A Meta-Analysis of Comparative Transcriptomic Data Reveals a Set of Key Genes Involved in the Tolerance to Abiotic Stresses in Rice.

Matteo Buti,Elena Baldoni,Elide Formentin,Annamaria Genga,Fiorella Lo Schiavo,Justyna Milc,Enrico Francia,Giovanna Frugis

doi:10.3390/ijms20225662

Abstract

Several environmental factors, such as drought, salinity, and extreme temperatures, negatively affect plant growth and development, which leads to yield losses. The tolerance or sensitivity to abiotic stressors are the expression of a complex machinery involving molecular, biochemical, and physiological mechanisms. Here, a meta-analysis on previously published RNA-Seq data was performed to identify the genes conferring tolerance to chilling, osmotic, and salt stresses, by comparing the transcriptomic changes between tolerant and susceptible rice genotypes. Several genes encoding transcription factors (TFs) were identified, suggesting that abiotic stress tolerance involves upstream regulatory pathways. A gene co-expression network defined the metabolic and signalling pathways with a prominent role in the differentiation between tolerance and susceptibility: (i) the regulation of endogenous abscisic acid (ABA) levels, through the modulation of genes that are related to its biosynthesis/catabolism, (ii) the signalling pathways mediated by ABA and jasmonic acid, (iii) the activity of the “Drought and Salt Tolerance” TF, involved in the negative regulation of stomatal closure, and (iv) the regulation of flavonoid biosynthesis by specific MYB TFs. The identified genes represent putative key players for conferring tolerance to a broad range of abiotic stresses in rice; a fine-tuning of their expression seems to be crucial for rice plants to cope with environmental cues.

Highlights

Environmental stresses are the most critical factors that affect crop growth and development, causing plant damages and injuries that may lead to yield loss [1]
Increased knowledge regarding the molecular mechanisms of adaptation to environmental constraints, which leads to the development of new resilient varieties, still represents the best strategy for coping with the erratic nature of stress caused by global change
The three couples of contrasting genotypes selected for chilling, osmotic, and salt stress experiments were different. This is an advantage for the meta-analysis here presented, since, for each experimental condition, two genotypes that highly differ in their physiological response to stress are available

Summary

Introduction

Environmental stresses are the most critical factors that affect crop growth and development, causing plant damages and injuries that may lead to yield loss [1]. During their life cycle, plants are frequently affected by several stresses that cause general or specific effects on growth and development [2]. When plants are exposed to abiotic constraints, the perception and transduction of stress signals induce the plant to activate stress-related genes, resulting in metabolic and physiological changes that adapt the organism to the new environmental conditions [2,3]. Increased knowledge regarding the molecular mechanisms of adaptation to environmental constraints, which leads to the development of new resilient varieties, still represents the best strategy for coping with the erratic nature of stress caused by global change

Objectives

Methods

Results

Conclusion