Trancript profiling of crown root less 1 stem base reveals new elements associated with crown root development in rice

Y Coudert , M Bes , Thi van Anh Le (1) , M Pre , E. Guiderdoni (2, 3) , Pascal Gantet (4)

1 LMI RICE
2 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
3 Cirad-BIOS - Département Systèmes Biologiques
4 UMR DIADE - Diversité, adaptation, développement des plantes

Background : In rice, the major part of the post-embryonic root system is made of stem-derived roots namedcrown roots (CR). Among the few characterized rice mutants affected in root development,crown rootless1mutantis unable to initiate crown root primordia. CROWN ROOTLESS1(CRL1) is induced by auxin and encodes an AS2/LOB-domain transcription factor that acts upstream of the gene regulatory network controlling CR development. Results : To identify genes involved in CR development, we compared global gene expression profile in stem basesofcrl1mutant and wild-type (WT) plants. Our analysis revealed that 250 and 236 genes are down- and up-regulated respectively in thecrl1mutant. Auxin inducesCRL1expression and consequently it is expected that auxinalso alters the expression of genes that are early regulated by CRL1. To identify genes under the early control ofCRL1, we monitored the expression kinetics of a selected subset of genes, mainly chosen among those exhibitingdifferential expression, incrl1and WT following exogenous auxin treatment. This analysis revealed that most ofthese genes, mainly related to hormone, water and nutrient, development and homeostasis, were likely notregulated directly by CRL1. We hypothesized that the differential expression for these genes observed in thecrl1mutant is likely a consequence of the absence of CR formation. Otherwise, threeCRL1-dependent auxin-responsivegenes:FSM (FLATENNED SHOOT MERISTEM)/ FAS1 (FASCIATA1), GTE4 (GENERAL TRANSCRIPTION FACTOR GROUP E4)andMAP(MICROTUBULE-ASSOCIATED PROTEIN) were identified.FSM/FAS1andGTE4are known in rice andArabidopsistobe involved in the maintenance of root meristem through chromatin remodelling and cell cycle regulationrespectively. Conclusion : Our data showed that the differential regulation of most genes incrl1versus WT may be an indirectconsequence ofCRL1inactivation resulting from the absence of CR in thecrl1mutant. Nevertheless some genes,FAS1/FSM,GTE4andMAP, requireCRL1to be induced by auxin suggesting that they are likely directly regulated byCRL1. These genes have a function related to polarized cell growth, cell cycle regulation or chromatin remodelling.This suggests that these genes are controlled by CRL1 and involved in CR initiation in rice.

Domaines: Sciences du Vivant [q-bio]

Y Coudert, M Bes, Thi van Anh Le, M Pre, E. Guiderdoni, et al.. Trancript profiling of crown root less 1 stem base reveals new elements associated with crown root development in rice. BMC Genomics, 2011, 12 (e387), ⟨10.1186/1471-2164-12-387⟩. ⟨hal-01324492⟩