Genomic selection without own phenotypes exploits new mutational variance less than BLUP selection

H.A. Mulder; S.H. Lee; Sam Clark; B. Hayes; Julius H.J. van der Werf

Abstract

De novo mutations (DNM) create new genetic variance and are an important driver for long-term selection response. We hypothesized that genomic selection without own phenotypes exploits new mutational variance less than pedigree-based BLUP selection. The objectives were to compare GBLUP selection without own phenotype (GBLUP), GBLUP selection with own phenotype (GBLUP_OP) and pedigree-based BLUP selection with own phenotype for 20 generations using Monte Carlo simulation. GBLUP resulted in the lowest genetic variance (24.7%
of total genetic variance) and response due to DNM after 20 generations (9.4% of total response). GBLUP_OP had the highest genetic variance due to new DNM (47.8% of total genetic variance) and selection response due to DNM
(30% of total response), while BLUP was in between with 27.1% of genetic variance due to DNM and 21.9% of response due to DNM. However, GBLUP_OP caused a rapid decline in total genetic variance, because the genetic
variance due to old QTL rapidly eroded. GBLUP had very little selection pressure on DNM and as a consequence, GBLUP had the highest number of DNM with negative effects that were still segregating 10 generations after a
DNM arose. Due to the decline in genetic variance for all selection strategies, selection limits are foreseen and these selection limits are lower for GBLUP (11.2 phenotypic SD from the base population mean) and GBLUP_OP (10.7
phenotypic SD) than for BLUP selection (11.8 phenotypic SD). It can be concluded that genomic selection without own phenotypes exploits new mutational variance less than BLUP selection with own phenotypes, it increases the
probability of DNM with negative effects and it lowers selection limits. Sustainable breeding strategies should consider optimal ways to exploit DNM.

Original language	English
Title of host publication	Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science
Place of Publication	Wageningen
Publisher	Wageningen Academic Publishers
Pages	123-123
ISBN (Electronic)	9789086868902
ISBN (Print)	9789086863396
Publication status	Published - 26 Aug 2019
Event	70th Annual Meeting of the European Federation of Animal Science - Ghent, Belgium Duration: 25 Aug 2019 → 31 Aug 2019

Publication series

Name	Book of Abstracts
Publisher	Wageningen Academic Publishers
ISSN (Electronic)	1382-6077

Conference

Conference	70th Annual Meeting of the European Federation of Animal Science
Country/Territory	Belgium
Period	25/08/19 → 31/08/19

Access to Document

https://www.wageningenacademic.com/doi/pdf/10.3920/978-90-8686-890-2#page=125

Cite this

Mulder, H. A., Lee, S. H., Clark, S., Hayes, B., & van der Werf, J. H. J. (2019). Genomic selection without own phenotypes exploits new mutational variance less than BLUP selection. In Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science (pp. 123-123). (Book of Abstracts). Wageningen Academic Publishers. https://www.wageningenacademic.com/doi/pdf/10.3920/978-90-8686-890-2#page=125

@inbook{e35f174dd6d3408ea7687bd792cc8794,

title = "Genomic selection without own phenotypes exploits new mutational variance less than BLUP selection",

abstract = "De novo mutations (DNM) create new genetic variance and are an important driver for long-term selection response. We hypothesized that genomic selection without own phenotypes exploits new mutational variance less than pedigree-based BLUP selection. The objectives were to compare GBLUP selection without own phenotype (GBLUP), GBLUP selection with own phenotype (GBLUP_OP) and pedigree-based BLUP selection with own phenotype for 20 generations using Monte Carlo simulation. GBLUP resulted in the lowest genetic variance (24.7% of total genetic variance) and response due to DNM after 20 generations (9.4% of total response). GBLUP_OP had the highest genetic variance due to new DNM (47.8% of total genetic variance) and selection response due to DNM (30% of total response), while BLUP was in between with 27.1% of genetic variance due to DNM and 21.9% of response due to DNM. However, GBLUP_OP caused a rapid decline in total genetic variance, because the genetic variance due to old QTL rapidly eroded. GBLUP had very little selection pressure on DNM and as a consequence, GBLUP had the highest number of DNM with negative effects that were still segregating 10 generations after a DNM arose. Due to the decline in genetic variance for all selection strategies, selection limits are foreseen and these selection limits are lower for GBLUP (11.2 phenotypic SD from the base population mean) and GBLUP_OP (10.7 phenotypic SD) than for BLUP selection (11.8 phenotypic SD). It can be concluded that genomic selection without own phenotypes exploits new mutational variance less than BLUP selection with own phenotypes, it increases the probability of DNM with negative effects and it lowers selection limits. Sustainable breeding strategies should consider optimal ways to exploit DNM.",

author = "H.A. Mulder and S.H. Lee and Sam Clark and B. Hayes and {van der Werf}, {Julius H.J.}",

year = "2019",

month = aug,

day = "26",

language = "English",

isbn = "9789086863396",

series = "Book of Abstracts",

publisher = "Wageningen Academic Publishers",

pages = "123--123",

booktitle = "Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science",

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Mulder, HA, Lee, SH, Clark, S, Hayes, B & van der Werf, JHJ 2019, Genomic selection without own phenotypes exploits new mutational variance less than BLUP selection. in Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. Book of Abstracts, Wageningen Academic Publishers, Wageningen, pp. 123-123, 70th Annual Meeting of the European Federation of Animal Science, Belgium, 25/08/19. <https://www.wageningenacademic.com/doi/pdf/10.3920/978-90-8686-890-2#page=125>

Genomic selection without own phenotypes exploits new mutational variance less than BLUP selection. / Mulder, H.A.; Lee, S.H.; Clark, Sam et al.
Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. Wageningen: Wageningen Academic Publishers, 2019. p. 123-123 (Book of Abstracts).

Research output: Chapter in Book/Report/Conference proceeding › Abstract

TY - CHAP

T1 - Genomic selection without own phenotypes exploits new mutational variance less than BLUP selection

AU - Mulder, H.A.

AU - Lee, S.H.

AU - Clark, Sam

AU - Hayes, B.

AU - van der Werf, Julius H.J.

PY - 2019/8/26

Y1 - 2019/8/26

N2 - De novo mutations (DNM) create new genetic variance and are an important driver for long-term selection response. We hypothesized that genomic selection without own phenotypes exploits new mutational variance less than pedigree-based BLUP selection. The objectives were to compare GBLUP selection without own phenotype (GBLUP), GBLUP selection with own phenotype (GBLUP_OP) and pedigree-based BLUP selection with own phenotype for 20 generations using Monte Carlo simulation. GBLUP resulted in the lowest genetic variance (24.7% of total genetic variance) and response due to DNM after 20 generations (9.4% of total response). GBLUP_OP had the highest genetic variance due to new DNM (47.8% of total genetic variance) and selection response due to DNM (30% of total response), while BLUP was in between with 27.1% of genetic variance due to DNM and 21.9% of response due to DNM. However, GBLUP_OP caused a rapid decline in total genetic variance, because the genetic variance due to old QTL rapidly eroded. GBLUP had very little selection pressure on DNM and as a consequence, GBLUP had the highest number of DNM with negative effects that were still segregating 10 generations after a DNM arose. Due to the decline in genetic variance for all selection strategies, selection limits are foreseen and these selection limits are lower for GBLUP (11.2 phenotypic SD from the base population mean) and GBLUP_OP (10.7 phenotypic SD) than for BLUP selection (11.8 phenotypic SD). It can be concluded that genomic selection without own phenotypes exploits new mutational variance less than BLUP selection with own phenotypes, it increases the probability of DNM with negative effects and it lowers selection limits. Sustainable breeding strategies should consider optimal ways to exploit DNM.

AB - De novo mutations (DNM) create new genetic variance and are an important driver for long-term selection response. We hypothesized that genomic selection without own phenotypes exploits new mutational variance less than pedigree-based BLUP selection. The objectives were to compare GBLUP selection without own phenotype (GBLUP), GBLUP selection with own phenotype (GBLUP_OP) and pedigree-based BLUP selection with own phenotype for 20 generations using Monte Carlo simulation. GBLUP resulted in the lowest genetic variance (24.7% of total genetic variance) and response due to DNM after 20 generations (9.4% of total response). GBLUP_OP had the highest genetic variance due to new DNM (47.8% of total genetic variance) and selection response due to DNM (30% of total response), while BLUP was in between with 27.1% of genetic variance due to DNM and 21.9% of response due to DNM. However, GBLUP_OP caused a rapid decline in total genetic variance, because the genetic variance due to old QTL rapidly eroded. GBLUP had very little selection pressure on DNM and as a consequence, GBLUP had the highest number of DNM with negative effects that were still segregating 10 generations after a DNM arose. Due to the decline in genetic variance for all selection strategies, selection limits are foreseen and these selection limits are lower for GBLUP (11.2 phenotypic SD from the base population mean) and GBLUP_OP (10.7 phenotypic SD) than for BLUP selection (11.8 phenotypic SD). It can be concluded that genomic selection without own phenotypes exploits new mutational variance less than BLUP selection with own phenotypes, it increases the probability of DNM with negative effects and it lowers selection limits. Sustainable breeding strategies should consider optimal ways to exploit DNM.

M3 - Abstract

SN - 9789086863396

T3 - Book of Abstracts

SP - 123

EP - 123

BT - Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science

PB - Wageningen Academic Publishers

CY - Wageningen

T2 - 70th Annual Meeting of the European Federation of Animal Science

Y2 - 25 August 2019 through 31 August 2019