Genome-Wide Transcript Profiling Reveals an Auxin-Responsive Transcription Factor, OsAP2/ERF-40, Promoting Rice Adventitious Root Development

Abstract

Unlike dicots, the robust root system in grass species largely originates from stem base during postembryonic development. The mechanisms by which plant hormone signaling pathways control the architecture of adventitious root remain largely unknown. Here, we studied the modulations in global genes activity in developing rice adventitious root by genome-wide RNA sequencing in response to external auxin and cytokinin signaling cues. We further analyzed spatiotemporal regulations of key developmental regulators emerged from our global transcriptome analysis. Interestingly, some of the key cell fate determinants such as homeodomain transcription factor (TF), OsHOX12, no apical meristem protein, OsNAC39, APETALA2/ethylene response factor, OsAP2/ERF-40 and WUSCHEL-related homeobox, OsWOX6.1 and OsWOX6.2, specifically expressed in adventitious root primordia. Functional analysis of one of these regulators, an auxin-induced TF containing AP2/ERF domain, OsAP2/ERF-40, demonstrates its sufficiency to confer the adventitious root fate. The ability to trigger the root developmental program is largely attributed to OsAP2/ERF-40-mediated dose-dependent transcriptional activation of genes that can facilitate generating effective auxin response, and OsERF3–OsWOX11–OsRR2 pathway. Our studies reveal gene regulatory network operating in response to hormone signaling pathways and identify a novel TF regulating adventitious root developmental program, a key agronomically important quantitative trait, upstream of OsERF3–OsWOX11–OsRR2 pathway.

Genome-Wide High Resolution Expression Map and Functions of Key Cell Fate Determinants Reveal the Dynamics of Crown Root Development in Rice

“…Oryza sativa var. IR-64 seed germination, growth, auxin treatment and sample collection were performed as described by Neogy et al, (2019). For LCM, the stem base tissue from 6-day old rice seedling was harvested in Carnoy's fluid (ethanol: chloroform: acetic acid glacial; 6:3:1), infiltrated twice under mild vacuum and dehydrated through graded ethanol series followed by replacement with xylene.…”

“…For generating DR5ev_erYFP transgenic rice lines, the DR5ev_erYFP-nosT (1.4kb) was PCR amplified using the plasmid pHm-DR5ev-erYFP_nosT2 as template (gift from Ari Pekka Mahonen's lab at Helsinki University, Finland) and cloned into pCAMBIA1390 vector. For LBA4404 and used to raise transgenic rice lines as described by Toki et al (2006) and Neogy et al (2019). The constructs for Arabidopsis transformation were cloned using Multisite gateway recombination cloning system (Invitrogen) using pCAMBIA 1300 destination vector.…”

“…Mutation in rice genes regulating auxin distribution and signaling such as CROWN-ROOTLESS4/OsGNOM1 (OsCRL4/OsGNOM1) and PINFORMED1 (OsPIN) display defects in CR development (Kitomi et al 2008, Liu et al 2009. Auxin signaling activates expression of TFs, they, in turn, regulate and integrate the signaling pathway during CR organogenesis , Liu et al 2005, Kitomi et al 2011b, Zhao et al 2009, Coudert et al 2015, Zhang et al, 2018, Lavarenne et al, 2019, Neogy et al, 2019Mao et al, 2020). In this study, we have investigated the global gene network operational during CRP specification and differentiation in rice.…”

Auxin-responsive (phospho)proteome analysis reveals regulation of cell cycle and ethylene signaling during rice crown root development

“…The copyright holder for this preprint this version posted March 31, 2021. ; https://doi.org/10.1101/2021.03.30.437660 doi: bioRxiv preprint 4 also regulate CR development (Inukai et al, 2005;Kitomi et al, 2008Kitomi et al, , 2011Zhao et al, 2009; 2015; Wang et al, 2016;Neogy et al, 2019;Shao et al, 2019;Garg et al, 2020).…”

Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice

“…Comparison between CR, large and fine lateral roots revealed a significant enrichment in transcripts associated with secondary cell wall metabolism, as well as increased levels of transcripts encoding auxin-signaling related genes in CR [11]. Recently, exogenous hormonal treatments and transcriptome analysis of rice stem base allowed the identification of a new gene involved in CR development [12].…”