Abiotic Stress-Responsive miRNA and Transcription Factor-Mediated Gene Regulatory Network in Oryza sativa: Construction and Structural Measure Study.

Rinku Sharma,Shashankaditya Upadhyay,Sudeepto Bhattacharya,Ashutosh Singh

doi:10.3389/fgene.2021.618089

Rinku Sharma, Shashankaditya Upadhyay + Show 2 more

Open Access

https://doi.org/10.3389/fgene.2021.618089

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Abstract

Climate changes and environmental stresses have a consequential association with crop plant growth and yield, meaning it is necessary to cultivate crops that have tolerance toward the changing climate and environmental disturbances such as water stress, temperature fluctuation, and salt toxicity. Recent studies have shown that trans-acting regulatory elements, including microRNAs (miRNAs) and transcription factors (TFs), are emerging as promising tools for engineering naive improved crop varieties with tolerance for multiple environmental stresses and enhanced quality as well as yield. However, the interwoven complex regulatory function of TFs and miRNAs at transcriptional and post-transcriptional levels is unexplored in Oryza sativa. To this end, we have constructed a multiple abiotic stress responsive TF-miRNA-gene regulatory network for O. sativa using a transcriptome and degradome sequencing data meta-analysis approach. The theoretical network approach has shown the networks to be dense, scale-free, and small-world, which makes the network stable. They are also invariant to scale change where an efficient, quick transmission of biological signals occurs within the network on extrinsic hindrance. The analysis also deciphered the existence of communities (cluster of TF, miRNA, and genes) working together to help plants in acclimatizing to multiple stresses. It highlighted that genes, TFs, and miRNAs shared by multiple stress conditions that work as hubs or bottlenecks for signal propagation, for example, during the interaction between stress-responsive genes (TFs/miRNAs/other genes) and genes involved in floral development pathways under multiple environmental stresses. This study further highlights how the fine-tuning feedback mechanism works for balancing stress tolerance and how timely flowering enable crops to survive in adverse conditions. This study developed the abiotic stress-responsive regulatory network, APRegNet database (http://lms.snu.edu.in/APRegNet), which may help researchers studying the roles of miRNAs and TFs. Furthermore, it advances current understanding of multiple abiotic stress tolerance mechanisms.

Highlights

Abiotic stresses such as drought, cold, and salt can reduce the productivity and yield of plants with a direct adverse impact on global food security (Myers et al, 2017)
We developed a comprehensive database, APRegNet database,1 whose construction is discussed for abiotic responsive gene regulatory networks at both transcriptional and post-transcriptional level for A. thaliana, 1http://lms.snu.edu.in/APRegNet
MiRNAs and transcription factors were woven into a complex inter-regulatory network within the cell liable for reprogramming gene expression in response to abiotic stresses in O. sativa deciphered through transcriptome meta-analysis

Summary

Introduction

Abiotic stresses such as drought, cold, and salt can reduce the productivity and yield of plants with a direct adverse impact on global food security (Myers et al, 2017). Researchers have estimated that around 1% of enhancement per annum in the O. sativa yield is required to fulfill increasing population demands (Normile, 2008). The literature on this subject includes several studies on rice, examining ways to enhance its nutritional quality and tolerance toward many diseases (Grover and Minhas, 2000). Increasing the yield of rice to meet this increasing demand is one of the most challenging aspects of this research, as various abiotic stresses adversely affect production (Mantri et al, 2012)

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