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Transcriptome Characterization of Gene Profiling During Early Stage of Nitric Oxide-Induced Adventitious Rooting in Mung Bean Seedlings

  • Shi-Weng LiEmail author
  • Yan Leng
  • Rui-Fang Shi
Article
  • 54 Downloads

Abstract

Nitric oxide (NO) functions as a signaling molecule modulating diverse developmental and physiological processes in plants. NO was recently shown to strongly induce the formation of adventitious roots in plants. A transcriptome analysis was performed using RNA-Seq and qRT-PCR technologies to obtain further insights into the gene expression profile underlying NO-induced adventitious rooting. Sodium nitroprusside (SNP), a widely used NO donor, significantly up-regulated the GO terms and pathways oxidoreductase activity, wounding response, water deprivation response, microtubule-based process, cell cycle, cell wall synthesis, photosynthesis, hydrolase activity at the root induction stage, response to stress, cell wall loosening and biogenesis, ethylene signaling at the root initiation stage. In total, 2582 and 2588 differentially expressed genes (DEGs, fold change ≥ 2) were selected in plants receiving the 6- and 24-h SNP treatments, respectively. The analysis of the most highly differentially expressed genes (RPKM ≥ 10 and fold change ≥ 2) shows that NO significantly regulated the expression of genes involved in nitrogen compound response, stress response, oxidative stress response, cell wall modification, signal transduction, protein processing, secondary metabolism, metabolic processes, and transcription factors (TFs), as well as plant hormone signaling. Notably, the expression of a large number of genes encoding peroxidase (POD) isoforms was significantly differentially regulated by SNP. Furthermore, qRT-PCR results indicated that NO significantly up-regulated the expression of several genes with known functions in pathways such as auxin signaling and stress response, as well as TF genes, at the root induction and initiation stages. The evidence obtained implies that NO up-regulated the expression of genes that are involved in the key cellular processes leading to the root formation.

Keywords

Vigna radiata (L.) R. Wilczek Adventitious roots Nitric oxide (NO) Transcriptome Gene expression 

Abbreviations

ABA

ABSCISIC ACID

ACC

1-Aminocyclopropane-1-carboxylic acid

ACO

1-Aminocyclopropane-1-carboxylic acid oxidase

ACS

1-Aminocyclopropane-1-carboxylic acid synthase

AHK

Arabidopsis histidine kinase

AOX

Alternative oxidase

AP2/ERF

Apetala2/Ethylene response factor

APX

Ascorbate peroxidase

ARF

Auxin response factor

AUX1/LAX

Auxin/IAA

BR

Brassinosteroid

BRI1

Brassinosteroid insensitive 1

BAK1

Brassinosteroid insensitive 1-associated receptor kinase 1-like

bHLH

Basic/helix-loop-helix

bZIP

Basic leucine zipper

CASPL

Casparian strip membrane protein-like

CAT

Catalase

cGMP

Cyclic guanosine monophosphate

CHS

Chalcone synthase

DEGs

Differentially expressed genes

DHAR

DHA reductase

Dof

Dof zinc finger protein

EBF1

EIN3-binding F-box protein 1-like

EIN

Ethylene-insensitive protein

ETO

Ethylene-overproduction protein

GA2/3OX2

Gibberellin 2/3-beta-dioxygenase

GA2/20OX

Gibberellins 2/20 oxidase

GATA

GATA transcription factor

GH

Glycoside hydrolase

GH3

Gretchen hagen 3

GO

Gene ontology

GPX

Glutathione peroxidase

GR

Glutathione reductase

GST

Glutathione S-transferase

HD-Zip

Homeobox-leucine zipper protein

HSPs

Heat shock proteins

HSFs

Heat shock transcription factors

IBA

Indole-3-butyric acid

KAAS

Automatic annotation server

KEGG

Kyoto encyclopedia of genes and genomes

KOG

Clusters of orthologous groups for eukaryotic complete genomes

LBD

Lateral organ boundaries-domain

LEA

Late embryogenesis abundant

LOB

Lateral organ boundaries

LRR

Leucine-rich repeat

MAPK

Mitogen-activated protein kinase

MDAR

Monodehydroascorbate reductase

NAC

NAM, ATAF, and CUC2

NAM

No apical meristem

NO

Nitric oxide

NR

NCBI non-redundant protein

PER

Peroxidase

PIN

PIN-formed

POD

Peroxidase

QORL

Quinone oxidoreductase-like protein

qRT-PCR

Real-time quantitative polymerase chain reaction

RAM

Root apical meristem

RNA-seq

RNA-sequencing

ROS

Reactive oxygen species

RPKM

Reads per kb per million reads

SAM

S-adenosylmethionine

SNP

Sodium nitroprusside

SOD

Superoxide dismutase

TFs

Transcription factors

WRKY

WRKYGQK domain protein

ZF

Zinc finger protein

Notes

Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (31760110 and 31560121).

Author Contributions

LSW conceived and designed the experimental plan, analyzed, and interpreted the sequence data, and drafted the manuscript. LY and SRF performed the experiments and analyzed the sequence data. All authors read and approved the final manuscript.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

344_2019_9993_MOESM1_ESM.pdf (107 kb)
Supplementary material 1 (PDF 107 kb)
344_2019_9993_MOESM2_ESM.xlsx (50 kb)
Supplementary material 2 (XLSX 49 kb). Table S2: Top list of the differentially regulated GOs
344_2019_9993_MOESM3_ESM.xlsx (16 kb)
Supplementary material 3 (XLSX 15 kb). Table S3: Top list of the differentially regulated KOs
344_2019_9993_MOESM4_ESM.xlsx (56 kb)
Supplementary material 4 (XLSX 56 kb). Table S4: List of DEGs in the sample pair NO6 vs. Wat6
344_2019_9993_MOESM5_ESM.xlsx (54 kb)
Supplementary material 5 (XLSX 54 kb). Table S5: List of DEGs in the sample pair NO24 vs. Wat24
344_2019_9993_MOESM6_ESM.xlsx (24 kb)
Supplementary material 6 (XLSX 24 kb). Table S6: List of differentially expressed genes of transcription factors
344_2019_9993_MOESM7_ESM.xlsx (13 kb)
Supplementary material 7 (XLSX 12 kb). Table S7: List of differentially expressed genes associated with plant hormone signaling
344_2019_9993_MOESM8_ESM.pdf (131 kb)
Supplementary material 8 (PDF 130 kb). Table S8: Comparation of DEGs that respond to SNP and IBA

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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.School of Environmental and Municipal Engineering, Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu ProvinceLanzhou Jiaotong UniversityLanzhouPeople’s Republic of China

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