Genome-wide identification and characterization of microRNAs by small RNA sequencing for low nitrogen stress in potato.

Jagesh Kumar Tiwari,Rasna Zinta,Shashi Rawat,Rajesh Kumar Singh,Swarup Kumar Chakrabarti,Aastha Saraswati,Tanuja Buckseth,Tapan Kumar Mondal

doi:10.1371/journal.pone.0233076

Abstract

Nitrogen is an important nutrient for plant growth and tuber quality of potato. Since potato crop requires high dose of N, improving nitrogen use efficiency (NUE) of plant is an inevitable approach to minimize N fertilization. The aim of this study was to identify and characterize microRNAs (miRNAs) by small RNA sequencing in potato plants grown in aeroponic under two contrasting N (high and low) regimes. A total of 119 conserved miRNAs belonging to 41 miRNAs families, and 1002 putative novel miRNAs were identified. From total, 52 and 54 conserved miRNAs, and 404 and 628 putative novel miRNAs were differentially expressed in roots and shoots, respectively under low N stress. Of total 34,135 predicted targets, the gene ontology (GO) analysis indicated that maximum targets belong to biological process followed by molecular function and cellular component. Eexpression levels of the selected miRNAs and targets were validated by real time-quantitative polymerase chain reaction (RT-qPCR) analysis. Two predicted targets of potential miRNAs (miR397 and miR398) were validated by 5’ RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). In general, predicted targets are associated with stress-related, kinase, transporters and transcription factors such as universal stress protein, heat shock protein, salt-tolerance protein, calmodulin binding protein, serine-threonine protein kinsae, Cdk10/11- cyclin dependent kinase, amino acid transporter, nitrate transporter, sugar transporter, transcription factor, F-box family protein, and zinc finger protein etc. Our study highlights that miR397 and miR398 play crucial role in potato during low N stress management. Moreover, study provides insights to modulate miRNAs and their predicted targets to develop N-use efficient potato using transgenic/genome-editing tools in future.

Highlights

Potato is the most important non-grain food crop in the world
Agronomic and soil management techniques have been applied to a great extent to improve nitrogen use efficiency (NUE) in crops, this study aimed to identify microRNAs involved in regulation of gene expression under N stress metabolism in potato [3, 4]
Improving NUE of potato plant is essential to reduce amount of N fertilizers applied to the crop, while maintaining tuber yield

Summary

Introduction

In India, potato crop requires high dose of nitrogen (180–240 kg ha-1) to produce high tuber yield (30–40 t ha-1) [1]. MiRNAs identification under low nitrogen stress in potato approach, which can utilize less nitrogen (N) to produce equivalent tuber yield. This approach is more important in developing countries where resources are limited like India [2]. Agronomic and soil management techniques have been applied to a great extent to improve NUE in crops, this study aimed to identify microRNAs (miRNAs) involved in regulation of gene expression under N stress metabolism in potato [3, 4]

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Conclusion