Fine Mapping without Phenotyping: Identification of Selection Targets in Secondary Evolve and Resequence Experiments

Area of Science:

• Evolutionary Biology
• Genetics
• Genomics

Background:

• Evolve and Resequence (E&R) studies map genomic regions under selection.
• Linkage disequilibrium in sexually reproducing organisms limits resolution in primary E&R studies.
• Secondary E&R aims to increase mapping resolution by allowing further recombination.

Purpose of the Study:

• To assess the impact of experimental design on the power and resolution of secondary E&R.
• To identify key factors for optimizing secondary E&R studies.
• To provide guidance for future experimental evolution research.

Main Methods:

• Computer simulations were used to model secondary E&R experiments.
• The effects of crossing schemes, population size, experimental duration, and replicates were evaluated.
• Power and resolution of candidate gene mapping were the primary metrics.

Main Results:

• Crossing scheme and population size critically influence secondary E&R power and resolution.
• Simple crossing schemes with few founder lines are more effective than complex ones.
• A minimum population size of 4,800 individuals is necessary for ≥75% power.

Conclusions:

• Experimental design, particularly crossing strategy and population size, is paramount for successful secondary E&R.
• Current E&R studies often use population sizes too small for high-resolution mapping.
• Optimized secondary E&R designs can improve the characterization of causative SNPs in experimental evolution.