DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds

M.N. Aldridge; J. Marjanovic; John Henshall; B. de Klerk; K.L.M. Peeters; Y. de Haas

doi:10.3920/978-90-8686-940-4_182

DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds

M.N. Aldridge, J. Marjanovic, John Henshall, B. de Klerk, K.L.M. Peeters, Y. de Haas

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

Abstract

It is generally economically unviable to individually genotype large quantities of commercial crossbred broilers to predict purebred breeding values for crossbred performance. Pooling DNA of crossbreds with similar phenotypes, and genotyping the pool, could be a cost-effective alternative. To test this hypothesis, we used a dataset from a broiler three-way cross experiment consisting of ~9,000 individual genotypes and constructed pools of four different sizes (5, 10, 25, and 50 individuals). Estimated SNP effects and predicted sire breeding values from pooled genotypes were compared to results from individual genotypes, where number of individual genotypes was equal to number of pools. The pool size of 50 and 58 pools had a reasonable accuracy and bias (0.45 and 0.76, respectively) compared to 58 genotyped individuals (0.14 and 0.24). Our results indicate that DNA pooling may be used as a cost-effective means to obtain information on commercial crossbreds for selection in purebreds.

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	781-784
ISBN (Electronic)	9789086869404
DOIs	https://doi.org/10.3920/978-90-8686-940-4_182
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

Access to Document

10.3920/978-90-8686-940-4_182Licence: CC BY

https://edepot.wur.nl/587887Licence: CC BY

AF-16022 Breed4Food II (BO-63-001-009, BO-47-001-021, BO-22.04-025-001, BO-22.04-011-001, BO-22.02-011-001)
Veerkamp, R. (Project Leader)
1/01/14 → 31/12/21
Project: LVVN project

Cite this

Aldridge, M. N., Marjanovic, J., Henshall, J., de Klerk, B., Peeters, K. L. M., & de Haas, Y. (2022). DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds. 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. 781-784). Article 182 Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-940-4_182

Aldridge, M.N. ; Marjanovic, J. ; Henshall, John et al. / DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds. 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. 781-784

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title = "DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds",

abstract = "It is generally economically unviable to individually genotype large quantities of commercial crossbred broilers to predict purebred breeding values for crossbred performance. Pooling DNA of crossbreds with similar phenotypes, and genotyping the pool, could be a cost-effective alternative. To test this hypothesis, we used a dataset from a broiler three-way cross experiment consisting of ~9,000 individual genotypes and constructed pools of four different sizes (5, 10, 25, and 50 individuals). Estimated SNP effects and predicted sire breeding values from pooled genotypes were compared to results from individual genotypes, where number of individual genotypes was equal to number of pools. The pool size of 50 and 58 pools had a reasonable accuracy and bias (0.45 and 0.76, respectively) compared to 58 genotyped individuals (0.14 and 0.24). Our results indicate that DNA pooling may be used as a cost-effective means to obtain information on commercial crossbreds for selection in purebreds.",

author = "M.N. Aldridge and J. Marjanovic and John Henshall and {de Klerk}, B. and K.L.M. Peeters and {de Haas}, Y.",

year = "2022",

doi = "10.3920/978-90-8686-940-4_182",

language = "English",

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

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

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Aldridge, MN, Marjanovic, J, Henshall, J, de Klerk, B, Peeters, KLM & de Haas, Y 2022, DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds. 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., 182, Wageningen Academic Publishers, Wageningen, pp. 781-784, 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_182

DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds. / Aldridge, M.N.; Marjanovic, J.; Henshall, John 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. 781-784 182.

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

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AU - Aldridge, M.N.

AU - Marjanovic, J.

AU - Henshall, John

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AU - Peeters, K.L.M.

AU - de Haas, Y.

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N2 - It is generally economically unviable to individually genotype large quantities of commercial crossbred broilers to predict purebred breeding values for crossbred performance. Pooling DNA of crossbreds with similar phenotypes, and genotyping the pool, could be a cost-effective alternative. To test this hypothesis, we used a dataset from a broiler three-way cross experiment consisting of ~9,000 individual genotypes and constructed pools of four different sizes (5, 10, 25, and 50 individuals). Estimated SNP effects and predicted sire breeding values from pooled genotypes were compared to results from individual genotypes, where number of individual genotypes was equal to number of pools. The pool size of 50 and 58 pools had a reasonable accuracy and bias (0.45 and 0.76, respectively) compared to 58 genotyped individuals (0.14 and 0.24). Our results indicate that DNA pooling may be used as a cost-effective means to obtain information on commercial crossbreds for selection in purebreds.

AB - It is generally economically unviable to individually genotype large quantities of commercial crossbred broilers to predict purebred breeding values for crossbred performance. Pooling DNA of crossbreds with similar phenotypes, and genotyping the pool, could be a cost-effective alternative. To test this hypothesis, we used a dataset from a broiler three-way cross experiment consisting of ~9,000 individual genotypes and constructed pools of four different sizes (5, 10, 25, and 50 individuals). Estimated SNP effects and predicted sire breeding values from pooled genotypes were compared to results from individual genotypes, where number of individual genotypes was equal to number of pools. The pool size of 50 and 58 pools had a reasonable accuracy and bias (0.45 and 0.76, respectively) compared to 58 genotyped individuals (0.14 and 0.24). Our results indicate that DNA pooling may be used as a cost-effective means to obtain information on commercial crossbreds for selection in purebreds.

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A2 - Veerkamp, R.F.

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ER -

Aldridge MN, Marjanovic J, Henshall J, de Klerk B, Peeters KLM, de Haas Y. DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds. 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. 781-784. 182 doi: 10.3920/978-90-8686-940-4_182

DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds

Abstract

Conference/symposium

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Projects

AF-16022 Breed4Food II (BO-63-001-009, BO-47-001-021, BO-22.04-025-001, BO-22.04-011-001, BO-22.02-011-001)

Cite this