Functional genomics of rice root development

Deciphering the genetic and molecular control of the development 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 constraints. These include i. the detection of QTLs involved in root system development though whole genome or targeted association mapping ii. the investigation of the molecular control of root meristem maintenance and function, tissue specification, and lateral and adventitious (nodal) root formation. Root typology, meristem organization and tissue specification have been investigated 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 (Rebouillat et al, in press). Recent progresses in two photon imaging now permit a non destructive in situ observation throughout the root tissue.in notably visualizing cell walls, nuclei and starch granules without specific staining. A 4D imaging of the rice root is under construction. This tool will allow to precisely analyze cell lineages using GFP-marked Enhancer Trap lines and will permit to study protein trafficking and interactions in specific cell types during root growth. A genome-wide comparison of A. thaliana root development genes through reverse genetics in rice has been undertaken. Using the phylogenomic database GreenPhylDB (http://www.greenphyldb.cirad.fr) 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. Functional analyses of A. thaliana and O. sativa orthologs are underway using a reverse genetics (http://www.orygenesdb.cirad.fr) approach and will give new insight on divergence/conservation on root meristem patterning and maintenance in both species. (Texte intégral