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The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations
Genetic selection has been applied for many generations in animal, plant, and experimental populations. Selection changes the allelic architecture of traits to create genetic gain. It remains unknown whether the changes in allelic architecture are different for the recently introduced technique of g...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10471209/ https://www.ncbi.nlm.nih.gov/pubmed/37506255 http://dx.doi.org/10.1093/genetics/iyad141 |
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author | Wientjes, Yvonne C J Bijma, Piter van den Heuvel, Joost Zwaan, Bas J Vitezica, Zulma G Calus, Mario P L |
author_facet | Wientjes, Yvonne C J Bijma, Piter van den Heuvel, Joost Zwaan, Bas J Vitezica, Zulma G Calus, Mario P L |
author_sort | Wientjes, Yvonne C J |
collection | PubMed |
description | Genetic selection has been applied for many generations in animal, plant, and experimental populations. Selection changes the allelic architecture of traits to create genetic gain. It remains unknown whether the changes in allelic architecture are different for the recently introduced technique of genomic selection compared to traditional selection methods and whether they depend on the genetic architectures of traits. Here, we investigate the allele frequency changes of old and new causal loci under 50 generations of phenotypic, pedigree, and genomic selection, for a trait controlled by either additive, additive and dominance, or additive, dominance, and epistatic effects. Genomic selection resulted in slightly larger and faster changes in allele frequencies of causal loci than pedigree selection. For each locus, allele frequency change per generation was not only influenced by its statistical additive effect but also to a large extent by the linkage phase with other loci and its allele frequency. Selection fixed a large number of loci, and 5 times more unfavorable alleles became fixed with genomic and pedigree selection than with phenotypic selection. For pedigree selection, this was mainly a result of increased genetic drift, while genetic hitchhiking had a larger effect on genomic selection. When epistasis was present, the average allele frequency change was smaller (∼15% lower), and a lower number of loci became fixed for all selection methods. We conclude that for long-term genetic improvement using genomic selection, it is important to consider hitchhiking and to limit the loss of favorable alleles. |
format | Online Article Text |
id | pubmed-10471209 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-104712092023-09-01 The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations Wientjes, Yvonne C J Bijma, Piter van den Heuvel, Joost Zwaan, Bas J Vitezica, Zulma G Calus, Mario P L Genetics Genomic Prediction Genetic selection has been applied for many generations in animal, plant, and experimental populations. Selection changes the allelic architecture of traits to create genetic gain. It remains unknown whether the changes in allelic architecture are different for the recently introduced technique of genomic selection compared to traditional selection methods and whether they depend on the genetic architectures of traits. Here, we investigate the allele frequency changes of old and new causal loci under 50 generations of phenotypic, pedigree, and genomic selection, for a trait controlled by either additive, additive and dominance, or additive, dominance, and epistatic effects. Genomic selection resulted in slightly larger and faster changes in allele frequencies of causal loci than pedigree selection. For each locus, allele frequency change per generation was not only influenced by its statistical additive effect but also to a large extent by the linkage phase with other loci and its allele frequency. Selection fixed a large number of loci, and 5 times more unfavorable alleles became fixed with genomic and pedigree selection than with phenotypic selection. For pedigree selection, this was mainly a result of increased genetic drift, while genetic hitchhiking had a larger effect on genomic selection. When epistasis was present, the average allele frequency change was smaller (∼15% lower), and a lower number of loci became fixed for all selection methods. We conclude that for long-term genetic improvement using genomic selection, it is important to consider hitchhiking and to limit the loss of favorable alleles. Oxford University Press 2023-07-28 /pmc/articles/PMC10471209/ /pubmed/37506255 http://dx.doi.org/10.1093/genetics/iyad141 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Genomic Prediction Wientjes, Yvonne C J Bijma, Piter van den Heuvel, Joost Zwaan, Bas J Vitezica, Zulma G Calus, Mario P L The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations |
title | The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations |
title_full | The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations |
title_fullStr | The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations |
title_full_unstemmed | The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations |
title_short | The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations |
title_sort | long-term effects of genomic selection: 2. changes in allele frequencies of causal loci and new mutations |
topic | Genomic Prediction |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10471209/ https://www.ncbi.nlm.nih.gov/pubmed/37506255 http://dx.doi.org/10.1093/genetics/iyad141 |
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