Rice Transcriptome Analysis Reveals Nitrogen Starvation Modulates Differential Alternative Splicing and Transcript Usage in Various Metabolism-Related Genes.

Saurabh Chaudhary,Meenu Kalkal

doi:10.3390/life11040285

Saurabh Chaudhary, Meenu Kalkal

Open Access

https://doi.org/10.3390/life11040285

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Journal: Life	Publication Date: Mar 27, 2021
Citations: 6	License type: CC BY 4.0

Affiliation: Cardiff University, National Institute of Malaria Research

Abstract

Nitrogen (N) is crucial for plant growth and development; however, excessive use of N fertilizers cause many problems including environmental damage, degradation of soil fertility, and high cost to the farmers. Therefore, immediate implementation is required to develop N efficient crop varieties. Rice being low nitrogen use efficiency (NUE) and a high demand staple food across the world has become a favorite crop to study the NUE trait. In the current study, we used the publicly available transcriptome data generated from the root and shoot tissues of two rice genotypes IR-64 and Nagina-22 (N-22) under optimum N supply (N+) and chronic N-starvation (N−). A stringent pipeline was applied to detect differentially expressed genes (DEGs), alternatively spliced (DAS) genes, differentially expressed transcripts (DETs) and differential transcript usage (DTU) transcripts in both the varieties and tissues under N+ and N− conditions. The DAS genes and DTU transcripts identified in the study were found to be involved in several metabolic and biosynthesis processes. We suggest alternative splicing (AS) plays an important role in fine-tuning the regulation of metabolic pathways related genes in genotype, tissue, and condition-dependent manner. The current study will help in understanding the transcriptional dynamics of NUE traits in the future.

Highlights

IntroductionPublisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations
The Principal Component Analysis (PCA) after removing batch effects of the biological replicates suggested differential expression at gene and transcript levels occurred in tissues and condition dependent manner in rice (Figure S3)
A total variance of 40.44% and 38.32% were detected at gene and transcript level, respectively, among the root and shoot tissues in both the varieties (IR-64 and N-22) (Figure S3)

Summary

Introduction

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Nitrogen (N) is a constituent of many biomolecules including amino acids, enzymes, growth hormones, nucleic acids, and proteins; its uptake from the soil, transportation among tissues, and metabolism is crucial to understand in plants. Nitrate (NO3 − ) and ammonium (NH4 + ) ions are the two most important forms of inorganic N required for plant growth and development [1]. NO3 − is considered as the major source of N for land plants while NH4 + is important for plants growing under anaerobic conditions like rice [2,3]

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