Analysis of chromosomes and nucleotides in rice to predict gene expression through codon usage pattern

Area of Science:

• Plant Genetics
• Molecular Biology
• Bioinformatics

Background:

• Amino acids are crucial for protein structure and function, impacting plant growth.
• Understanding codon usage patterns in rice plastid chromosomes is key to predicting gene expression.

Purpose of the Study:

• To analyze nucleotide, synonymous codon, and amino acid usage in rice plastid chromosomes.
• To predict gene expression through codon usage patterns.
• To provide insights for rice breeding and genetics.

Main Methods:

• Analysis of codon adaptation index (CAI) across 12 rice chromosomes.
• Evaluation of guanine and cytosine (GC) content.
• Calculation of modified relative codon bias (rCDNA) and relative synonymous codon usage (RSCU).

Main Results:

• Codon Adaptation Index values ranged from 0.631 to 0.733.
• GC content varied from 37% to 60%.
• Eight chromosomes showed modified relative codon bias above the 0.66 threshold, with specific amino acid over-representation (asparagine, aspartate, cysteine, glutamate, phenylalanine) observed across all chromosomes.

Conclusions:

• Codon usage patterns in rice plastid chromosomes offer a platform for gene expression prediction.
• Findings support rice breeding programs by identifying desirable genes for trait improvement.
• Results facilitate codon optimization for developing improved rice varieties.