Benefits of testing in both bio-secure and production environments in genomic selection breeding programs for commercial broiler chicken

Thinh T. Chu, Setegn W. Alemu, Elise Norberg, Anders C. Sørensen, John Henshall, Rachel Hawken, Just Jensen

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

Background: A breeding program for commercial broiler chicken that is carried out under strict biosecure conditions can show reduced genetic gain due to genotype by environment interactions (G × E) between bio-secure (B) and commercial production (C) environments. Accuracy of phenotype-based best linear unbiased prediction of breeding values of selection candidates using sib-testing in C is low. Genomic prediction based on dense genetic markers may improve accuracy of selection. Stochastic simulation was used to explore the benefits of genomic selection in breeding schemes for broiler chicken that include birds in both B and C for assessment of phenotype. Results: When genetic correlations (r-{g} r g) between traits measured in B and C were equal to 0.5 and 0.7, breeding schemes with 15, 30 and 45% of birds assessed in C resulted in higher genetic gain for performance in C compared to those without birds in C. The optimal proportion of birds phenotyped in C for genetic gain was 30%. When the proportion of birds in C was optimal and genotyping effort was limited, allocating 30% of the genotyping effort to birds in C was also the optimal genotyping strategy for genetic gain. When r-{g} r g was equal to 0.9, genetic gain for performance in C was not improved with birds in C compared to schemes without birds in C. Increasing the heritability of traits assessed in C increased genetic gain significantly. Rates of inbreeding decreased when the proportion of birds in C increased because of a lower selection intensity among birds retained in B and a reduction in the probability of co-selecting close relatives. Conclusions: If G × E interactions (r-{g} r g of 0.5 and 0.7) are strong, a genomic selection scheme in which 30% of the birds hatched are phenotyped in C has larger genetic gain for performance in C compared to phenotyping all birds in B. Rates of inbreeding decreased as the proportion of birds moved to C increased from 15 to 45%.

LanguageEnglish
Article number52
JournalGenetics Selection Evolution
Volume50
Issue number1
DOIs
Publication statusPublished - 3 Nov 2018

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marker-assisted selection
Birds
Breeding
Chickens
genomics
broiler chickens
breeding
bird
birds
genetic improvement
testing
genotyping
Inbreeding
inbreeding
phenotype
programme
Phenotype
selection intensity
Tocopherols
prediction

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Chu, Thinh T. ; Alemu, Setegn W. ; Norberg, Elise ; Sørensen, Anders C. ; Henshall, John ; Hawken, Rachel ; Jensen, Just. / Benefits of testing in both bio-secure and production environments in genomic selection breeding programs for commercial broiler chicken. In: Genetics Selection Evolution. 2018 ; Vol. 50, No. 1.
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title = "Benefits of testing in both bio-secure and production environments in genomic selection breeding programs for commercial broiler chicken",
abstract = "Background: A breeding program for commercial broiler chicken that is carried out under strict biosecure conditions can show reduced genetic gain due to genotype by environment interactions (G × E) between bio-secure (B) and commercial production (C) environments. Accuracy of phenotype-based best linear unbiased prediction of breeding values of selection candidates using sib-testing in C is low. Genomic prediction based on dense genetic markers may improve accuracy of selection. Stochastic simulation was used to explore the benefits of genomic selection in breeding schemes for broiler chicken that include birds in both B and C for assessment of phenotype. Results: When genetic correlations (r-{g} r g) between traits measured in B and C were equal to 0.5 and 0.7, breeding schemes with 15, 30 and 45{\%} of birds assessed in C resulted in higher genetic gain for performance in C compared to those without birds in C. The optimal proportion of birds phenotyped in C for genetic gain was 30{\%}. When the proportion of birds in C was optimal and genotyping effort was limited, allocating 30{\%} of the genotyping effort to birds in C was also the optimal genotyping strategy for genetic gain. When r-{g} r g was equal to 0.9, genetic gain for performance in C was not improved with birds in C compared to schemes without birds in C. Increasing the heritability of traits assessed in C increased genetic gain significantly. Rates of inbreeding decreased when the proportion of birds in C increased because of a lower selection intensity among birds retained in B and a reduction in the probability of co-selecting close relatives. Conclusions: If G × E interactions (r-{g} r g of 0.5 and 0.7) are strong, a genomic selection scheme in which 30{\%} of the birds hatched are phenotyped in C has larger genetic gain for performance in C compared to phenotyping all birds in B. Rates of inbreeding decreased as the proportion of birds moved to C increased from 15 to 45{\%}.",
author = "Chu, {Thinh T.} and Alemu, {Setegn W.} and Elise Norberg and S{\o}rensen, {Anders C.} and John Henshall and Rachel Hawken and Just Jensen",
year = "2018",
month = "11",
day = "3",
doi = "10.1186/s12711-018-0430-x",
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Benefits of testing in both bio-secure and production environments in genomic selection breeding programs for commercial broiler chicken. / Chu, Thinh T.; Alemu, Setegn W.; Norberg, Elise; Sørensen, Anders C.; Henshall, John; Hawken, Rachel; Jensen, Just.

In: Genetics Selection Evolution, Vol. 50, No. 1, 52, 03.11.2018.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Benefits of testing in both bio-secure and production environments in genomic selection breeding programs for commercial broiler chicken

AU - Chu, Thinh T.

AU - Alemu, Setegn W.

AU - Norberg, Elise

AU - Sørensen, Anders C.

AU - Henshall, John

AU - Hawken, Rachel

AU - Jensen, Just

PY - 2018/11/3

Y1 - 2018/11/3

N2 - Background: A breeding program for commercial broiler chicken that is carried out under strict biosecure conditions can show reduced genetic gain due to genotype by environment interactions (G × E) between bio-secure (B) and commercial production (C) environments. Accuracy of phenotype-based best linear unbiased prediction of breeding values of selection candidates using sib-testing in C is low. Genomic prediction based on dense genetic markers may improve accuracy of selection. Stochastic simulation was used to explore the benefits of genomic selection in breeding schemes for broiler chicken that include birds in both B and C for assessment of phenotype. Results: When genetic correlations (r-{g} r g) between traits measured in B and C were equal to 0.5 and 0.7, breeding schemes with 15, 30 and 45% of birds assessed in C resulted in higher genetic gain for performance in C compared to those without birds in C. The optimal proportion of birds phenotyped in C for genetic gain was 30%. When the proportion of birds in C was optimal and genotyping effort was limited, allocating 30% of the genotyping effort to birds in C was also the optimal genotyping strategy for genetic gain. When r-{g} r g was equal to 0.9, genetic gain for performance in C was not improved with birds in C compared to schemes without birds in C. Increasing the heritability of traits assessed in C increased genetic gain significantly. Rates of inbreeding decreased when the proportion of birds in C increased because of a lower selection intensity among birds retained in B and a reduction in the probability of co-selecting close relatives. Conclusions: If G × E interactions (r-{g} r g of 0.5 and 0.7) are strong, a genomic selection scheme in which 30% of the birds hatched are phenotyped in C has larger genetic gain for performance in C compared to phenotyping all birds in B. Rates of inbreeding decreased as the proportion of birds moved to C increased from 15 to 45%.

AB - Background: A breeding program for commercial broiler chicken that is carried out under strict biosecure conditions can show reduced genetic gain due to genotype by environment interactions (G × E) between bio-secure (B) and commercial production (C) environments. Accuracy of phenotype-based best linear unbiased prediction of breeding values of selection candidates using sib-testing in C is low. Genomic prediction based on dense genetic markers may improve accuracy of selection. Stochastic simulation was used to explore the benefits of genomic selection in breeding schemes for broiler chicken that include birds in both B and C for assessment of phenotype. Results: When genetic correlations (r-{g} r g) between traits measured in B and C were equal to 0.5 and 0.7, breeding schemes with 15, 30 and 45% of birds assessed in C resulted in higher genetic gain for performance in C compared to those without birds in C. The optimal proportion of birds phenotyped in C for genetic gain was 30%. When the proportion of birds in C was optimal and genotyping effort was limited, allocating 30% of the genotyping effort to birds in C was also the optimal genotyping strategy for genetic gain. When r-{g} r g was equal to 0.9, genetic gain for performance in C was not improved with birds in C compared to schemes without birds in C. Increasing the heritability of traits assessed in C increased genetic gain significantly. Rates of inbreeding decreased when the proportion of birds in C increased because of a lower selection intensity among birds retained in B and a reduction in the probability of co-selecting close relatives. Conclusions: If G × E interactions (r-{g} r g of 0.5 and 0.7) are strong, a genomic selection scheme in which 30% of the birds hatched are phenotyped in C has larger genetic gain for performance in C compared to phenotyping all birds in B. Rates of inbreeding decreased as the proportion of birds moved to C increased from 15 to 45%.

U2 - 10.1186/s12711-018-0430-x

DO - 10.1186/s12711-018-0430-x

M3 - Article

VL - 50

JO - Genetics, Selection, Evolution

T2 - Genetics, Selection, Evolution

JF - Genetics, Selection, Evolution

SN - 0999-193X

IS - 1

M1 - 52

ER -