Ghat: An R package for identifying adaptive polygenic traits

Abstract

AbstractIdentifying selection on polygenic complex traits in crops and livestock is key to understanding evolution and helps prioritize important characteristics for breeding. However, the QTL that contribute to polygenic trait variation exhibit small or infinitesimal effects. This hinders the ability to detect QTL controlling polygenic traits because enormously high statistical power is needed for their detection. Recently, we circumvented this challenge by introducing a method to identify selection on complex traits by evaluating the relationship between genome-wide changes in allele frequency and estimates of effect-size. The method involves calculating a composite-statistic across all markers that captures this relationship, followed by implementing a linkage disequilibrium-aware permutation test to evaluate if the observed pattern differs from that expected due to drift during evolution and population stratification. In this manuscript, we describe “Ghat”, an R package developed to implement the method to test for selection on polygenic traits. We demonstrate the package by applying it to test for polygenic selection on 15 published European winter wheat traits including yield, biomass, quality, morphological characteristics, and disease resistance traits. The results highlight the power of Ghat to identify selection on complex traits. The Ghat package is accessible on CRAN, The Comprehensive R Archival Network, and on GitHub.