ArticleGenetics, selection, evolution : GSE2014
Allele frequency changes due to hitch-hiking in genomic selection programs.
Article in Genetics, selection, evolution : GSE, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 51 citations in OpenAlex.
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- Changes in allele frequencies and genetic architecture due to selection in two pig populations.Genetics, selection, evolution : GSE · 2024Article
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- Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection.Genetics, selection, evolution : GSE · 2021Article
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- Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein-Friesian breeding program from 1986 to 2015.Genetics, selection, evolution : GSE · 2018Article
- Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle.BMC genomics · 2018Article
- Unlocking new alleles for leaf rust resistance in the Vavilov wheat collection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Single-Step BLUP with Varying Genotyping Effort in Open-PollinatedG3 (Bethesda, Md.) · 2017Article
- Genetic Gains in Yield and Yield Related Traits under Drought Stress and Favorable Environments in a Maize Population Improved Using Marker Assisted Recurrent Selection.Frontiers in plant science · 2017Article
- Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny.Genetics, selection, evolution : GSE · 2016Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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