The fate of new mutations: genomic selection exploits new mutation variance to a much smaller degree than traditional selection

H.A. Mulder, S.H. Lee, B.J. Hayes, J.H.J. van der Werf

Research output: Chapter in Book/Report/Conference proceedingConference paper

Abstract

New mutations create new genetic variance in populations and contribute to long-term response to selection. We hypothesize that genomic selection exploits new mutational variance much less than traditional selection methods, because new mutations are not in linkage disequilibrium with markers on the current SNP chips, while animals with a favourable mutation have a selective advantage with mass and pedigree-based BLUP selection. We used Monte Carlo simulation using real sequence data to generate the base generation to test this hypothesis. Genomic selection increased response to selection due to old QTL by 33% and 1% in generation 5 and 20 compared to mass selection, respectively, while response to selection from new mutations was 65-85% and 61% lower than with mass selection in generation 5 and 20, respectively. In genomic selection, genetic variance due to old QTL was much faster eroded, while new mutational variance did not increase much, resulting in a 65% and 43% lower total genetic variance in generation 20 with genomic selection, compared to mass and pedigree-based BLUP selection. In summary, we showed that genomic selection hardly exploits new mutational variance and erodes genetic variance much faster than mass and BLUP selection. Future research should focus on developing sustainable genomic selection strategies to optimize long-term response to selection, exploiting new mutational variance. Keywords: de novo mutation, genomic selection, long-term selection response, selection
Original languageEnglish
Title of host publicationProceedings of the 11th World Congress on Genetics Applied to Livestock Production
Subtitle of host publicationVolume Genetic Gain - Breeding Strategies 1
PublisherWCGALP
Number of pages5
Publication statusPublished - Feb 2018
Event11th World Congress on Genetics Applied to Livestock Production - Auckland, New Zealand
Duration: 11 Feb 201816 Feb 2018

Conference

Conference11th World Congress on Genetics Applied to Livestock Production
CountryNew Zealand
CityAuckland
Period11/02/1816/02/18

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marker-assisted selection
mutation
genetic variance
selection response
pedigree
quantitative trait loci
selection methods
linkage disequilibrium
animals
testing

Cite this

Mulder, H. A., Lee, S. H., Hayes, B. J., & van der Werf, J. H. J. (2018). The fate of new mutations: genomic selection exploits new mutation variance to a much smaller degree than traditional selection. In Proceedings of the 11th World Congress on Genetics Applied to Livestock Production: Volume Genetic Gain - Breeding Strategies 1 [415] WCGALP.
Mulder, H.A. ; Lee, S.H. ; Hayes, B.J. ; van der Werf, J.H.J. / The fate of new mutations: genomic selection exploits new mutation variance to a much smaller degree than traditional selection. Proceedings of the 11th World Congress on Genetics Applied to Livestock Production: Volume Genetic Gain - Breeding Strategies 1. WCGALP, 2018.
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abstract = "New mutations create new genetic variance in populations and contribute to long-term response to selection. We hypothesize that genomic selection exploits new mutational variance much less than traditional selection methods, because new mutations are not in linkage disequilibrium with markers on the current SNP chips, while animals with a favourable mutation have a selective advantage with mass and pedigree-based BLUP selection. We used Monte Carlo simulation using real sequence data to generate the base generation to test this hypothesis. Genomic selection increased response to selection due to old QTL by 33{\%} and 1{\%} in generation 5 and 20 compared to mass selection, respectively, while response to selection from new mutations was 65-85{\%} and 61{\%} lower than with mass selection in generation 5 and 20, respectively. In genomic selection, genetic variance due to old QTL was much faster eroded, while new mutational variance did not increase much, resulting in a 65{\%} and 43{\%} lower total genetic variance in generation 20 with genomic selection, compared to mass and pedigree-based BLUP selection. In summary, we showed that genomic selection hardly exploits new mutational variance and erodes genetic variance much faster than mass and BLUP selection. Future research should focus on developing sustainable genomic selection strategies to optimize long-term response to selection, exploiting new mutational variance. Keywords: de novo mutation, genomic selection, long-term selection response, selection",
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Mulder, HA, Lee, SH, Hayes, BJ & van der Werf, JHJ 2018, The fate of new mutations: genomic selection exploits new mutation variance to a much smaller degree than traditional selection. in Proceedings of the 11th World Congress on Genetics Applied to Livestock Production: Volume Genetic Gain - Breeding Strategies 1., 415, WCGALP, 11th World Congress on Genetics Applied to Livestock Production, Auckland, New Zealand, 11/02/18.

The fate of new mutations: genomic selection exploits new mutation variance to a much smaller degree than traditional selection. / Mulder, H.A.; Lee, S.H.; Hayes, B.J.; van der Werf, J.H.J.

Proceedings of the 11th World Congress on Genetics Applied to Livestock Production: Volume Genetic Gain - Breeding Strategies 1. WCGALP, 2018. 415.

Research output: Chapter in Book/Report/Conference proceedingConference paper

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AB - New mutations create new genetic variance in populations and contribute to long-term response to selection. We hypothesize that genomic selection exploits new mutational variance much less than traditional selection methods, because new mutations are not in linkage disequilibrium with markers on the current SNP chips, while animals with a favourable mutation have a selective advantage with mass and pedigree-based BLUP selection. We used Monte Carlo simulation using real sequence data to generate the base generation to test this hypothesis. Genomic selection increased response to selection due to old QTL by 33% and 1% in generation 5 and 20 compared to mass selection, respectively, while response to selection from new mutations was 65-85% and 61% lower than with mass selection in generation 5 and 20, respectively. In genomic selection, genetic variance due to old QTL was much faster eroded, while new mutational variance did not increase much, resulting in a 65% and 43% lower total genetic variance in generation 20 with genomic selection, compared to mass and pedigree-based BLUP selection. In summary, we showed that genomic selection hardly exploits new mutational variance and erodes genetic variance much faster than mass and BLUP selection. Future research should focus on developing sustainable genomic selection strategies to optimize long-term response to selection, exploiting new mutational variance. Keywords: de novo mutation, genomic selection, long-term selection response, selection

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Mulder HA, Lee SH, Hayes BJ, van der Werf JHJ. The fate of new mutations: genomic selection exploits new mutation variance to a much smaller degree than traditional selection. In Proceedings of the 11th World Congress on Genetics Applied to Livestock Production: Volume Genetic Gain - Breeding Strategies 1. WCGALP. 2018. 415