Revealing Shared and Distinct Genes Responding to JA and SA Signaling in Arabidopsis by Meta-Analysis.

Nailou Zhang,Dongyan Yang,Zhijin Fan,Shuang Zhou

doi:10.3389/fpls.2020.00908

Abstract

Plant resistance against biotrophic and necrotrophic pathogens is mediated by mutually synergistic and antagonistic effects of salicylic acid (SA) and jasmonic acid (JA) signals. However, the unique and shared genes responding to the defense mediated by JA/SA signals were largely unclear. To reveal discrete, synergistic and antagonistic JA/SA responsive genes in Arabidopsis thaliana, Meta-Analysis was employed with 257 publicly available Arabidopsis thaliana RNA-Seq gene expression profiles following treatment of mock, JA or SA analogs. JA/SA signalings were found to co-induce broad-spectrum disease-response genes, co-repress the genes related to photosynthesis, auxin, and gibberellin, and reallocate resources of growth toward defense. JA might attenuate SA induced immune response by inhibiting the expression of resistance genes and receptor-like proteins/kinases. Strikingly, co-expression network analysis revealed that JA/SA uniquely regulated genes showing highly coordinated co-expression only in their respective treatment. Using principal component analysis, and hierarchical cluster analysis, JA/SA analogs were segregated into separate entities based on the global differential expression matrix rather than the expression matrix. To accurately classify JA/SA analogs with as few genes as possible, 87 genes, including the SA receptor NPR4, and JA biosynthesis gene AOC1 and JA response biomarkers VSP1/2, were identified by three feature selection algorithms as JA/SA markers. The results were confirmed by independent datasets and provided valuable resources for further functional analyses in JA- or SA- mediated plant defense. These methods would provide cues to build a promising approach for probing the mode of action of potential elicitors.

Highlights

Plants, as sessile organisms, are constantly threatened by a diverse and variable array of pathogens and herbivores occurring simultaneously or sequentially
We wondered if the jasmonic acid (JA)/salicylic acid (SA) functional analogs could be grouped into two classes based on the global gene expression matrix since both phytohormones were traditionally thought to be mutually antagonistic
principal component analysis (PCA) was implemented to explore the data structures using publicly available RNA-Seq gene expression profiles generated from plants treated with JA analogs [coronatine (COR), MeJA], SA analogs (benzo(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH), 2,4-dichloro-6-{(E)-[(3-methoxyphenyl) imino]methyl}phenol (DPMP), 2,6-dichloro-isonicotinic acid (INA), SA), and mock (Supplementary Table S1)

Summary

Introduction

As sessile organisms, are constantly threatened by a diverse and variable array of pathogens and herbivores occurring simultaneously or sequentially. SA is a primary defense hormone, mediating resistance against biotrophic and hemibiotrophic pathogens (feeding on living tissue). Antagonistic and synergistic effects between JA/SA signaling pathways are considered to provide plants with a regulatory potential to survive under their complex biological environments in a resource costeffective manner (Thaler et al, 2012; Coolen et al, 2016). This manner can be realized by shifting defense responses to either the SA- or JA- signaling pathway according to the lifestyle of the particular invading pathogen (Pieterse et al, 2012). Identification of the genes related to the cross-talk of JA/SA signals in plants is of importance to develop plants with an increased disease resistance property (Shigenaga et al, 2017)

Methods

Results

Conclusion