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Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset

Broiler breeding programs rely on crossbreeding. With genomic selection, widespread use of crossbred performance in breeding programs comes within reach. Commercial crossbreds, however, may have unknown pedigrees and their genomes may include DNA from 2 to 4 different breeds. Our aim was, for a broi...

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Autores principales: Calus, Mario P L, Vandenplas, Jérémie, Hulsegge, Ina, Borg, Randy, Henshall, John M, Hawken, Rachel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Poultry Science Association, Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6870559/
https://www.ncbi.nlm.nih.gov/pubmed/31393589
http://dx.doi.org/10.3382/ps/pez458
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author Calus, Mario P L
Vandenplas, Jérémie
Hulsegge, Ina
Borg, Randy
Henshall, John M
Hawken, Rachel
author_facet Calus, Mario P L
Vandenplas, Jérémie
Hulsegge, Ina
Borg, Randy
Henshall, John M
Hawken, Rachel
author_sort Calus, Mario P L
collection PubMed
description Broiler breeding programs rely on crossbreeding. With genomic selection, widespread use of crossbred performance in breeding programs comes within reach. Commercial crossbreds, however, may have unknown pedigrees and their genomes may include DNA from 2 to 4 different breeds. Our aim was, for a broiler dataset with a limited number of sires having both purebred and crossbred offspring generated using natural mating, to rapidly derive parentage, assess the distribution of the sire contribution to the offspring generation, and to assess breed-of-origin of alleles in crossbreds. The dataset contained genotypes for 56,075 SNPs for 5,882 purebred and 10,943 3-way crossbred offspring generated by natural mating of 164 purebred sires to 1,016 purebred and 1,386 F1 crossbred hens. Using our algorithm FindParents, joint parentage derivation for the offspring and parent generations required only 1 m 29 s to retrieve parentage for 20,253 animals considering 4,504 possible parents. FindParents was similarly accurate as a maximum likelihood based method, apart from situations where settings of FindParents did not match the genotyping error rate in the data. Numbers of offspring per sire had a very skewed distribution, ranging from 1 to 270 crossbreds and 1 to 154 purebreds. Derivation of breed-of-origin of alleles relied on phasing all genotypes, including 8,205, 372, and 720 animals from the 3 pure lines involved, and allocating haplotypes in the crossbreds to purebred lines based on observed frequencies in the purebred lines. Breed-of-origin could be derived for 96.94% of the alleles of the 1,386 F1 crossbred hens and for 91.88% of the alleles of the 10,943 3-way crossbred offspring, of which 49.49% to the sire line. The achieved percentage of assignment to the sire line was sufficient to proceed with subsequent analyses requiring only the breed-of-origin of the paternal alleles to be known. Although required number of animals may be population dependent, to increase the total percentage of assigned alleles, it seems advisable to use at least approx. 1,000 genotyped purebred animals for each of the lines involved.
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spelling pubmed-68705592019-11-27 Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset Calus, Mario P L Vandenplas, Jérémie Hulsegge, Ina Borg, Randy Henshall, John M Hawken, Rachel Poult Sci Genetics and Genomics Broiler breeding programs rely on crossbreeding. With genomic selection, widespread use of crossbred performance in breeding programs comes within reach. Commercial crossbreds, however, may have unknown pedigrees and their genomes may include DNA from 2 to 4 different breeds. Our aim was, for a broiler dataset with a limited number of sires having both purebred and crossbred offspring generated using natural mating, to rapidly derive parentage, assess the distribution of the sire contribution to the offspring generation, and to assess breed-of-origin of alleles in crossbreds. The dataset contained genotypes for 56,075 SNPs for 5,882 purebred and 10,943 3-way crossbred offspring generated by natural mating of 164 purebred sires to 1,016 purebred and 1,386 F1 crossbred hens. Using our algorithm FindParents, joint parentage derivation for the offspring and parent generations required only 1 m 29 s to retrieve parentage for 20,253 animals considering 4,504 possible parents. FindParents was similarly accurate as a maximum likelihood based method, apart from situations where settings of FindParents did not match the genotyping error rate in the data. Numbers of offspring per sire had a very skewed distribution, ranging from 1 to 270 crossbreds and 1 to 154 purebreds. Derivation of breed-of-origin of alleles relied on phasing all genotypes, including 8,205, 372, and 720 animals from the 3 pure lines involved, and allocating haplotypes in the crossbreds to purebred lines based on observed frequencies in the purebred lines. Breed-of-origin could be derived for 96.94% of the alleles of the 1,386 F1 crossbred hens and for 91.88% of the alleles of the 10,943 3-way crossbred offspring, of which 49.49% to the sire line. The achieved percentage of assignment to the sire line was sufficient to proceed with subsequent analyses requiring only the breed-of-origin of the paternal alleles to be known. Although required number of animals may be population dependent, to increase the total percentage of assigned alleles, it seems advisable to use at least approx. 1,000 genotyped purebred animals for each of the lines involved. Poultry Science Association, Inc. 2019-12 2019-08-08 /pmc/articles/PMC6870559/ /pubmed/31393589 http://dx.doi.org/10.3382/ps/pez458 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Poultry Science Association. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.
spellingShingle Genetics and Genomics
Calus, Mario P L
Vandenplas, Jérémie
Hulsegge, Ina
Borg, Randy
Henshall, John M
Hawken, Rachel
Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset
title Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset
title_full Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset
title_fullStr Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset
title_full_unstemmed Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset
title_short Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset
title_sort assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset
topic Genetics and Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6870559/
https://www.ncbi.nlm.nih.gov/pubmed/31393589
http://dx.doi.org/10.3382/ps/pez458
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