Overexpression of OsbHLH044 transcription factor controls a negative regulatory module associated with plant cell death and stress inhibition in rice crown root development

Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by genetics and functional genomics approaches. The CROWN ROOTLESS1 (CRL1) transcription factor is necessary for crown root initiation in rice. The basic helix-loop-helix 044 (OsbHLH044) transcription factor was identified as a CRL1-regulated gene. In this study, we aimed to determine OsbHLH044-regulated genes, with transcriptome analysis of OsbHLH44 overexpressing plants in crl1 mutant background. We analysed the transcriptional profile of overexpressing lines stem bases in comparison with corresponding null segregant sister control lines. 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/ . Stem bases of six days old plantlets were used. The experiment was repeated independently three times with 2 pC5300.OE-OsbHLH044 overexpression lines and with their coresponding null segregant sister lines. For each biological replicate, ten to fifteen stem bases were collected and immediately frozen in liquid nitrogen. After grounding stem bases in liquid nitrogen, RNA were extracted and quantified at 260 nm with a ND-1000 spectrophotometer (Thermo-Fisher, Waltham, MA, USA).