Ghat

Ghat detects selection on polygenic complex traits by relating genome-wide allele frequency changes to marker effect-size estimates.

Key Features:

• Implementation: Implemented as an R package.
• Scope: Targets detection of selection on polygenic complex traits in organisms such as crops and livestock.
• Genome-wide allele-effect analysis: Evaluates the relationship between genome-wide changes in allele frequency and estimates of effect size across all genetic markers.
• Composite statistic: Calculates a composite statistic that summarizes the genome-wide allele-frequency and effect-size relationship.
• Statistical testing: Assesses significance using a linkage disequilibrium-aware permutation test to account for LD, drift, and population stratification.

Scientific Applications:

• Wheat trait analysis: Applied to 15 published European wheat traits, including yield, biomass, quality, morphological characteristics, and disease resistance.
• Simulated populations: Applied to simulated populations with differing breeding histories and genetic architectures to evaluate performance under varied scenarios.
• Quantifying selection: Used to quantify evolution and selection on complex traits across genomes.
• Breeding prioritization: Supports prioritization of important characteristics for breeding programs by identifying adaptive polygenic signals.

Methodology:

Evaluates genome-wide allele frequency changes against marker effect-size estimates across all genetic markers, computes a composite statistic summarizing that relationship, and assesses significance with a linkage disequilibrium-aware permutation test.