Allele frequency changes due to hitch-hiking in genomic selection programs.

Huiming Liu,Theo He Meuwissen,Anders C Sørensen,Peer Berg

doi:10.1186/1297-9686-46-8

Abstract

BackgroundGenomic selection makes it possible to reduce pedigree-based inbreeding over best linear unbiased prediction (BLUP) by increasing emphasis on own rather than family information. However, pedigree inbreeding might not accurately reflect loss of genetic variation and the true level of inbreeding due to changes in allele frequencies and hitch-hiking. This study aimed at understanding the impact of using long-term genomic selection on changes in allele frequencies, genetic variation and level of inbreeding.MethodsSelection was performed in simulated scenarios with a population of 400 animals for 25 consecutive generations. Six genetic models were considered with different heritabilities and numbers of QTL (quantitative trait loci) affecting the trait. Four selection criteria were used, including selection on own phenotype and on estimated breeding values (EBV) derived using phenotype-BLUP, genomic BLUP and Bayesian Lasso. Changes in allele frequencies at QTL, markers and linked neutral loci were investigated for the different selection criteria and different scenarios, along with the loss of favourable alleles and the rate of inbreeding measured by pedigree and runs of homozygosity.ResultsFor each selection criterion, hitch-hiking in the vicinity of the QTL appeared more extensive when accuracy of selection was higher and the number of QTL was lower. When inbreeding was measured by pedigree information, selection on genomic BLUP EBV resulted in lower levels of inbreeding than selection on phenotype BLUP EBV, but this did not always apply when inbreeding was measured by runs of homozygosity. Compared to genomic BLUP, selection on EBV from Bayesian Lasso led to less genetic drift, reduced loss of favourable alleles and more effectively controlled the rate of both pedigree and genomic inbreeding in all simulated scenarios. In addition, selection on EBV from Bayesian Lasso showed a higher selection differential for mendelian sampling terms than selection on genomic BLUP EBV.ConclusionsNeutral variation can be shaped to a great extent by the hitch-hiking effects associated with selection, rather than just by genetic drift. When implementing long-term genomic selection, strategies for genomic control of inbreeding are essential, due to a considerable hitch-hiking effect, regardless of the method that is used for prediction of EBV.

Highlights

Genomic selection makes it possible to reduce pedigree-based inbreeding over best linear unbiased prediction (BLUP) by increasing emphasis on own rather than family information
Genomic information used by Bayesian Lasso (BL) and genomic BLUP (GBLUP) increased the average frequency of favourable QTL alleles, p, only marginally compared to BLUP and phenotypic selection (PS) at higher heritability, while the differences in p between all selection criteria were more pronounced at lower heritability
The results showed that at lower heritability, i.e. 0.05, genetic drift was more pronounced for Genomic selection (GS) and BLUP because the emphasis on sib information in these selection criteria was high, so co-selection of relatives increased as the heritability decreased, in contrast to PS [6]

Summary

Introduction

Genomic selection makes it possible to reduce pedigree-based inbreeding over best linear unbiased prediction (BLUP) by increasing emphasis on own rather than family information. Pedigree inbreeding might not accurately reflect loss of genetic variation and the true level of inbreeding due to changes in allele frequencies and hitch-hiking. Pedersen et al [13] found that for selection based on BLUP EBV, the rate of genomic inbreeding at all linked neutral loci across a chromosome that contains a major QTL was significantly higher than the rate of pedigree inbreeding. This indicates that, due to hitch-hiking effects, there are no neutral loci on a chromosome that contains a QTL

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