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

Mario P.L. Calus*, Jérémie Vandenplas, Ina Hulsegge, Randy Borg, John M. Henshall, Rachel Hawken

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

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.

Original languageEnglish
Pages (from-to)6270-6280
Number of pages11
JournalPoultry Science
Volume98
Issue number12
DOIs
Publication statusPublished - 1 Dec 2019

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sires
purebreds
crossbreds
broiler chickens
alleles
breeds
parentage
natural mating
hens
animals
genotype
marker-assisted selection
pedigree
reproductive performance
haplotypes
genome
breeding
DNA

Keywords

  • breed-of-origin
  • broiler
  • crossbred
  • parentage

Cite this

@article{31f8f759cb5b483ba8cc3c9655fa7248,
title = "Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset",
abstract = "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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author = "Calus, {Mario P.L.} and J{\'e}r{\'e}mie Vandenplas and Ina Hulsegge and Randy Borg and Henshall, {John M.} and Rachel Hawken",
year = "2019",
month = "12",
day = "1",
doi = "10.3382/ps/pez458",
language = "English",
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pages = "6270--6280",
journal = "Poultry Science",
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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.

In: Poultry Science, Vol. 98, No. 12, 01.12.2019, p. 6270-6280.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset

AU - Calus, Mario P.L.

AU - Vandenplas, Jérémie

AU - Hulsegge, Ina

AU - Borg, Randy

AU - Henshall, John M.

AU - Hawken, Rachel

PY - 2019/12/1

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AB - 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.

KW - breed-of-origin

KW - broiler

KW - crossbred

KW - parentage

U2 - 10.3382/ps/pez458

DO - 10.3382/ps/pez458

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VL - 98

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JO - Poultry Science

JF - Poultry Science

SN - 0032-5791

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ER -