Accuracy of genomic estimated breeding values for crossbred performance in broilers using a purebred or crossbred reference population

P. Duenk, M.P.L. Calus, Y.C.J. Wientjes, Vivian Breen, John Henshall, Rachel Hawken, P. Bijma

Research output: Chapter in Book/Report/Conference proceedingConference paper

Abstract

In breeding programs of pigs and poultry, selection is typically applied at the level of the purebred (PB) animals using PB data. This may result in a suboptimal response at the crossbred (CB) level when the genetic correlation between PB and CB performance () is lower than one. The objectives of this study, therefore, were to (1) estimate the , and (2) compare the accuracy of genomic estimated breeding values (GEBVs) for CB body weight in broilers using a PB reference population (RP) or a CB RP. Phenotype and genotype data were available for 5,274 PB and 10,395 CB offspring, and genotype data for their 163 PB sires. For comparison of cross-validation (CV) GEBV accuracies, the size of the CB RP was reduced to approximately match the size of the PB RP. Because the number of sires was
limited, validation was also performed on GEBVs of CB offspring of the sires. The estimated was 0.94 (0.04). The results show that the accuracy of sire GEBVs was slightly higher with a CB RP (0.43) compared to a PB RP (0.40). Similarly, the accuracy of CB offspring GEBVs was higher with a CB RP (0.47) compared to a PB RP (0.25). These results are likely due to (1) the that is lower than one, and (2) differences in genomic relationships between reference and validation animals. In finalizing this work, we will develop an equation that uses the accuracy of CB GEBVs for CB performance to predict the accuracy of PB GEBVs for CB
performance.
Original languageEnglish
Title of host publicationProceedings of the 11th World Congress on Genetics Applied to Livestock Production
Subtitle of host publication Volume Methods and Tools - Prediction 3
PublisherWCGALP
Number of pages5
Publication statusPublished - 11 Feb 2018
EventWorld Congress on Genetics Applied to Livestock Production - Auckland, New Zealand
Duration: 11 Feb 201816 Feb 2018

Conference

ConferenceWorld Congress on Genetics Applied to Livestock Production
Abbreviated titleWCGALP 2018
CountryNew Zealand
CityAuckland
Period11/02/1816/02/18

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purebreds
breeding value
crossbreds
broiler chickens
genomics
sires
genotype
genetic correlation
animals
poultry
phenotype

Cite this

Duenk, P., Calus, M. P. L., Wientjes, Y. C. J., Breen, V., Henshall, J., Hawken, R., & Bijma, P. (2018). Accuracy of genomic estimated breeding values for crossbred performance in broilers using a purebred or crossbred reference population. In Proceedings of the 11th World Congress on Genetics Applied to Livestock Production: Volume Methods and Tools - Prediction 3 [220] WCGALP.
Duenk, P. ; Calus, M.P.L. ; Wientjes, Y.C.J. ; Breen, Vivian ; Henshall, John ; Hawken, Rachel ; Bijma, P. / Accuracy of genomic estimated breeding values for crossbred performance in broilers using a purebred or crossbred reference population. Proceedings of the 11th World Congress on Genetics Applied to Livestock Production: Volume Methods and Tools - Prediction 3. WCGALP, 2018.
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abstract = "In breeding programs of pigs and poultry, selection is typically applied at the level of the purebred (PB) animals using PB data. This may result in a suboptimal response at the crossbred (CB) level when the genetic correlation between PB and CB performance () is lower than one. The objectives of this study, therefore, were to (1) estimate the , and (2) compare the accuracy of genomic estimated breeding values (GEBVs) for CB body weight in broilers using a PB reference population (RP) or a CB RP. Phenotype and genotype data were available for 5,274 PB and 10,395 CB offspring, and genotype data for their 163 PB sires. For comparison of cross-validation (CV) GEBV accuracies, the size of the CB RP was reduced to approximately match the size of the PB RP. Because the number of sires waslimited, validation was also performed on GEBVs of CB offspring of the sires. The estimated was 0.94 (0.04). The results show that the accuracy of sire GEBVs was slightly higher with a CB RP (0.43) compared to a PB RP (0.40). Similarly, the accuracy of CB offspring GEBVs was higher with a CB RP (0.47) compared to a PB RP (0.25). These results are likely due to (1) the that is lower than one, and (2) differences in genomic relationships between reference and validation animals. In finalizing this work, we will develop an equation that uses the accuracy of CB GEBVs for CB performance to predict the accuracy of PB GEBVs for CBperformance.",
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Duenk, P, Calus, MPL, Wientjes, YCJ, Breen, V, Henshall, J, Hawken, R & Bijma, P 2018, Accuracy of genomic estimated breeding values for crossbred performance in broilers using a purebred or crossbred reference population. in Proceedings of the 11th World Congress on Genetics Applied to Livestock Production: Volume Methods and Tools - Prediction 3., 220, WCGALP, World Congress on Genetics Applied to Livestock Production, Auckland, New Zealand, 11/02/18.

Accuracy of genomic estimated breeding values for crossbred performance in broilers using a purebred or crossbred reference population. / Duenk, P.; Calus, M.P.L.; Wientjes, Y.C.J.; Breen, Vivian; Henshall, John; Hawken, Rachel; Bijma, P.

Proceedings of the 11th World Congress on Genetics Applied to Livestock Production: Volume Methods and Tools - Prediction 3. WCGALP, 2018. 220.

Research output: Chapter in Book/Report/Conference proceedingConference paper

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AU - Calus, M.P.L.

AU - Wientjes, Y.C.J.

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AU - Henshall, John

AU - Hawken, Rachel

AU - Bijma, P.

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N2 - In breeding programs of pigs and poultry, selection is typically applied at the level of the purebred (PB) animals using PB data. This may result in a suboptimal response at the crossbred (CB) level when the genetic correlation between PB and CB performance () is lower than one. The objectives of this study, therefore, were to (1) estimate the , and (2) compare the accuracy of genomic estimated breeding values (GEBVs) for CB body weight in broilers using a PB reference population (RP) or a CB RP. Phenotype and genotype data were available for 5,274 PB and 10,395 CB offspring, and genotype data for their 163 PB sires. For comparison of cross-validation (CV) GEBV accuracies, the size of the CB RP was reduced to approximately match the size of the PB RP. Because the number of sires waslimited, validation was also performed on GEBVs of CB offspring of the sires. The estimated was 0.94 (0.04). The results show that the accuracy of sire GEBVs was slightly higher with a CB RP (0.43) compared to a PB RP (0.40). Similarly, the accuracy of CB offspring GEBVs was higher with a CB RP (0.47) compared to a PB RP (0.25). These results are likely due to (1) the that is lower than one, and (2) differences in genomic relationships between reference and validation animals. In finalizing this work, we will develop an equation that uses the accuracy of CB GEBVs for CB performance to predict the accuracy of PB GEBVs for CBperformance.

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M3 - Conference paper

BT - Proceedings of the 11th World Congress on Genetics Applied to Livestock Production

PB - WCGALP

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Duenk P, Calus MPL, Wientjes YCJ, Breen V, Henshall J, Hawken R et al. Accuracy of genomic estimated breeding values for crossbred performance in broilers using a purebred or crossbred reference population. In Proceedings of the 11th World Congress on Genetics Applied to Livestock Production: Volume Methods and Tools - Prediction 3. WCGALP. 2018. 220