Genomic and Transcriptomic Analysis Provide Insights Into Root Rot Resistance in <i>Panax notoginseng</i>

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Abstract

Panax notoginseng ( Panax notoginseng (Burk.) F.H. Chen), a plant of high medicinal value, is severely affected by root rot during cultivation. Here, we generated a reference genome of P. notoginseng, with a contig N50 size of 241.268 kb, and identified 66 disease-resistance genes (R-genes) as candidate genes for breeding disease-resistant varieties. We then investigated the molecular mechanism underlying the responses of resistant and susceptible P. notoginseng genotypes to Fusarium oxysporum infection at six time points by RNA-seq. Functional analysis of the genes differentially expressed between the two genotypes indicated that genes involved in the defense response biological process like hormone transduction and plant-pathogen interaction are continuously and highly expressed in resistant genotype during infection. Moreover, salicylic acid and jasmonic acid levels gradually increased during infection in the resistant genotype. Coexpression analysis showed that PnWRKY22 acts as a hub gene in the defense response of the resistant genotype. Finally, transiently overexpressing PnWRKY22 increased salicylic acid levels in P. notoginseng leaves. Our findings provide a theoretical basis for studying root rot resistance in P. notoginseng.

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Most cited references 46

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Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

Kenneth Livak, Thomas D. Schmittgen (2001)

The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).

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Effector-triggered immunity: from pathogen perception to robust defense.

Haitao Cui, Kenichi Tsuda, Jane Parker (2015)

In plant innate immunity, individual cells have the capacity to sense and respond to pathogen attack. Intracellular recognition mechanisms have evolved to intercept perturbations by pathogen virulence factors (effectors) early in host infection and convert it to rapid defense. One key to resistance success is a polymorphic family of intracellular nucleotide-binding/leucine-rich-repeat (NLR) receptors that detect effector interference in different parts of the cell. Effector-activated NLRs connect, in various ways, to a conserved basal resistance network in order to transcriptionally boost defense programs. Effector-triggered immunity displays remarkable robustness against pathogen disturbance, in part by employing compensatory mechanisms within the defense network. Also, the mobility of some NLRs and coordination of resistance pathways across cell compartments provides flexibility to fine-tune immune outputs. Furthermore, a number of NLRs function close to the nuclear chromatin by balancing actions of defense-repressing and defense-activating transcription factors to program cells dynamically for effective disease resistance.

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WRKY transcription factors in plant responses to stresses.

Jingjing Jiang, Shenghui Ma, Nenghui Ye … (2017)

The WRKY gene family is among the largest families of transcription factors (TFs) in higher plants. By regulating the plant hormone signal transduction pathway, these TFs play critical roles in some plant processes in response to biotic and abiotic stress. Various bodies of research have demonstrated the important biological functions of WRKY TFs in plant response to different kinds of biotic and abiotic stresses and working mechanisms. However, very little summarization has been done to review their research progress. Not just important TFs function in plant response to biotic and abiotic stresses, WRKY also participates in carbohydrate synthesis, senescence, development, and secondary metabolites synthesis. WRKY proteins can bind to W-box (TGACC (A/T)) in the promoter of its target genes and activate or repress the expression of downstream genes to regulate their stress response. Moreover, WRKY proteins can interact with other TFs to regulate plant defensive responses. In the present review, we focus on the structural characteristics of WRKY TFs and the research progress on their functions in plant responses to a variety of stresses.

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Author and article information

Contributors

Yuxin Zhou: URI : http://loop.frontiersin.org/people/952894/overview

Linlin Dong: URI : http://loop.frontiersin.org/people/363151/overview

Shilin Chen: URI : http://loop.frontiersin.org/people/317930/overview

Journal

Journal ID (nlm-ta): Front Plant Sci

Journal ID (iso-abbrev): Front Plant Sci

Journal ID (publisher-id): Front. Plant Sci.

Title: Frontiers in Plant Science

Publisher: Frontiers Media S.A.

ISSN (Electronic): 1664-462X

Publication date (Electronic): 15 December 2021

Publication date Collection: 2021

Volume: 12

Electronic Location Identifier: 775019

Affiliations

[1] ¹Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing, China

[2] ²College of Biological and Pharmaceutical Sciences, China Three Gorges University , Yichang, China

[3] ³Wenshan Miaoxiang Notoginseng Technology, Co., Ltd. , Wenshan, China

[4] ⁴Institute of Sanqi Research, Wenshan University , Wenshan, China

Author notes

Edited by: Youlian Pan, National Research Council Canada (NRC-CNRC), Canada

Reviewed by: Lei Zhang, Second Military Medical University, China; Fangcheng Bi, Guangdong Academy of Agricultural Sciences, China

*Correspondence: Linlin Dong, lldong@ 123456icmm.ac.cn

Shilin Chen, slchen@ 123456icmm.ac.cn

^†These authors have contributed equally to this work and share first authorship

This article was submitted to Plant Pathogen Interactions, a section of the journal Frontiers in Plant Science

Article

DOI: 10.3389/fpls.2021.775019

PMC ID: 8714957

PubMed ID: 34975957

SO-VID: df633733-8673-4af9-abfe-606c2076d605

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

History

Date received : 13 September 2021

Date accepted : 23 November 2021

Page count

Figures: 6, Tables: 1, Equations: 0, References: 46, Pages: 13, Words: 7980

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Genomic and Transcriptomic Analysis Provide Insights Into Root Rot Resistance in Panax notoginseng

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Arabidopsis genomics

Most cited references 46

Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

Effector-triggered immunity: from pathogen perception to robust defense.

WRKY transcription factors in plant responses to stresses.

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