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Article

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

1
Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
2
Parasite-Host Biology, National Institute of Malaria Research, Dwarka, New Delhi 110077, India
*
Author to whom correspondence should be addressed.
Academic Editors: Tatyana V. Savchenko and Andrej Frolov
Life 2021, 11(4), 285; https://doi.org/10.3390/life11040285
Received: 26 February 2021 / Revised: 23 March 2021 / Accepted: 24 March 2021 / Published: 27 March 2021
(This article belongs to the Special Issue Metabolism of Photosynthetic Organisms)
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. View Full-Text
Keywords: alternative splicing; gene expression; N-starvation; NUE; metabolism; transcript usage; rice alternative splicing; gene expression; N-starvation; NUE; metabolism; transcript usage; rice
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MDPI and ACS Style

Chaudhary, S.; Kalkal, M. Rice Transcriptome Analysis Reveals Nitrogen Starvation Modulates Differential Alternative Splicing and Transcript Usage in Various Metabolism-Related Genes. Life 2021, 11, 285. https://doi.org/10.3390/life11040285

AMA Style

Chaudhary S, Kalkal M. Rice Transcriptome Analysis Reveals Nitrogen Starvation Modulates Differential Alternative Splicing and Transcript Usage in Various Metabolism-Related Genes. Life. 2021; 11(4):285. https://doi.org/10.3390/life11040285

Chicago/Turabian Style

Chaudhary, Saurabh, and Meenu Kalkal. 2021. "Rice Transcriptome Analysis Reveals Nitrogen Starvation Modulates Differential Alternative Splicing and Transcript Usage in Various Metabolism-Related Genes" Life 11, no. 4: 285. https://doi.org/10.3390/life11040285

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