left: 2D electrophoresis gel of (MALDI-TOF MS), - screening for candidate genes involved in the regulation of Arabidopsis thaliana root proteins. sequencing (ESI MS/MS, adaptive responses; Upper right: bio-informatic analysis sequencer). - separation of general and specific pathways of the response to 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, [email protected] of a polypeptide digestion in 2D electrophoresis (MaldiTof) analysing post-translational 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, [email protected] Heterologous expression system Agropolis - May 2001 - May Agropolis 21 Biology of the development of cultivated perennial plants Perennial plants are subject to he biology of plant development Development environmental changes and to embraces knowledge of all the T molecular, cellular and and optimized competition in cultivated structural processes leading from the populations, and adapt to zygote to the reproductively viable exploitation of trees adult plant (embryogenesis, juvenile these changes through more or and adult development phases). The primary goal of the "Biology of less marked alterations in In cultivated perennial species, Development of Cultivated Perennial development. These alterations account should be taken of specific Plants" (BDPPC) research group is to features linked to the perenniality of enhance understanding of the may be accelerated through crops, the length of the juvenile development of ligneous plants using genetic improvement. phase, the process of lignification, temperate and tropical species, in and establishment of a perennial order to master their functioning, plant architecture. their genetic usefulness, and their 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 Montpellier II. Thousands of rubber Co-ordinator: Françoise Dosba, [email protected], trees born in fax: +33 (0)4 99 61 26 16 Website: the laboratory 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, [email protected] Agropolis - May 2001 - May Agropolis 22 M.-P. Carron, © Cirad-CP Ct ’vie,clonePB260, (Côte d’Ivoire), Heveavitroclone infieldtest 3 yearsold Biology 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, Filao is a tropical tree from Oceania which belongs to the - to develop the technologies needed 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 erosion, and the restoration of the fertility of degraded relations between the development zones. Filao lives in nitrogen-fixing symbiosis with a and life cycle of perennial plants and 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, [email protected]

Filao symbiotic genes are studied to improve symbiosis efficiency Agropolis - May 2001 - May Agropolis 24 morphogenetic responses to regeneration systemstostudy - plants. transformation adaptedtoperennial role ofgrowth regulators; genetic stagesofgrowthof theimportant and environmental changes;identification - modulating genomeexpression. ofthemechanisms description species withaviewtoimprovement, understand thearchitecture ofthese their expression, usethesegenesto and toinvestigatetheregulation of of developmentperennial plants genes involvedinthedifferent phases - structural levels: pursued atthree complementary This research iscurrently being to architecture From gene Eucalyptus. the laboratory " specific topics, hevea(seepage22 coffee andbanana,formore trees tofixnitrogen Casuarina - and peartree; specific topics, tree, apricot olivetree of fruits " right - studies are: The perennial speciesusedinthese genes concerned. the expression andregulation ofthe the geneticmechanismsunderlying between architectural features and environmental conditions, relations relation togenotypeand development andarchitecture in Thousands ofrubbertrees bornin molecular: whole plant: cellular: tropical species: temperate species: Architecture oftrees andquality ") andvine, andformore development ofinvitro (see left" identification ofthe "), cacaoand root andbranch oil palm, "), coconutpalm, Genes thatallowGenes apple tree (see for twoappletree of theFujivariety Consequence for tree architecture “solaxe”growth differently (free Comparison of

that have been Evelyne Coste, © INRA distribution. growth left, managed fruit size fruit right). and fruitquality and Treesarchitecture otc:EeyeCse,[email protected] Evelyne Costes, Contact: environmentally costly. culture systemsthatrequire lessinputandare less allow selectedmaterialtoevolve towards more integrated morphological characteristicsgoverning yield to necessary itwillbe Inthelongerterm, genetic transformation systems. willinvolvemorphogenesis ofcaulesorroots.This theuseof notably thoseinvolved in stages andintheirregulation, manipulate thegenesinvolved inthedifferent development we shallidentifyand Usingtheapple tree, environmental value. the architecture andfunctioningofplantseconomicor basis ofenhancedunderstandingthemechanismsunderpinning components. genetic determinismoftheprincipalarchitectural The BDPPCresearch goal group's isto primary agronomists andplant biotechnologistsfrom INRA. ecophysiologists, physiologists, together morphologists, approach multidisciplinary brings thinning outthefruits.This notably tree shaping and into accountmanagementpractices, will enhanceunderstandingoffruitquality.This approach takes woodin thefoliage andthecharacteristicsofsupporting Knowledge ofthepositioningfruits interest today. particular the overproduction, aneconomicbackground of growth andfructification.Against based onin-depthknowledge oftherulesgoverning varietal integrate intobreeding schemes We plantomake geneticimprovements onthe production ofquality fruits This work leadstopropose given species. and itssustainabilityoftrees ofa governing early stagesofproduction, study andanalysis oftherules The maingoals ofthiswork are the from morphologicalmarkers. ofthetree's developmenthistory analysis allows toreconstitute the and initstemporalcontext.This tree, This involves INRA and Agro.M atMontpellier. Species" research group ofthe Functioning ofFruit-bearing by the"Architecture and to temperatefruit-bearingspecies isbeingapplied intertropical forest, plants, The architectural analysis of adaptive management practices which isconsidered globally developed inthe1960s observation ofthe observation study the is of and to 25 Agropolis - May 2001 26 Agropolis - May 2001 Plants underEnvironmental Stresses” ha.Headway canbemade ahead. The“Laboratory ofEcophysiologyThe“Laboratory of researchers from Agro.M andINRA. biotechnology andmodelling biotechnology adaptation ofplantstowater deficit isvitalforagricultural Team andco-ordinator oodntr François Tardieu, Co-ordinator: research group comprises13 production inthedecades a:+33(0)467524443 fax: of plantgeneregulation. [email protected], The search forbetter through theuseof drought-resistant progress. inevitable, regardless ofanygenetic "water forcarbondioxide" trade offis but alsoreduces photosynthesis. The leaf growth. This avoidsdehydration by closingthestomataandreducing of water, itmustslow itstranspiration the plantcannottakeupthisamount plant's weight adayinsummer).If large quantities(uptothree timesthe through whichwateristranspired in microscopic pores, thestomata, Carbon dioxide entersleavesthrough possible ifthere istranspiration. photosynthesis andgrowth are only A water supply: inplants, water supply: contingent onaminimum gricultural production isclearly .ade,©INRA F.Tardieu, © of leaf growthleaf of rateDroughtand otc:Brrn ulr m Muller, Bertrand Contact: environmental response. willenableustorelate geneallelestoeach maize.This set ofenvironmental conditionsfor 100recombinant linesof now evaluating thegeneticvariabilityofresponses toeach conditions tothemeasured growth rate(photograph).We are by relating theenvironmental andinthe field, in thelaboratory modelhasbeentestedboth temperature ofthemeristem.This andthe airhumidity, leaf growth ratetosoilwaterstatus, A modelhasbeenestablishedwhichpredicts theresponses of growth rate towater deficitintheairandsoil Natural geneticvariability intheresponse offoliage Creation of experimental experimental resistant toanother. Apurely be willnotnecessarily scenario genotype resistant toonedrought according tolocation,andsoa or afewgenes. This isbecause: which dependsonthetransfer ofone resistance toadiseaseorherbicide, that followed forothertraits, suchas improvement cannotbethesameas given watersupply. The strategy for as tomaximize production fora growth anddevelopmentofplantsso in optimizingthephotosynthesis, Research ondrought tolerance consists deter a multifactorial Tolerance ofdrought: the climate varies yearthe climatevaries onyear and plants? [email protected] minism four-pronged approach isused: with screening forgenesofinterest. A To achievethis, we combinemodelling lower reduced risk, potentialyield). strong response (betterprotection, toa ofahigherrisk) yield attheprice transpiration: maximized potential photosynthesis, growth and weak response (maintenanceof several waterdeficitscenarios, from a exhibiting contrasting responses to andevaluate genotypes construct Environmental Stresses) seeksto Ecophysiology ofPlants under for The LEPSE(Laboratory lower potentialyield. andthereforeagainst risks settlefora yield, ortomaximize protection oftotalloss ahighrisk running maximize thepotentialyield,thereby a genotype, mayseekto thefarmer strategy.the farmer's When choosing qualitative characteristic, andinvolves difficult thanthesearch fora economic reasons. hardly feasibleforpractical and require dozens ofyears, whichis evaluation ofagenotypewould INRA F. Tardieuet T. © Simonneau, the search foranoptimumismore shortage. of inthecapacity genotypic variability Similar research isexploring groups atMoulon and Versailles). (collaboration withtheINRAgenetics and waterdeficitinthesoil temperature, humidity, atmospheric characteristic oftheresponse to individual identificationofthealleles Quantitative Trait Loci)allows and geneticanalysis(search for micrometeorological measurements combination ofdevelopmentmodels, Dactylis Arabidopsis thaliana, deficit inthesoilandair growth anddevelopment towater variability intheresponses of Exploration ofthenaturalgenetic Dactylis ••• to survive severeto survive water of transgenesisof effects Predictingthe water shortage transpiration andthe water statusofplantssubjectto Modelling theeffectofagenetictransformation on (maize, ). The synthesis of ABA. varies only intherateof which model (seepicture), predicted by meansofasingle conditions testedcanbe transformants underallthe behaviours ofthe ABA.All wild relatives orfed artificial deficits orwere graftedonto subjected todifferent water enzyme-deficient plantswere Partially close theirstomata. plants loseallcapacity to resulting enzyme-deficient of abscissicacid(ABA).The gene involved inthesynthesis have beentransformed ata Nicotiana plumbaginifolia [email protected] Simonneau, Contact:Thierry plants 27 Agropolis - May 2001 28 Agropolis - May 2001 Three-dimensional computer ecotypes have beensystematically compared for thearchitecture effects onplantbehaviour ofstress and/oranallelicvariation.A programme isunderway torepresent inreal timetheadaptive responses ofsunflower and otcs ééi eou,[email protected] JérémieLecoeur, Contacts: Modelling thearchitecture ofsunflower and Arabidopsis Creation of Computer modellingisessentialinsimulating thelong-term aitosi niomna odtos In variations inenvironmental conditions. Arabidopsis thaliana simulating resistancesimulating representations of thaliana subjectedtoenvironmental constraints drought-resistant Virtual plants in plants Virtual © H. Rey, Cirad-AMAP et J. Lecoeur, INRA Arabidopsis genotypes totransient to stressto plants? model parameters. Arabidopsis e,r Rey, e [email protected] several , Hervé , pedoclimatic scenarios given genotypeinalargenumberof plants subjecttowatershortage. controls transpiration andgrowth in that in thesynthesisofonehormone the manipulationofageneinvolved genotype. The maintestconsistedin essential characteristics ofeach complexity oftheresponses tothe Modelling reduces theapparent phenotype are functionallyrelated. several characterizing the variables Because theplantisaregulated system, environmental conditions the genotype'sresponses to effects ofagenemanipulationon cycle geneandtherate ofcelldivision). (for example, expression ofacell in different environmental scenarios expression andaquantitativevariable correspondences between gene blots, analysisofactivity)toestablish microarrays) andproteins (Western 18), we assessmRNA(cDNA the B&BMPresearch group (seepage measurements. In collaboration with to advances inmicrometeorological done inthefieldorlaboratory, thanks Gene expression analysiscannow be Dactylis Arabidopsis, environmental conditions plants subjecttoknown associated withadaptationsin with theCirad-INRA-AMAP unit). rate offoliagegrowth (incollaboration functions, suchastranspiration orthe correspondence forthesimplest is already possibletoestablishthis and asimulationofyield.However, it a correspondence between onegene stages, andasyet we cannotestablish genotype. This work isinitsearly associatedwitha calculate therisks and large numberofscenarios therefore itispossibletosimulatea operation hasalow marginal cost, uptake, biomassproduction, etc. This computer inorder tocalculatewater and genotypictraits are fedintoa The microclimatic characteristics sunflower) Modelling ofthebehaviour ofa Systematic assessmentofthe Analysis oftheexpression ofgenes ) ( Arabidopsis (maize, , new constraints onagriculture. prospects forintegrated pestmanagement interactions Plant-parasite to encourage useofalternative solutions mustbefoundtothe htsntr ramns and treatments, phytosanitary BGPI) comprises25researchers from oodntr Jean-Loup Notteghem, Co-ordinator: demands forqualityfoodand et.Theseresearch activities pests. The andGeneticsofPlant- “Biology Parasite Interactionsfor Integrated Team andco-ordinator methods thatlimittheuseof Protection” research group (UMR approaches suchasvarietal Ever-increasing consumer [email protected] resistance todiseasesand goM CiradandINRA. Agro.M, a:+33(0)467545977 fax: environment meanthat should beparalleled by decision-making aids. It iscrucialtodevelop preservation ofthe development of yielding approaches andtoolsthat research onsuitablemodelsare and atthepopulationlevel.Basic oftheunderlyingmechanisms terms of plant-parasite interactions in We aimtoenhanceunderstanding combinations ofbiocontrol methods. management approaches to research group isdevelopingnovel T .L otge,©INRA J.-L. Notteghem,© (center row) and resistant variety ietil witha rice trial, evaluation ina Blast damage varieties (side susceptible Integrated Control (BGPI) Plant-Parasite Interactions for he Biology andGeneticsof rows) through improved integrated pest otc:Dde hreu thar DidierTharreau, Contact: mechanisms ofrice. being usedtoidentifyandclonegenesinvolved inthedefence Genomicsisnow of aresistance geneiscurrently underway. cloning andothersare now beingstudied.The has beencloned, oneoftheavirulence genes Scientific Research) research group, collaboration withan Aventis-CNRS (NationalCentre for Ina resistance andvirulencegeneshave beenmapped. New The mechanismsofinteractionhave alsobeenstudied. Asia. populationsof Chineseandfertile European, worldwide, levels: work hasbeen conducted atdifferenttheir evolution.This and isusedinstudiesof large collectionofisolateshasbeenassembled research teams.A Rice blastcausedby Rice blastisaresearch modelfor numerous international prohibitive for mostricegrowers. andthecostoffungicidesis quickly overcome by thepathogen, in Latin resistance ofanew variety isingeneral America.The particularly andgreatly limitsproduction, fungal diseaseofrice, a researchmodel a grisea Rice- The Magnaporthe grisea Magnaporthe population fluctuations. - mathematicalmodellingof - - allow progress in: genetics ofinteractions, population genetics, .grisea M. pathosystem as pathosystem Magnaporthe r [email protected] population structures and is themostimportant ••• 29 Agropolis - May 2001 30 Agropolis - May 2001 Red leafmottle induced bythe Peanut Clump in sugarcane Virus (PCV) Virus

P. Baudin, © Cirad-CA Our group is pursuing three lines Narrow-leaved ragwort- of research: rust interactions to • In studying the mechanisms of 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 This species is sensitive to a rust fungus from Australia, (see page 16). Puccinia lagenophorae, which reached France some thirty years ago.We are studying the • The study of the factors of viral 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 Jacques Maillet, © Agro.M diversity of viral populations, host could be used as a biocontrol agent.This resistance, geographical project strengthens ongoing collaborations of the BGPI Damage caused fragmentation of cultivated regions, research group with associate members of Agropolis and by Puccinia insect control methods. This work is being done in close collaboration with local laboratories of Australian (CSIRO1) and American lagenephorae with farmers and technical institutes (EBCL-USDA-ARS2) organizations specialized in biocontrol (rust) on narrow-leaved specializing in this field. (1) CSIRO: Commonwealth Scientific and Industrial Research Organization (2) EBCL: European Biological Control Laboratory - USDA-ARS: United States Department of Agriculture - ragwort Agricultural Research Services • The study of the population Contact: Jacques Maillet,Agro-Montpellier, genetics of phytoparasitic fungi, [email protected] bacteria and nematodes, and of 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 microorganisms that attack cultures of banana, sugar cane, cacao, Applications of the research projects vegetable crops, palm trees including coconut palms. New detection include diagnosis of plant diseases 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 new pathogens.Through these studies we hope to limit vector transmission of viral develop diagnostic kits for onsite use by our infection. partners.

(1) VIC-INIBAP:Virus Indexing Center of the International Network for the Improvement M. Chatenet, © Cirad-CA of Banana and Plantain Contact : Michel Peterschmitt,Cirad, Peanut Clump [email protected] Virus (PCV) infecting sugar cane Agropolis - May 2001 - May Agropolis 31 Dissemination of innovations From research to applications

Improved seeds and plants are Facilitating the then doubled to restore fertility. For the traditional and most creation of new instance, a cross between such pure favoured way of transferring lines is currently used to produce genetic advances to producers. varieties hybrids of tropical or temperate rice. Plant biotechnologies have The creation of a new variety is • Somatic fusions and hybridizations greatly accelerated and time-consuming and costly. The exchange of genetic material enhanced this transfer.The Numerous techniques now improve between different varieties during the performance of traditional reproduction is an important source research groups of the methods, and some of these are of variability, but some species Languedoc-Roussillon region presented below. hybridize poorly and are therefore participate actively in the difficult to improve by classical • Haploid methods methods. Somatic fusions and development of these new The use of pure lines is often hybridizations enable mixing in the technologies. They have necessary when the goal of the laboratory of the genetic and fine-tuned methods and breeding programmes is to create cytoplasmic structures of plants by hybrids. Traditional methods need fusing protoplasts, thereby increasing processes that are available eight to ten years, whereas haploid the genetic diversity of certain from Agropolis, and some of methods (haploid-diploidization) species. At Agropolis, this technique these have been transferred to rapidly yield hybrid varieties by is used with citrus fruits. generating pure lines in a single the private sector and the generation. Plants with only half of • Marker-assisted selection countries of the South. the genetic make-up are produced by To ensure that a cultivated hybrid has 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 coffee vitroclone mixtures of mineral salts, sugars, Contact: Marc Berthouly, Cirad, [email protected], 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 Agropolis - May 2001 - May Agropolis 32 Vitropic: a laboratory for production of vitroplants of tropical species in Languedoc-Roussillon interest, difficult and often Vitropic S.A., a subsidiary of Cirad, is 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 during crossing and selection by in vitro culture). It was set up in through their association with Matthieu, ©Yvan S.A. Vitropic 1986 and now has an annual turnover 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 characteristics, and is now increasingly West Indies and Africa.Vitropic is a used for quantitative traits, which are leader in these foreign markets and 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 difficult by natural means, but it is biotechnology improves now possible to transfer the gene production controlling the relevant characteristic The production of vitroplants does 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 are much debated in Europe, yet at Use of banana this early stage much remains to be vitroclones in test tubes.The miniature banana plantlets produced under discovered. Among the varieties increases the protected laboratory conditions are disease-free and are selected, increasing use is made of production with shipped from Montpellier to the production zones.Their transfer of a valuable trait to a plant less pesticides 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, [email protected] Agropolis - May 2001 - May Agropolis 33 Multiplying the most interesting palm tree in large numbers to fix useful agronomical characteristics fruits andrice.fruits technique hasbeenusedwith citrus cultivated and thussaved. This stage, soonafterfertilization, canberescuedEmbryos atanearly between "incompatible"species. from thefirstcellsofacrosshybrids rescue allows theproduction of improve cultivated varieties. Embryo stage. Yet this type ofcross would does notdevelopbeyond acertain resulting isoftenunviableor embryo may sometimesbecrossed, butthe Similar butpoorlycompatiblespecies • including: Other techniquesare beingimproved, microcutting andmicrografting. and widespread techniquein mediumisalongstanding nutrient In vitro culture ofplantsinasterile techniques Multiplication led xed by meansofcontrol- useful agronomic traitscanonly befi themost Becauseofthis, selected seedsavailable togrowers. lead tosubstantialheterogeneity intheplantsgrown from reproduction andthetimeneededfor geneticimprovement modeof cross-pollination andseed-only propagation.The grafts)donotexistfor thisplantwithitsobligate shoots, Conventional techniquesofvegetative propagation (cuttings, itaccountsfor 20%ofworld oilseedproduction. tons, 20millions anannual outputofca. intertropical zone.With The oilpalmisthemajorsource ofvegetable fatinthehumid palm oil of producetruecopies vitrocultureto In Yves Duval, © IRD Embryo rescueEmbryo artificial vegetativeartificial propagation techniques usingcellbiology plant thatgavetheexplants. It canbe genetically identicaltothemother yields alarge numberofplantlets ofvegetativepropagation This form • palm, coconutpalm...).Despite naturally propagate vegetatively(oil useful whentheplantdoesnot in transgenic systems. It isespecially multiplication rates. It isalso usable technique asitallows enormous leaf orstem. This isahighlypromising copies ofaplantfrom afragment of used toreproduce millionsofidentical which wasdesignedtoimprove the which facilitatesinvitro culture RITA (seepage32" teams atAgropolis. Anexampleis invented oradaptedby theresearch techniques isneeded,andhasbeen new equipmentforallthese Appropriate andofficiallyapproved procedure atMontpellier. plantlets havebeenproduced by this trees, cottonplantsandbanana of thousandspalmtrees, hevea technicaldifficulties,certain hundreds Somatic embryogenesis ia anapparatus Rita, ftems aubepat.Large-scalemultiplication and of themostvaluableplants. ensuring large-scaleproduction oftruecopiesreproduction UMR BDPPC(seepage 22) otc:vsDvl ia-R,yv Cirad-IRD, Contact:Yves Duval, Montpellier Génopole(seepage16). notably throughtechniques available the at Agropolis, usingmolecularapproaches basedoncutting-edge Malaysia, depth intandemwithresearch teams from Great Britainand known assomaclonal variationandisnow beingstudiedin phenomenonis resulting from regeneration.This or variants, off-types approach.We have alsonotedtheexistenceofsterile, thusunderscoringthevalueofthis a 20to30%yieldincrease, leadingto andvariouscloneshave beenidentified, been planted, hundred thousandoilpalmplantletsregenerated invitro have Several Indonesia) for pilottesting. Malaysia, (Côte d’Ivoire, and have beentransferred tothemainproducing countries since theearly 1980s incollaborationbetween IRDandCirad, regeneration have usingsomaticembryogenesis beendeveloped "), [email protected] Cirad, JacquesMeunier, Co-ordinator: range ofpotentialapplications. vitro cultures, whichhaveawide this area, regarding particularly in possess considerable know-how in Agropolis memberinstitutions andAsia. been builtinAfrica culture rooms, several ofwhichhave as confinementgreenhouses and medium-sized localcompanies, such collaboration withsmall-and equipment hasbeendevelopedin growth ofinvitro cultures. Other [email protected] d.fr , 35 Agropolis - May 2001 36 Agropolis - May 2001 Education andtraining Bac +5 Bac +5 Bac +4 Bac +3 à 8 Level professionally postgraduate graduate graduate graduate Doctoral oriented degrees Under- studies Post- Post- nvriiso otele Iado epga,aswellAgro of Universities ofMontpellier IIandofPerpignan, otele Ar.) offernumerous coursesinplantgenomics, Montpellier (Agro.M), Agropolis isoneofthemajorFrench andEuropean training pole Doctorat (bac+8) DEA (bac+5) modules ereCourses Degree Special DESS DAA MSc BSc narclue giuiesadrrldvlpet The agribusinessandrural development. in agriculture, The impactofbiotechnologies advanced plantbiotechnology Regulating agriculture: example Plant production engineering: Cell biologyandappliedplant genetic diversityoforganisms of integrated pestmanagement Conservation ofbiodiversity: Conservation at Agropolis Cell biologyandphysiology: Plant geneticresources and on theseedandbreeding Applied plantphysiology Genetics, genomicsand biological interactions Evolution andecology Plant development INA-PG: seeds andplants and adaptation physiology Agro.M: Biology: sectors INH: NationalAgronomic Institute –ParisGrignon genetic resources andbiotechnology. DEUG: DESS: NationalInstitute ofHorticulture (Angers) NationalAgronomy School atMontpellier Degree of General UniversityStudies Degree of Specialized Higher Studies DAA: Degree UM II: UM II/Agro.M UM II/Agro.M Agro.M /INH UM II/UP Degree in Advanced Agr DEA: nttt Director Institute INA-PG / Agro.M Agro.M Agro.M Agro.M Abbreviations UP: MI Yves Sauvaires UM II UM II UM II University ofMontpellier II Degree of Higher Studies University ofPerpignan courses Dominique This Claude Grignon J.-L. Notteghem Isabelle Oliviéri Michel Delseny Jacques Maillet Francine Casse André Charrier André Charrier Michel Lebrun Michel Lebrun Bernard Delay Notteghem Jean-Loup onomy higher-education system The evolving French ESDEA DESS Frenchsystem Maîtrise Licence DEUG Doctorat acluétEndofhighschool Baccalauréat Bac+1 years +8 years +7 years +6 years +5 years +4 years +3 years +2 years li ia,©IRD-Cirad-CP Alain Rival,© International system International MSc PhD BSc Training at Montpellier in molecular biology ietr hlpeJure,[email protected] PhilippeJoudrier, Director: campus. Site:Agro.M higher-education training. open tostudentswiththebaccalaureate plustwo years of education. professionally orienteddegree canbefollowed incontinuing Please notethat http://www.agropolis.fr/formation/servicesfc.html seeourwebsite: informationFor onpersonalizedtraining, further in oroutsideMontpellier. thesecourseswilltake place Depending ondemandandcontent, andsoforth. training of trainers, on-fieldtraining, work, laboratory suchasseminars, collective andindividualrequirements, Agropolis canorganizespecificeducationalevents tailored to Continuing Customized training " Introduction tomolecularbiology " research doctoral oriented studies. or professionally oriented curriculum, term students havetochoosebetween ashort level) andDoctorat (PhD level).Postgraduate degrees: Licence(BSclevel),Master (MSc European area; itemphasizes onthree main teachingandtrainingharmonize withinthe system beguninlate1998isintendedto The reform oftheFrench higher education modules from doctoralstudiesand education one-week course , 37 Agropolis - May 2001 38 Agropolis - May 2001 - DEA"Evolution andEcology". - DEA"Development and Adaptation ofPlants" - DEA"PlantGeneticResources and BiologicalInteractions" genomicsandgeneticresources: plant biotechnologies, Three doctoralcoursesare more specifically orientedtowards IRDatMontpellier). INRA, CNRS, research institutes(Cirad, researchsome thirty groups inuniversities (UMII/ Agro.M) and PhDstudentswork in are almost200PhDstudentsinall.The andthere Some 60graduatesbeginthePhDcourseevery year, withanannual intake of75-80students. leading toaDEAdegree, The GraduateSchool offers“Integrative seven Biology” courses systems andprocesses. applied tobiological • Mathematicsandinformation technology the bioticandabioticenvironment. • Physiology andecophysiology ofrelations between plantsand changes. global communities andecosystems; ofpopulations, • Ecology • Host-parasiteinteractionsandsymbiotichosts. functionalgenomics. function andregulation, gene structure andorganizationofthegenome, • Genomics: geneticresources. mechanismsof evolution, • Biodiversity, school'ssixscientificprioritiesare:biotechnology.The sustainable development andagriculture andtheprogress in protection oftheenvironment, ofbiodiversity, to conservation withaview processes andtheinteractionsofbiologicalsystems, Montpellier IIfocuses ontheintegrationinbiological The GraduateSchool attheUniversity“Integrative of Biology” training andpreparing themfor theirprofessional career. have thetwofold purposeofimproving thestudents'scientific modules for modules the three years ofthesispreparation.These scientificconferences andtraining training involving seminars, year oftheDEA(baccalauréat+5)andcontinues withadditional coursebeginsinthe courses thatleadtothePhDdegree.This The GraduateSchool(GS)embracesalllecture andpractical "IntegrativeBiology" Graduateschool - Continuing education and services toforeign- Continuing students educationandservices - personaltutoring. - additional required coursesdefinedwiththetrainingadvisor, training, - laboratory - French courses, periodmay anintroductory comprise: the coursechosen, Dependingon for foreignpersonalized setofservices students. alsooffers a specializedcourses,Agropolis For certain activities… cultural publictransport, - campusfacilitiesandrestaurants, - applying for housingbenefit, - findingaccommodation, - how toobtaina resident orstudentpermit, and traineeson: Agropolis provides information andguidancefor foreign students traineesand students foreignWelcoming A,ie atotalof135studentsonvariouspostgraduatecourses. i.e. DAA, 15 15DESS, 30DEA, 75PhDstudents, - Studentpopulation: 20-25peryear. and geneticresources: genomics - Numberofthesiscompletedinplantbiotechnologies, figures…Some Training inavinecollection(Agro.M) and trainees: - DEAandGraduateSchool “Integrative Biology”: nr hrirAr.,achar André Charrier,Agro.M, a:+33(0)467047599 fax: agr http://www a:+33(0)467045415 fax: opolis@agr Contact .agr opolis.fr opolis.fr [email protected] heading"training", , , .L ory,©Agro.M J.-L. Porreye,© This 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 Place Eugène Bataillon pour le développement 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 imprimerie AGROPOLIS 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 : [email protected] http://www.agropolis.fr