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Rice transcriptome analysis reveals nitrogen starvation modulates differential alternative splicing and transcript usage in various metabolism-related genes

Chaudhary, Saurabh and Kalkal, Meenu 2021. Rice transcriptome analysis reveals nitrogen starvation modulates differential alternative splicing and transcript usage in various metabolism-related genes. Life 11 (4) , 285. 10.3390/life11040285

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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.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Biosciences
Additional Information: This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).
Publisher: MDPI
ISSN: 2075-1729
Date of First Compliant Deposit: 29 March 2021
Date of Acceptance: 24 March 2021
Last Modified: 30 Mar 2021 09:00
URI: https://orca.cardiff.ac.uk/id/eprint/140154

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