RNA-Seq Transcriptome Analysis of Rice Primary Roots Reveals the Role of Flavonoids in Regulating the Rice Primary Root Growth.

Yu Xu,Junjie Zou,Miaoyun Xu,Hongyan Zheng,Xuefeng Zong,Lei Wang

doi:10.3390/genes10030213

Abstract

Flavonoids play important roles in root development and in its tropic responses, whereas the flavonoids-mediated changes of the global transcription levels during root growth remain unclear. Here, the global transcription changes in quercetin-treated rice primary roots were analyzed. Quercetin treatment significantly induced the inhibition of root growth and the reduction of H2O2 and O2− levels. In addition, the RNA-seq analysis revealed that there are 1243 differentially expressed genes (DEGs) identified in quercetin-treated roots, including 1032 up-regulated and 211 down-regulated genes. A gene ontology (GO) enrichment analysis showed that the enriched GO terms are mainly associated with the cell wall organization, response to oxidative stress, and response to hormone stimulus. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway analysis showed that the enriched DEGs are involved in phenylpropanoid biosynthesis, glutathione metabolism, and plant hormone signal transduction. Moreover, the quercetin treatment led to an increase of the antioxidant enzyme activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) in rice roots. Also, the quercetin treatment altered the DR5:GUS expression pattern in the root tips. All of these data indicated that the flavonoids-mediated transcription changes of genes are related to the genes involved in cell wall remodeling, redox homeostasis, and auxin signaling, leading to a reduced cell division in the meristem zone and cell elongation in the elongation zone of roots.

Highlights

Flavonoids are a large group of secondary metabolites and are widely distributed throughout plants
The genes for “response to hormone stimulus (GO:0009725)” contain Os11g0137000 (OsPIN1B), Os06g0166500 (OsIAA20), and Os05g0500900 (OsGH3-4), which are involved in the auxin transport and signaling (Table S5). These results indicate that quercetin functions in the root growth, mainly through regulating the transcription levels of the genes involved in cell wall remodeling, redox homeostasis, and auxin signaling
The quantitative real-time PCR (qRT-PCR) results showed that the transcription levels of down-regulated by by quercetin treatment, consistent with the RNA Sequencing (RNA-seq) results levels of these thesegenes geneswere were down-regulated quercetin treatment, consistent with the RNA-seq. These results indicated that quercetin mediates the gene expression levels involved in results (Figure 6A). These results indicated that quercetin mediates the gene expression levels regulating the auxin metabolism, auxin transport, and auxin signal transduction

Summary

Introduction

Flavonoids are a large group of secondary metabolites and are widely distributed throughout plants. The flavonoids are synthesized through the phenylpropanoid pathway, and can be classified into six major subgroups, including chalcones, flavonols, flavones, flavandiols, anthocyanines, and proanthocyanins, or condensed tannins [1,2]. In Arabidopsis, the flavonoid biosynthesis is directly regulated by several key enzymes, and is finely controlled by multiple transcription factors [3,4]. Flavonoids are considered as effective compounds involved in protecting plants against UV-B radiation [5], and as antioxidants to reduce the reactive oxygen species (ROS) levels in plants [6]. Flavonoids function as important regulators in different biological processes, including defense against pathogen infection, nodulation, pollen fertility, and stomatal. The abundance of flavonoids can be rapidly and profoundly regulated in response to environmental stimulus, growth, and developmental signals

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Results

Conclusion