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

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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 ( rg ) 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 rg 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 ( rg 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%.
Original languageEnglish
Article number52
JournalGenetics Selection Evolution
Volume50
Number of pages13
ISSN0999-193X
DOIs
Publication statusPublished - 3 Nov 2018

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