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

M N Aldridge; J Marjanovic; J M Henshall; B de Klerk; K 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
, J M Henshall
, B de Klerk
, K Peeters
, Y de Haas

Animal Genetics and Breeding Unit

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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)
Editors	R F Veerkamp, Y de Haas
Place of Publication	Wageningen, The Netherlands
Publisher	Wageningen Academic
Pages	781-784
ISBN (Print)	9789086869404
DOIs	https://doi.org/10.3920/978-90-8686-940-4_182
Publication status	Published - 31 Dec 2022
Event	WCGALP 2022: 12th World Congress on Genetics Applied to Livestock Production - De Doelen International Conference Center Rotterdam, Rotterdam, The Netherlands Duration: 3 Jul 2022 → 8 Jul 2022

Conference

Conference	WCGALP 2022: 12th World Congress on Genetics Applied to Livestock Production
City	Rotterdam, The Netherlands
Period	3/07/22 → 8/07/22

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https://hdl.handle.net/1959.11/59350

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Aldridge, M. N., Marjanovic, J., Henshall, J. M., de Klerk, B., Peeters, K., & 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. D. Haas (Eds.), Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP) (pp. 781-784). Article 182 Wageningen Academic. https://doi.org/10.3920/978-90-8686-940-4_182

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

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Aldridge, MN, Marjanovic, J, Henshall, JM, de Klerk, B, Peeters, K & de Haas, Y 2022, DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds. in RF Veerkamp & YD Haas (eds), Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)., 182, Wageningen Academic, Wageningen, The Netherlands, pp. 781-784, WCGALP 2022: 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, The 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, J M et al.
Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP). ed. / R F Veerkamp; Y de Haas. Wageningen, The Netherlands: Wageningen Academic, 2022. p. 781-784 182.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AU - Aldridge, M N

AU - Marjanovic, J

AU - Henshall, J M

AU - de Klerk, B

AU - Peeters, K

AU - de Haas, Y

PY - 2022/12/31

Y1 - 2022/12/31

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

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ER -

Aldridge MN, Marjanovic J, Henshall JM, de Klerk B, Peeters K, de Haas Y. DNA pooling is a cost effective method of including commercial crossbred data in selection of purebreds. In Veerkamp RF, Haas YD, editors, Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP). Wageningen, The Netherlands: Wageningen Academic. 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

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