On the use of SNPs of large effect to improve prediction accuracy in pigs

M.S. Lopes; M. Derks; M. van Son; A.B. Gjuvsland; C.A. Sevillano; E. Grindflek; E.F. Knol

doi:10.3920/978-90-8686-940-4_282

On the use of SNPs of large effect to improve prediction accuracy in pigs

M.S. Lopes, M. Derks, M. van Son, A.B. Gjuvsland, C.A. Sevillano, E. Grindflek, E.F. Knol

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

Abstract

The aim of this study was to develop a strategy for selecting SNPs that could receive higher weight than other SNPs in a GBLUP approach due to their expected association with important pig phenotypes. In addition, we aimed to investigate if such a strategy yields improved prediction accuracy compared to a traditional GBLUP approach. Four prediction accuracy scenarios were evaluated using three production traits in two pig populations. Our results show that adding extra weight to SNPs that are expected to be (close to) causal variants in the G matrix increases the prediction accuracy of genomic prediction. The advantage of weighted G matrix compared to a traditional one is not very large, but the added value is consistent.

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	1189-1192
ISBN (Electronic)	9789086869404
DOIs	https://doi.org/10.3920/978-90-8686-940-4_282
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

Access to Document

10.3920/978-90-8686-940-4_282Licence: CC BY

https://edepot.wur.nl/588178Licence: CC BY

Cite this

Lopes, M. S., Derks, M., van Son, M., Gjuvsland, A. B., Sevillano, C. A., Grindflek, E., & Knol, E. F. (2022). On the use of SNPs of large effect to improve prediction accuracy in pigs. 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. 1189-1192). Article 282 Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-940-4_282

Lopes, M.S. ; Derks, M. ; van Son, M. et al. / On the use of SNPs of large effect to improve prediction accuracy in pigs. 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. 1189-1192

@inproceedings{62487cc4c8134156825787f5ff92a583,

title = "On the use of SNPs of large effect to improve prediction accuracy in pigs",

abstract = "The aim of this study was to develop a strategy for selecting SNPs that could receive higher weight than other SNPs in a GBLUP approach due to their expected association with important pig phenotypes. In addition, we aimed to investigate if such a strategy yields improved prediction accuracy compared to a traditional GBLUP approach. Four prediction accuracy scenarios were evaluated using three production traits in two pig populations. Our results show that adding extra weight to SNPs that are expected to be (close to) causal variants in the G matrix increases the prediction accuracy of genomic prediction. The advantage of weighted G matrix compared to a traditional one is not very large, but the added value is consistent.",

author = "M.S. Lopes and M. Derks and {van Son}, M. and A.B. Gjuvsland and C.A. Sevillano and E. Grindflek and E.F. Knol",

year = "2022",

doi = "10.3920/978-90-8686-940-4_282",

language = "English",

pages = "1189--1192",

editor = "R.F. Veerkamp and {de Haas}, Y.",

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

publisher = "Wageningen Academic Publishers",

address = "Netherlands",

note = "World Congress on Genetics Applied to Livestock Production: WCGALP 2022 ; Conference date: 03-07-2022 Through 08-07-2022",

}

Lopes, MS, Derks, M, van Son, M, Gjuvsland, AB, Sevillano, CA, Grindflek, E & Knol, EF 2022, On the use of SNPs of large effect to improve prediction accuracy in pigs. 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., 282, Wageningen Academic Publishers, Wageningen, pp. 1189-1192, 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_282

On the use of SNPs of large effect to improve prediction accuracy in pigs. / Lopes, M.S.; Derks, M.; van Son, M. 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. 1189-1192 282.

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

TY - GEN

T1 - On the use of SNPs of large effect to improve prediction accuracy in pigs

AU - Lopes, M.S.

AU - Derks, M.

AU - van Son, M.

AU - Gjuvsland, A.B.

AU - Sevillano, C.A.

AU - Grindflek, E.

AU - Knol, E.F.

PY - 2022

Y1 - 2022

N2 - The aim of this study was to develop a strategy for selecting SNPs that could receive higher weight than other SNPs in a GBLUP approach due to their expected association with important pig phenotypes. In addition, we aimed to investigate if such a strategy yields improved prediction accuracy compared to a traditional GBLUP approach. Four prediction accuracy scenarios were evaluated using three production traits in two pig populations. Our results show that adding extra weight to SNPs that are expected to be (close to) causal variants in the G matrix increases the prediction accuracy of genomic prediction. The advantage of weighted G matrix compared to a traditional one is not very large, but the added value is consistent.

AB - The aim of this study was to develop a strategy for selecting SNPs that could receive higher weight than other SNPs in a GBLUP approach due to their expected association with important pig phenotypes. In addition, we aimed to investigate if such a strategy yields improved prediction accuracy compared to a traditional GBLUP approach. Four prediction accuracy scenarios were evaluated using three production traits in two pig populations. Our results show that adding extra weight to SNPs that are expected to be (close to) causal variants in the G matrix increases the prediction accuracy of genomic prediction. The advantage of weighted G matrix compared to a traditional one is not very large, but the added value is consistent.

U2 - 10.3920/978-90-8686-940-4_282

DO - 10.3920/978-90-8686-940-4_282

M3 - Conference paper

SP - 1189

EP - 1192

BT - Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)

A2 - Veerkamp, R.F.

A2 - de Haas, Y.

PB - Wageningen Academic Publishers

CY - Wageningen

T2 - World Congress on Genetics Applied to Livestock Production: WCGALP 2022

Y2 - 3 July 2022 through 8 July 2022

ER -

Lopes MS, Derks M, van Son M, Gjuvsland AB, Sevillano CA, Grindflek E et al. On the use of SNPs of large effect to improve prediction accuracy in pigs. 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. 1189-1192. 282 doi: 10.3920/978-90-8686-940-4_282

On the use of SNPs of large effect to improve prediction accuracy in pigs

Abstract

Conference

Access to Document

Fingerprint

Cite this