In broiler breeding, genotype-by-environment interaction is known to result in a genetic correlation between body weight measured in bio-secure and commercial environments that is substantially less than 1. Thus, measuring body weights on sibs of selection candidates in a commercial environment and genotyping them could increase genetic progress. Using real data, the aim of this study was to evaluate which genotyping strategy and which proportion of sibs placed in the commercial environment should be genotyped to optimize a sib-testing breeding program in broilers. Phenotypic body weight and genomic information were collected on all sibs raised in a commercial environment, which allowed to retrospectively analyze different sampling strategies and genotyping proportions. Accuracies of genomic estimated breeding values (GEBV) obtained with the different genotyping strategies were assessed by computing their correlation with GEBV obtained when all sibs in the commercial environment were genotyped. Results showed that, compared to random sampling (RND), genotyping sibs with extreme phenotypes (EXT) resulted in higher GEBV accuracy across all genotyping proportions, especially for genotyping proportions of 12.5% or 25%, which resulted in correlations of 0.91 vs 0.88 for 12.5% and 0.94 vs 0.91 for 25% genotyped. Including pedigree on birds with phenotype in the commercial environment that were not genotyped increased accuracy at lower genotyping proportions, especially for the RND strategy (correlations of 0.88 vs 0.65 at 12.5% and 0.91 vs 0.80 at 25%), and a smaller but still substantial increase in accuracy for the EXT strategy (0.91 vs 0.79 for 12.5% and 0.94 vs 0.88 for 25% genotyped). Dispersion bias was virtually absent for RND if 25% or more birds were genotyped. However, GEBV were considerably inflated for EXT, especially when the proportion genotyped was low, which was further exacerbated if the pedigree of non-genotyped sibs was excluded. When less than 75% of all animals placed in a commercial environment are genotyped, it is recommended to use the EXT strategy, because it yields the highest accuracy. However, caution should be taken when interpreting the resulting GEBV because they will be over-dispersed. When 75% or more of the animals are genotyped, random sampling is recommended because it yields virtually no bias of GEBV and results in similar accuracies as the EXT strategy.

中文翻译：

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肉种鸡计划同胞测试方案的选择性基因分型策略

在肉鸡育种中，已知基因型与环境的相互作用会导致在生物安全环境和商业环境中测得的体重之间的遗传相关性大大小于 1。因此，在商业环境中测量候选者同胞的体重并对它们进行基因分型可以增加遗传进展。使用真实数据，本研究的目的是评估哪种基因分型策略以及商业环境中的同胞比例应该进行基因分型，以优化肉鸡的同胞测试育种计划。收集了在商业环境中饲养的所有同胞的表型体重和基因组信息，从而可以回顾性分析不同的采样策略和基因分型比例。通过计算它们与商业环境中所有同胞进行基因分型时获得的 GEBV 的相关性，评估了使用不同基因分型策略获得的基因组估计育种值 (GEBV) 的准确性。结果表明，与随机抽样 (RND) 相比，具有极端表型 (EXT) 的基因分型同胞在所有基因分型比例中均具有更高的 GEBV 准确性，尤其是对于 12.5% 或 25% 的基因分型比例，这导致 0.91 与 0.88 的相关性12.5% 和 0.94 对比 25% 基因分型的 0.91。包括在商业环境中具有表型但未进行基因分型的鸟类的谱系提高了较低基因分型比例的准确性，特别是对于 RND 策略（相关性 0.88 对 0.65 在 12.5% 和 0.91 对 0.80 在 25%），并且 EXT 策略的准确性有较小但仍然显着的提高（0.91 对 12.5% 的 0.79 和 0.94 对 25% 基因分型的 0.88）。如果对 25% 或更多的鸟类进行基因分型，则 RND 几乎不存在离散偏差。然而，GEBV 因 EXT 而显着膨胀，尤其是当基因分型比例较低时，如果排除非基因分型同胞的家系，这种情况会进一步加剧。当放置在商业环境中的所有动物中只有不到 75% 被基因分型时，建议使用 EXT 策略，因为它产生的准确性最高。但是，在解释生成的 GEBV 时应谨慎，因为它们会过度分散。当 75% 或更多的动物进行基因分型时，建议进行随机抽样，因为它几乎不会产生 GEBV 偏差，并且会产生与 EXT 策略相似的准确性。