The long-term effects of genomic selection: allele frequency changes and fixation of loci

Y.C.J. Wientjes; P. Bijma; J. van den Heuvel; B.J. Zwaan; Z.G. Vitezica; M.P.L. Calus

doi:10.3920/978-90-8686-940-4_199

The long-term effects of genomic selection: allele frequency changes and fixation of loci

Y.C.J. Wientjes, P. Bijma, J. van den Heuvel, B.J. Zwaan, Z.G. Vitezica, M.P.L. Calus

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Academic

Abstract

Allele frequencies change due to drift and selection. We investigated those changes for different selection methods. We simulated a livestock population with 50 generations of selection for an additive trait controlled by 2,000 segregating loci at the start of selection. Our results show that the average absolute change in allele frequency with genomic selection was slightly higher than with pedigree selection, and considerably higher than with mass selection. Genomic and pedigree selection both resulted in fixation of roughly three times more loci than mass selection, and roughly five times more loci became fixed for the unfavourable allele. While this was mainly a result of increased genetic drift, genomic selection also lost additional favourable alleles due to hitchhiking. This suggests that genomic selection can limit long-term genetic gain.

Original language	English
Title of host publication	Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)
Subtitle of host publication	Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges
Editors	R.F. Veerkamp, Y. de Haas
Place of Publication	Wageningen
Publisher	Wageningen Academic Publishers
Pages	849-852
ISBN (Electronic)	9789086869404
DOIs	https://doi.org/10.3920/978-90-8686-940-4_199
Publication status	Published - 2022
Event	World Congress on Genetics Applied to Livestock Production: WCGALP 2022 - Rotterdam, Netherlands Duration: 3 Jul 2022 → 8 Jul 2022

Conference

Conference	World Congress on Genetics Applied to Livestock Production: WCGALP 2022
Country/Territory	Netherlands
City	Rotterdam
Period	3/07/22 → 8/07/22

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10.3920/978-90-8686-940-4_199Licence: CC BY

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Wientjes, Y. C. J., Bijma, P., van den Heuvel, J., Zwaan, B. J., Vitezica, Z. G., & Calus, M. P. L. (2022). The long-term effects of genomic selection: allele frequency changes and fixation of loci. In R. F. Veerkamp, & Y. de Haas (Eds.), Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges (pp. 849-852). [199] Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-940-4_199

Wientjes, Y.C.J. ; Bijma, P. ; van den Heuvel, J. et al. / The long-term effects of genomic selection: allele frequency changes and fixation of loci. Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. editor / R.F. Veerkamp ; Y. de Haas. Wageningen : Wageningen Academic Publishers, 2022. pp. 849-852

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title = "The long-term effects of genomic selection: allele frequency changes and fixation of loci",

abstract = "Allele frequencies change due to drift and selection. We investigated those changes for different selection methods. We simulated a livestock population with 50 generations of selection for an additive trait controlled by 2,000 segregating loci at the start of selection. Our results show that the average absolute change in allele frequency with genomic selection was slightly higher than with pedigree selection, and considerably higher than with mass selection. Genomic and pedigree selection both resulted in fixation of roughly three times more loci than mass selection, and roughly five times more loci became fixed for the unfavourable allele. While this was mainly a result of increased genetic drift, genomic selection also lost additional favourable alleles due to hitchhiking. This suggests that genomic selection can limit long-term genetic gain.",

author = "Y.C.J. Wientjes and P. Bijma and {van den Heuvel}, J. and B.J. Zwaan and Z.G. Vitezica and M.P.L. Calus",

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doi = "10.3920/978-90-8686-940-4_199",

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booktitle = "Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)",

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Wientjes, YCJ , Bijma, P , van den Heuvel, J , Zwaan, BJ, Vitezica, ZG & Calus, MPL 2022, The long-term effects of genomic selection: allele frequency changes and fixation of loci. in RF Veerkamp & Y de Haas (eds), Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges., 199, Wageningen Academic Publishers, Wageningen, pp. 849-852, World Congress on Genetics Applied to Livestock Production: WCGALP 2022, Rotterdam, Netherlands, 3/07/22. https://doi.org/10.3920/978-90-8686-940-4_199

The long-term effects of genomic selection: allele frequency changes and fixation of loci. / Wientjes, Y.C.J.; Bijma, P.; van den Heuvel, J. et al.

Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. ed. / R.F. Veerkamp; Y. de Haas. Wageningen : Wageningen Academic Publishers, 2022. p. 849-852 199.

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Academic

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N2 - Allele frequencies change due to drift and selection. We investigated those changes for different selection methods. We simulated a livestock population with 50 generations of selection for an additive trait controlled by 2,000 segregating loci at the start of selection. Our results show that the average absolute change in allele frequency with genomic selection was slightly higher than with pedigree selection, and considerably higher than with mass selection. Genomic and pedigree selection both resulted in fixation of roughly three times more loci than mass selection, and roughly five times more loci became fixed for the unfavourable allele. While this was mainly a result of increased genetic drift, genomic selection also lost additional favourable alleles due to hitchhiking. This suggests that genomic selection can limit long-term genetic gain.

AB - Allele frequencies change due to drift and selection. We investigated those changes for different selection methods. We simulated a livestock population with 50 generations of selection for an additive trait controlled by 2,000 segregating loci at the start of selection. Our results show that the average absolute change in allele frequency with genomic selection was slightly higher than with pedigree selection, and considerably higher than with mass selection. Genomic and pedigree selection both resulted in fixation of roughly three times more loci than mass selection, and roughly five times more loci became fixed for the unfavourable allele. While this was mainly a result of increased genetic drift, genomic selection also lost additional favourable alleles due to hitchhiking. This suggests that genomic selection can limit long-term genetic gain.

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Wientjes YCJ , Bijma P , van den Heuvel J , Zwaan BJ, Vitezica ZG, Calus MPL. The long-term effects of genomic selection: allele frequency changes and fixation of loci. In Veerkamp RF, de Haas Y, editors, Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. Wageningen: Wageningen Academic Publishers. 2022. p. 849-852. 199 doi: 10.3920/978-90-8686-940-4_199

The long-term effects of genomic selection: allele frequency changes and fixation of loci

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