Codon Usage Provide Insights into the Adaptation of Rice Genes under Stress Condition

Tyagi, S and Kabade, P G and Gnanapragasam, N and Singh, U M and Gurjar, A K S and Rai, A and Sinha, P and Kumar, A and Singh, V K (2023) Codon Usage Provide Insights into the Adaptation of Rice Genes under Stress Condition. International Journal of Molecular Sciences (TSI), 24 (2). pp. 1-18. ISSN 1422-0067

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Abstract

Plants experience different stresses, i.e., abiotic, or biotic, and to combat them, plants re-program the expression of growth-, metabolism-, and resistance-related genes. These genes differ in their synonymous codon usage frequency and show codon usage bias. Here, we investigated the correlation among codon usage bias, gene expression, and underlying mechanisms in rice under abiotic and biotic stress conditions. The results indicated that genes with higher expression (up- or downregulated) levels had high GC content (≥60%), a low effective number of codon usage (≤40), and exhibited strong biases towards the codons with C/G at the third nucleotide position, irrespective of stress received. TTC, ATC, and CTC were the most preferred codons, while TAC, CAC, AAC, GAC, and TGC were moderately preferred under any stress (abiotic or biotic) condition. Additionally, downregulated genes are under mutational pressure (R2 ≥ 0.5) while upregulated genes are under natural selection pressure (R2 ≤ 0.5). Based on these results, we also identified the possible target codons that can be used to design an optimized set of genes with specific codons to develop climate-resilient varieties. Conclusively, under stress, rice has a bias towards codon usage which is correlated with GC content, gene expression level, and gene length.

Item Type:	Article
Divisions:	Others
CRP:	UNSPECIFIED
Uncontrolled Keywords:	codon usage bias, abiotic stress, gene expression, mutational pressure, natural selection
Subjects:	Others > Abiotic Stress Others > Rice
Depositing User:	Mr Nagaraju T
Date Deposited:	06 Mar 2024 07:56
Last Modified:	06 Mar 2024 07:56
URI:	http://oar.icrisat.org/id/eprint/12544
Official URL:	https://www.mdpi.com/1422-0067/24/2/1098
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	The authors express sincere thanks to the Department of Biotechnology (DBT), Government of India for financial support under the project ‘Development of superior haplotype based near isogenic lines (Haplo-NILs) for enhanced genetic gain in rice’ grant (BT/PR32853/AGill/103/1159/2019). This work has been undertaken as part of the ICAR-IRRI collaborative research project. IRRI is a member of the CGIAR Consortium.
Links:	Google Scholar

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