Evaluating the suitability of subjectively defined base populations

J. ten Napel; J. Vandenplas; M. Calus; I. Strandén; M. Lidauer; R. Veerkamp

doi:10.3920/978-90-8686-940-4_327

Evaluating the suitability of subjectively defined base populations

J. ten Napel, J. Vandenplas, M. Calus, I. Strandén, M. Lidauer, R. Veerkamp

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

Abstract

Defining multiple base populations for a genetic evaluation is subjective and there is generally no feedback on the suitability of the defined base populations prior to model validation. We present a number of statistics that can be used to evaluate defined base populations. Application of these statistics to one simulated and two practical datasets showed that in practical datasets the number of base animals per base population was in one case very low. In many cases the available genotype information for different base populations was coming from exactly the same genotyped animals. Both issues are likely to complicate genomic evaluation. A tool to estimate these statistics is available in the MiXBLUP software suite.

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	1372-1375
ISBN (Electronic)	9789086869404
DOIs	https://doi.org/10.3920/978-90-8686-940-4_327
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/symposium

Conference/symposium	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_327Licence: CC BY

https://edepot.wur.nl/588147Licence: CC BY

Cite this

ten Napel, J., Vandenplas, J., Calus, M., Strandén, I., Lidauer, M., & Veerkamp, R. (2022). Evaluating the suitability of subjectively defined base populations. 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. 1372-1375). Article 327 Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-940-4_327

ten Napel, J. ; Vandenplas, J. ; Calus, M. et al. / Evaluating the suitability of subjectively defined base populations. 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. 1372-1375

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title = "Evaluating the suitability of subjectively defined base populations",

abstract = "Defining multiple base populations for a genetic evaluation is subjective and there is generally no feedback on the suitability of the defined base populations prior to model validation. We present a number of statistics that can be used to evaluate defined base populations. Application of these statistics to one simulated and two practical datasets showed that in practical datasets the number of base animals per base population was in one case very low. In many cases the available genotype information for different base populations was coming from exactly the same genotyped animals. Both issues are likely to complicate genomic evaluation. A tool to estimate these statistics is available in the MiXBLUP software suite.",

author = "{ten Napel}, J. and J. Vandenplas and M. Calus and I. Strand{\'e}n and M. Lidauer and R. Veerkamp",

year = "2022",

doi = "10.3920/978-90-8686-940-4_327",

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pages = "1372--1375",

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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",

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ten Napel, J , Vandenplas, J , Calus, M, Strandén, I, Lidauer, M & Veerkamp, R 2022, Evaluating the suitability of subjectively defined base populations. 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., 327, Wageningen Academic Publishers, Wageningen, pp. 1372-1375, 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_327

Evaluating the suitability of subjectively defined base populations. / ten Napel, J.; Vandenplas, J.; Calus, 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. 1372-1375 327.

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

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AB - Defining multiple base populations for a genetic evaluation is subjective and there is generally no feedback on the suitability of the defined base populations prior to model validation. We present a number of statistics that can be used to evaluate defined base populations. Application of these statistics to one simulated and two practical datasets showed that in practical datasets the number of base animals per base population was in one case very low. In many cases the available genotype information for different base populations was coming from exactly the same genotyped animals. Both issues are likely to complicate genomic evaluation. A tool to estimate these statistics is available in the MiXBLUP software suite.

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ten Napel J , Vandenplas J , Calus M, Strandén I, Lidauer M, Veerkamp R. Evaluating the suitability of subjectively defined base populations. 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. 1372-1375. 327 doi: 10.3920/978-90-8686-940-4_327

Evaluating the suitability of subjectively defined base populations

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