Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes.

Zhongyu Wang,Qinghui Yu,Huan Wang,Ning Li

doi:10.3390/ijms222212238

Abstract

Soil salinization is a major environmental stress that causes crop yield reductions worldwide. Therefore, the cultivation of salt-tolerant crops is an effective way to sustain crop yield. Tomatoes are one of the vegetable crops that are moderately sensitive to salt stress. Global market demand for tomatoes is huge and growing. In recent years, the mechanisms of salt tolerance in tomatoes have been extensively investigated; however, the molecular mechanism through which non-coding RNAs (ncRNAs) respond to salt stress is not well understood. In this study, we utilized small RNA sequencing and whole transcriptome sequencing technology to identify salt-responsive microRNAs (miRNAs), messenger RNAs (mRNAs), and circular RNAs (circRNAs) in roots of M82 cultivated tomato and Solanum pennellii (S. pennellii) wild tomato under salt stress. Based on the theory of competitive endogenous RNA (ceRNA), we also established several salt-responsive ceRNA networks. The results showed that circRNAs could act as miRNA sponges in the regulation of target mRNAs of miRNAs, thus participating in the response to salt stress. This study provides insights into the mechanisms of salt tolerance in tomatoes and serves as an effective reference for improving the salt tolerance of salt-sensitive cultivars.

Highlights

We identified saltresponsive miRNAs, messenger RNAs (mRNAs), and circRNAs in cultivated tomato M82 and wild tomato
To identify salt-responsive miRNAs in M82 and S. pennellii, eight small RNA libraries were constructed with two replicates for the roots of cultivated tomato M82 and wild tomato S. pennellii with and without salt treatment
We identified salt-responsive DE-miRNAs, DE-mRNAs, and DE-circRNAs in the roots of cultivated and wild tomatoes under salt treatment and established several putative salt-responsive competitive endogenous RNA (ceRNA) networks based on the potential interaction relationships between RNAs

Summary

Introduction

Salt stress can affect the germination and growth of plants, which leads to the reduction of crop yield [1,2,3,4,5]. Research on salt-tolerant crops has important ecological and economic significance. In the course of evolution, many plants have evolved various salt-tolerance mechanisms to adapt to alkaline soil environments [6]. Plants have evolved a series of mechanisms to protect themselves from the effects of salt stress, such as osmotic adjustment, ion transport, and antioxidants. These mechanisms may be ubiquitous in most plants. Studying the salt-tolerance mechanisms of wild tomatoes is of momentous significance

Methods

Results

Conclusion