Time-series transcript profiling analysis in stem base of rice crown rootless 1 mutant after ectopic expression induction by dexamethasone of the CRL1 gene

Lateral Organ Boundary Domain (LBD) transcription factors are specific of plants and are involved in the control of development. One LBD clade is related to the control of root development (Coudert et al., 2013, Mol. Biol. Evol. 30, 569-572). Belonging to this clade, CROWN ROOTLESS 1 controls the initiation of crown roots in rice (Inukai Plant Cell, 17, 1387-1396, Liu et al., 2005, Plant J., 43, 47-56). The aim of this study was to identify the genes that are regulated by CRL1 in a time-dependant manner after its induction. A total of 1748 differentially expressed genes (DEG) were identified, 1034 of them upregulated, and 706 downregulated, and 14 both upregulated and downregulated at some point during the time series. Data analysis revealed three distinct phases in the time series that can represent three developemntal stage during crown root primordia formation. Affymetrix microarrays were processed in the Microarray Core Facility “Transcriptome“ of the Institute in Regenerative Medicine and Biotherapy, CHU de Montpellier-INSERM-UM Montpellier, http://irmb.chu-montpellier.fr/ . We transformed the crl1 mutant with a construction allowing the control of CRL1 expression by exogenous dexamethasone (DXC line) and with an empty construction as a control (DX line). Transcriptome profiling were conducted in both lines each 3 hours from 0 to 45 hour after dexamethasone addition (hours after induction : hai). After 5 hours dexamethasome was removed by renewing the liquid culture media. 3 independent experiments were carried out (rep1 to rep3)