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

Jérémy Lavarenne,Mikael Lucas,Jean-Luc Verdeil,Hélène Adam,Marie Javelle,Pascal Gantet,Marc Lartaud,Christophe Sallaud,Mathieu Gonin,Laurent Laplaze,Jacques Rouster,Antony Champion,Geneviève Conejéro

doi:10.1371/journal.pone.0238736

Abstract

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 functional genomics approaches. Nevertheless, these approaches are impaired by functional redundancy and mutant lethality. To overcome these limitations, organ targeted transcriptome analysis can help to identify genes involved in crown root formation and early development. In this study, we generated an atlas of genes expressed in developing crown root primordia in comparison with adjacent stem cortical tissue at three different developmental stages before emergence, using laser capture microdissection. We identified 3975 genes differentially expressed in crown root primordia. About 30% of them were expressed at the three developmental stages, whereas 10.5%, 19.5% and 12.8% were specifically expressed at the early, intermediate and late stages, respectively. Sorting them by functional ontology highlighted an active transcriptional switch during the process of crown root primordia formation. Cross-analysis with other rice root development-related datasets revealed genes encoding transcription factors, chromatin remodeling factors, peptide growth factors, and cell wall remodeling enzymes that are likely to play a key role during crown root primordia formation. This atlas constitutes an open primary data resource for further studies on the regulation of crown root initiation and development.

Highlights

Crown roots (CR) are a type of adventitious roots making up most of the root system in rice [1,2]
A progressive shift in transcriptional regulation occurring during crown root formation activates peptide mediated signaling cascades elements and repress specific cell wall metabolism genes
Because of the large proportion of Differentially expressed genes (DEG) encoding transcription factors in our dataset (S3 Fig), we investigated the TF differentially expressed during CR development associated to root development (Table 1)

Summary

Introduction

Crown roots (CR) are a type of adventitious roots making up most of the root system in rice [1,2]. These roots develop post-embryonically from the stem and play an important role in the adaptation of plants to the soil hydro-mineral status [3,4]. Genetics and functional genomics approaches revealed several genes involved in CR development in rice [5,6]. These approaches are impaired by functional redundancies, and by lethality of some mutants.

Methods

Results

Conclusion