Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Synonymous mutations can alter codon tRNA adaptation index (tAI) and local translation rates.
• It is hypothesized that synonymous mutations enhancing tAI are favored by natural selection.

Purpose of the Study:

• To investigate whether synonymous mutations affecting tAI are under selection in the maize genome.
• To determine the direction and strength of selection acting on synonymous mutations based on their impact on tAI.

Main Methods:

• Analysis of synonymous mutations in the maize (Zea mays) genome.
• Comparison of fixed-to-polymorphic ratios and derived/minor allele frequencies for tAI-increasing versus tAI-decreasing mutations.
• Utilizing both tRNA adaptation index (tAI) and codon adaptation index (CAI) to assess selection.

Main Results:

• Synonymous mutations that increase tAI exhibit higher fixed-to-polymorphic ratios compared to those decreasing tAI.
• Mutations increasing tAI show significantly higher derived allele frequencies (DAF) or minor allele frequencies (MAF) than those decreasing tAI.
• Similar patterns of selection were observed when using codon adaptation index (CAI) instead of tAI.

Conclusions:

• Synonymous mutations in maize are not neutral and are subject to natural selection.
• Mutations increasing tAI are positively selected, while those decreasing tAI are under purifying selection.
• The identified selection forces, though potentially weak, are significant and should not be disregarded in evolutionary studies.