Mapping the Salt Stress-Induced Changes in the Root miRNome in Pokkali Rice.

Kavita Goswami,Sudhir K Sopory,Budhayash Gautam,Neeti Sanan-Mishra,Deepti Mittal

doi:10.3390/biom10040498

Abstract

A plant’s response to stress conditions is governed by intricately coordinated gene expression. The microRNAs (miRs) have emerged as relatively new players in the genetic network, regulating gene expression at the transcriptional and post-transcriptional level. In this study, we performed comprehensive profiling of miRs in roots of the naturally salt-tolerant Pokkali rice variety to understand their role in regulating plant physiology in the presence of salt. For comparisons, root miR profiles of the salt-sensitive rice variety Pusa Basmati were generated. It was seen that the expression levels of 65 miRs were similar for roots of Pokkali grown in the absence of salt (PKNR) and Pusa Basmati grown in the presence of salt (PBSR). The salt-induced dis-regulations in expression profiles of miRs showed controlled changes in the roots of Pokkali (PKSR) as compared to larger variations seen in the roots of Pusa Basmati. Target analysis of salt-deregulated miRs identified key transcription factors, ion-transporters, and signaling molecules that act to maintain cellular Ca2+ homeostasis and limit ROS production. These miR:mRNA nodes were mapped to the Quantitative trait loci (QTLs) to identify the correlated root traits for understanding their significance in plant physiology. The results obtained indicate that the adaptability of Pokkali to excess salt may be due to the genetic regulation of different cellular components by a variety of miRs.

Highlights

Unfavorable environmental changes exert abiotic stresses on plants, which hamper their development, negatively influence their life span, and cause yield losses [1]
Root tissues were harvested from four sets of 15-day-old seedlings grown in the absence and presence of salt, viz. Pusa Basmati normal root (PBNR), Pokkali normal root (PKNR), Pusa Basmati salt-grown root (PBSR), and Pokkali salt-grown root (PKSR)
The small RNA and transcriptome profiles of PK and PB root tissues grown in the presence and absence of salt were analyzed and it was observed that the miR levels in PK roots are maintained to levels that favor stress tolerance physiology of the plant

Summary

Introduction

Unfavorable environmental changes exert abiotic stresses on plants, which hamper their development, negatively influence their life span, and cause yield losses [1]. Soil salt (mainly NaCl) is an important abiotic stress factor that creates osmotic imbalance, ion toxicity, and water deficiency in plants [2,3]. This affects the enzymatic and metabolic activities [4,5], leading to improper growth and nutritional deficiency [6]. The components of stress response pathways involve signal transduction molecules, ion transporters, ROS scavengers, and cellular machinery for maintaining osmotic homeostasis. The glyoxylase (Gly) pathway has been associated with the salt stress response in plants as it acts by removing the cellular toxicity and regulating glutathione (GSH) homeostasis [10]. Among the well-understood pathways are calcium-responsive SOS3-SOS2 protein kinases that activate the SOS1 ion transporters [11,12]

Methods

Results

Discussion

Conclusion