The coding loci of evolution and domestication: current knowledge and implications for bio-inspired genome editing

Area of Science:

• Genetics
• Genomics
• Bioengineering

Background:

• CRISPR/Cas9 technology offers potential for targeted mutations in domesticated organisms.
• Identifying specific genes and mutations for desired traits remains a significant challenge in crop and livestock improvement.

Purpose of the Study:

• To explore the potential of bio-inspired genome editing by utilizing naturally occurring mutations.
• To identify and analyze genes and mutations associated with evolutionary and domestication changes across eukaryotes.

Main Methods:

• Utilized Gephebase, a curated database of genes responsible for evolutionary and domesticated changes.
• Examined over 1200 mutations in coding regions of more than 700 genes across animals, plants, and yeasts.
• Analyzed mutation types, focusing on protein-null alleles (nonsense and frameshift mutations).

Main Results:

• Genetic knowledge varies by trait; xenobiotic resistance is well-studied, while others are less understood.
• Protein-null alleles constitute a substantial portion of identified domestication mutations (42%), compared to intraspecific (27%) and interspecific evolution (11%).
• A significant number of identified coding mutations are protein-null alleles.

Conclusions:

• The Gephebase compilation provides insights into potential targets for bio-inspired and transgene-free genome editing.
• Natural mutations, especially large-effect ones, offer promising avenues for genetic improvement in domesticated species.
• Understanding evolutionary and domestication mutations can guide future genome editing strategies.