Montpellier Scientific Community



Plant development and genetic improvement (DAP)

Director: Emmanuel Guiderdoni
Deputy-directors:
Frédéric de Lamotte (lamotte@supagro.inra.fr)

Research area
The JRU Plant Development and Genetic Improvement (DAP) focuses on the study, management and use of the agro-biodiversity of Mediterranean and tropical crops to identify superior combination of alleles of genes of agronomic interest for delivery in plant breeding schemes. Using quantitative and molecular genetics and genomic technologies, DAP investigates the genetic and molecular control of major agronomical traits (resistance to important diseases and product quality). We participate in the deciphering of the genetic and molecular mechanisms of vegetative development of major plants and their adaptation to abiotic stresses (drought, salinity, oxidative stress, cutting, tapping...) aiming at a continuum from gene to organ, thanks to cutting edge functional analysis, cell imaging and modelling approaches. The integration of genetic and molecular data in a range of dicotyledonous (Apple tree, Olive tree, Cocoa, Coffee, Rubber tree, Cotton, Groundnut) and monocotyledonous (Coconut, oil palm, banana, sugarcane, sorghum, bread wheat and rice) crops, that can be polyploids derived from interspecific hybridizations, allows to study the incidence of evolutive, adaptive and domestication processes on genome diversity in a scale ranging from the structural rearrangements to sequence variation in alleles subjected to these pressures.
Research highlights
Our unit has been a pioneer in the construction of the very first molecular maps in tropical crops namely banana, cocoa, sugarcane, oil palm, coconut, rubber tree and has contributed to major advances in those of cotton, coffee and sorghum. A large effort of construction of the first BAC libraries in these crops has also been accomplished. Structural genomics of the polyploids banana and sugarcane, using molecular cytogenetics, have allowed to a better understanding of recombinations and translocations occurring in these complex genomes. Comparative genomics in the andropogonae has allowed an early establishment of synteny relationships between sorghum and sugarcane by our teams. These resources are being used for mapping resistance to major diseases and quality traits while candidate genes are being pinpointed through mapping of large cDNA resources constructed in our unit. We have largely contributed to the understanding of the structuration of the diversity in target crops of the generation challenge program (GCP) conducting to the constitution of core collections that are precious resources for linking nucleotide variation to phenotypic variation. This association genetics allows to capture genes involved in major trait variation. We are also major stakeholder in international genomics consortia that are conducting the sequencing and functional analysis of the genome of the main tropical crops. In the field of functional genomics, our unit has contributed major resources such as rice insertion line libraries, and information systems and comparative genomics tools linking molecular genetics to gene function across species. We have participated in the understanding of the role small proteins involved in wheat grain quality notably using structural biology, and in the deciphering of the genetic and molecular control of stress tolerance in rubber and of adaptive development of roots in rice. The virtual plants group has an internationally recognized expertise in the modelling of meristem function and of the elaboration of plant shape such as the branched apple tree canopy. Last but not least, DAP hosts genotyping, cell imaging, bioinformatics , rice functional genomics and modelling platforms which are well recognized in the international community.

Staff profile
Total permanent staff Total Scientists Scientists with "HDR"[1] Post-doc fellows PhD
117
70
15
5
16
[1] French university degree for confirmed thesis supervisor
Research teams
Thematic field "Genetics and breeding"
  • Structure of genetic resources
  • Structure and evolution of genomes
  • Genome and breeding
  • Data integration for comparative genomics
  • Adaptive development of rice
  • Development of wheat grain
  • Architecture and functioning of fruit species
  • Cell biology of response to abiotic and biotic stress in tropical perennial species
  • Virtual Plants
Platforms and other tools
  • Plant histology and Cell Imaging platform (PHIV)
  • Genotyping and robotics
  • Bioinformatics
  • Functional genomics
  • OpenALEA software platform
Most important international partnerships
Univ. of Calgary (Canada), UC Davis, TIGR, (USA) HortResearch (New-Zealand), ACPFG, U. Queensland, BSES CSIRO (Australia), VARTC (Vanuatu), Bologna U, Milano U, (Italy) Leiden University, (Netherlands) U. Nottingham, U. Aberdeen, John Innes Centre, Rothamsted Research (UK), CSIC-IRTA Barcelona, IVIA Valencia, (Spain) MPIPMP Gölm (Germany) SwissProt (Switzerland) IRIEC, IOPRI (Indonesia), Kasetsart U, Prince of Songkla U., Rubber Research Institute of Thailand ; (Thailand) HZAU, BRI (China), Institut de Génétique Agronomique, Institut Polytechnique de Hanoi, (Vietnam), MPOB (Malaysia), CBS, Sfax, (Tunisia), U. Bel Abes (Algeria, IRAD (Cameroon), SASRI (South Africa), EMBRAPA Cenargen, IAPAR, INCAPER, UEL, UESC, UNESP-FCAV , UNICAMP ,UESC ,CEPLAC (Brazil), CRU (Trinidad)
Facts and figures
Publications in international ranking journals
2008: 83
2007: 69
2006: 64
2005: 72
Representative publications
Droc, G, Ruiz, M, Larmande, P, Pereira, A, Piffanelli, P, Morel, JB, Dievart, A, Courtois, B, Guiderdoni, E, Périn, C, (2006) OryGenesDB: a database for rice reverse genetics. Nucleic Acids Res, Jan-1, D736-40

Barbier de Reuille, P.; Bohn-Courseau, I.; Ljung, K.; Morin, H.; Carraro, N.; Godin, C., Traas, J. (2006) Computer simulations reveal properties of the cell-cell signaling network at the shoot apex in Arabidopsis. Proc Natl Acad Sci U S A, 2006, 103, 1627-1632

Boutrot F, Chantret N, Gautier MF. (2008) Genome-wide analysis of the rice and Arabidopsis non-specific lipid transfer protein (nsLtp) gene family and identification of wheat nsLtp genes by EST data mining. BMC Genomics 9: 86 (DOI:10.1186/1471-2164-9-86)).

de Alencar Figueiredo L.F., Calatayud C., Dupuits C., Billot C., Rami J.F., Brunel D., Perrier X., Courtois B, Deu M.,. Glaszmann (2008) Phylogeographic Evidence of Crop Neo-Diversity in Sorghum. Genetics (in press)

Marcano M, Pugh T, Cros E, Morales S, Portillo Páez E, Courtois B, Glaszmann J, Engels M, Phillips W, Astorga C, Risterucci AM, Fouet O, González V, Rosenberg K, Vallat I, Dagert M and C Lanaud (2007) Adding value to cocoa Theobroma cacao L germplasm information with domestication history and admixture mapping. Theor Appl Gen 114: 877-884.

Blanc G, Baptiste C, Oliver G, Martin F, Montoro P. (2006) Efficient Agrobacterium tumefaciens-mediated transformation of embryogenic calli and regeneration of Hevea brasiliensis Müll Arg. plants. Plant Cell Rep. 2006 Jan;24(12):724-33.

Jannoo N, Grivet L, Chantret N, Garsmeur O, Glaszmann JC, Arruda P, D'Hont A (2007) Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome. Plant J.,50(4):574-85.

Piffanelli P., Droc G., Mieulet D., Lanau N., Bès M., Bourgeois E., Rouvière C., Gavory F., Cruaud C., Ghesquière A., Guiderdoni E. (2007). Large-scale characterization of Tos17 insertion sites in a rice T-DNA mutant library. Plant Molecular Biology 65(5) 587-601

Segura, V., Cilas C., Costes E. 2008. Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: mixed linear modelling of repeated spatial and temporal measures. New Phytologist 178(2): 302-314.

Massonnet C, Regnard JL, Lauri PÉ, Costes E, Sinoquet H. 2008. Contributions of foliage distribution and leaf functions to light interception, transpiration and photosynthetic capacities in two apple cultivars at branch and tree scales. Tree Physiology 28: 665-678.

Verdeil JL, Alemanno L, Niemenak N, Tranbarger TJ. 2007. Pluripotent versus totipotent plant stem cells: dependence versus autonomy? Trends Plant Sci. June 2007, 12(6):245-52.
Total Annual Budget
2007 2008
Total annual budget (k€- including salaries for Cirad) 8 624 8 768
External contracts (k€): 2 109 2 221
ANR 454 928
EU 77 86
Private sector 502 349
Others 636 GCP, 170 USDA Rest MAE , Expertises
 426 GC P, 113 USDA Rest MAE, Expertises, 194 Agropolis Fondation