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Open Access Research article

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

Yoan Coudert1, Martine Bès2, Thi Van Anh Le34, Martial Pré3, Emmanuel Guiderdoni2 and Pascal Gantet1345*

Author Affiliations

1 Université Montpellier 2, UMR DAP, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France

2 CIRAD, UMR DAP, Avenue Agropolis TA A-96/03, 34398 Montpellier Cedex 5, France

3 Université Montpellier 2, UMR DIADE, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France

4 University of Sciences and Technology of Hanoi, Department of Biotechnology and Pharmacology, Institute of Agricultural Genetics, Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Ha Noi, Viet Nam

5 IRD, UMR DIADE, Avenue Agropolis, 34398 Montpellier Cedex 5, France

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BMC Genomics 2011, 12:387  doi:10.1186/1471-2164-12-387

Published: 1 August 2011

Abstract

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.