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

• Main Authors: Van Anh Le Thi, Bès Martine, Coudert Yoan, Pré Martial, Guiderdoni Emmanuel, Gantet Pascal
• Format: Article
• Language: English
• Published: BMC 2011-08-01
• Series: BMC Genomics
• Online Access: http://www.biomedcentral.com/1471-2164/12/387

<p>Abstract</p> <p>Background</p> <p>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, <it>crown rootless1 </it>mutant is unable to initiate crown root primordia. <it>CROWN ROOTLESS1 </it>(<it>CRL1</it>) is induced by auxin and encodes an AS2/LOB-domain transcription factor that acts upstream of the gene regulatory network controlling CR development.</p> <p>Results</p> <p>To identify genes involved in CR development, we compared global gene expression profile in stem bases of <it>crl1 </it>mutant and wild-type (WT) plants. Our analysis revealed that 250 and 236 genes are down- and up-regulated respectively in the <it>crl1 </it>mutant. Auxin induces <it>CRL1 </it>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 <it>crl1 </it>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 <it>crl1 </it>mutant is likely a consequence of the absence of CR formation. Otherwise, three <it>CRL1-</it>dependent auxin-responsive genes: <it>FSM (FLATENNED SHOOT MERISTEM)/FAS1 (FASCIATA1), GTE4 (GENERAL TRANSCRIPTION FACTOR GROUP E4) </it>and <it>MAP </it>(<it>MICROTUBULE-ASSOCIATED PROTEIN</it>) were identified. <it>FSM/FAS1 </it>and <it>GTE4 </it>are known in rice and <it>Arabidopsis </it>to be involved in the maintenance of root meristem through chromatin remodelling and cell cycle regulation respectively.</p> <p>Conclusion</p> <p>Our data showed that the differential regulation of most genes in <it>crl1 </it>versus WT may be an indirect consequence of <it>CRL1 </it>inactivation resulting from the absence of CR in the <it>crl1 </it>mutant. Nevertheless some genes, <it>FAS1/FSM</it>, <it>GTE4 </it>and <it>MAP</it>, require <it>CRL1 </it>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.</p>