Ghat: an R package for identifying adaptive polygenic traits.
G3 (Bethesda)
; 13(2)2023 02 09.
Article
en En
| MEDLINE
| ID: mdl-36454082
ABSTRACT
Identifying selection on polygenic complex traits in crops and livestock is important for understanding evolution and helps prioritize important characteristics for breeding. Quantitative trait loci (QTL) that contribute to polygenic trait variation often 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 approach involves calculating a composite statistic across all markers that capture 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 this method to test for selection on polygenic traits. We demonstrate the package by applying it to test for polygenic selection on 15 published European wheat traits including yield, biomass, quality, morphological characteristics, and disease resistance traits. Moreover, we applied Ghat to different simulated populations with different breeding histories and genetic architectures. 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.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Herencia Multifactorial
/
Fitomejoramiento
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
G3 (Bethesda)
Año:
2023
Tipo del documento:
Article
País de afiliación:
Alemania