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Background  In rice, the major part of the post-embryonic root system is made of stem-derived roots named crown roots (CR). Among the few characterized rice mutants affected in root development,  crown rootless1  mutant is 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 bases of  crl1  mutant and wild-type (WT) plants. Our analysis revealed that 250 and 236 genes are down- and up-regulated respectively in the  crl1  mutant. Auxin induces  CRL1  expression and consequently it is expected that auxin also alters the expression of genes that are early regulated by CRL1. To identify genes under the early control of CRL1, we monitored the expression kinetics of a selected subset of genes, mainly chosen among those exhibiting differential expression, in  crl1  and WT following exogenous auxin treatment. This analysis revealed that most of these genes, mainly related to hormone, water and nutrient, development and homeostasis, were likely not regulated directly by CRL1. We hypothesized that the differential expression for these genes observed in the  crl1  mutant is likely a consequence of the absence of CR formation. Otherwise, three  CRL1- dependent auxin-responsive genes:  FSM (FLATENNED SHOOT MERISTEM)/FAS1 (FASCIATA1), GTE4 (GENERAL TRANSCRIPTION FACTOR GROUP E4)  and  MAP  ( MICROTUBULE-ASSOCIATED PROTEIN ) were identified.  FSM/FAS1  and  GTE4  are known in rice and  Arabidopsis  to be involved in the maintenance of root meristem through chromatin remodelling and cell cycle regulation respectively.    Conclusion  Our data showed that the differential regulation of most genes in  crl1  versus WT may be an indirect consequence of  CRL1  inactivation resulting from the absence of CR in the  crl1  mutant. Nevertheless some genes,  FAS1/FSM ,  GTE4  and  MAP , require  CRL1  to be induced by auxin suggesting that they are likely directly regulated by CRL1. 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.

Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice