Functional genomics of rice root development

Perin Christophe, Dievart Anne, Gantet Pascal, Conte Matthieu, Lanau Nadège, Guiderdoni Emmanuel. 2007. Functional genomics of rice root development. In : Frontier Research in Model Plant, Taipei, Taiwan, October 11-12, 2007. s.l. : s.n., Résumé, pp. 17-18. Frontier Research in Model Plants, Taipei, Taïwan / (République de Chine (Taïwan)), 11 October 2007/12 October 2007.

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Abstract : Deciphering the genetic and molecular control of the develot of the root system and its adaptive response to the availability of nutrients and water is of primary importance for the sustainable establishment of the rice crop under adverse environments. Rice displays a complex root structure-comprising several root types and a large variation in root architecture that reflects adaptation to cropping systems. Our group is exploring various approaches to investigate the control of constitutive development of roots and its adaptation in response to abiotic stresses. Root typology, meristem organization and tissue specification have been investigated first in comparison to Arabidopsis. Specific anatomical features include radial patterning, variation in number of radial cells, number of cells constituting the quiescent centre and tissues participating in lateral root formation. Recent progresses in bi photon imaging now permit a non destructive in situ observation throughout the root tissue. This allows to precisely analyze cell lineages using GFP-marked Enhancer Trap lines and will permit to study protein trafficking and interactions in specific cell types. Cloning and characterization of architectural genes identified both through QTL analysis and screening of insertion mutants altered in root development is underway. A genome-wide comparison of A. thaliana root development genes through reverse genetics in rice is undertaken. We first developed a comparative database for genome-wide comparison of A. thaliana and O. sativa genic repertoire. GreenPhylDB ( nowadays comprises the most complete list of plant gene families (6,421 families) which have been manually curated. GreenPhylDB also contains all the phylogenomic relations computed for 4,375 families. We extracted rice orthologs for a total of 60 genes involved in root development in A. thaliana. Based on the reference rice root typology and root meristem fate we identified surprisingly several important genes missing in rice. For instance, the PLT genes involved in stem-cell niche establishment in A.thaliana were all missing in rice suggeetinn Pither extensive redtinrlánry in A. thaliana or alternative molecular mechanism for root meristem maintenance in rice. Moreover, several genes involved in root hair pattering in A. thaliana were missing in rice and this feature can be tentatively linked to the absence of root hair radial pattering in rice. By using a thew phylogenomics tool integrated in GreenPhylDB (i-GOST for iterative Greenphyl Ortholog Search Tool) we also identify moss (Physcomitrella patens) orthologs for most of the A. thaliana root hairs genes suggesting that rhizoids in moss and root hairs in angiosperm are truly homologs structures. Functional analyses of A. thaliana and O. sativa orthologs are underway using a reverse genetics ( approach and will give new insight on divergence/conservation on root meristem patterning and maintenance in both species. (Texte intégral)

Mots-clés Agrovoc : Oryza sativa, Arabidopsis thaliana

Classification Agris : F30 - Plant genetics and breeding
F62 - Plant physiology - Growth and development

Auteurs et affiliations

  • Perin Christophe, CIRAD-BIOS-UMR DAP (FRA)
  • Dievart Anne, INRA (FRA) ORCID: 0000-0001-9460-4638
  • Gantet Pascal, UM2 (FRA)
  • Conte Matthieu, CIRAD-BIOS-UMR DAP (FRA)
  • Lanau Nadège, CIRAD-BIOS-UMR DAP (FRA)
  • Guiderdoni Emmanuel, CIRAD-BIOS-UMR DAP (FRA)

Source : Cirad - Agritrop (

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