Büttgen Lisa, Simianer Henner, Pook Torsten
Animal Breeding and Genetics Group, Department of Animal Sciences, Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany.
Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.
Genet Sel Evol. 2025 Apr 7;57(1):18. doi: 10.1186/s12711-025-00948-4.
Genomic selection has become an integral component of modern animal breeding programs, having the potential to improve the efficiency of layer breeding programs both by obtaining higher prediction accuracies and reducing the generation interval, particularly for males, who cannot be phenotyped for sex-limited traits such as laying performance. In the current study, we investigate different strategies to reduce the generation interval either for both sexes or only for the male side of the breeding scheme based on stochastic simulation using the software MoBPS. Additionally, prediction accuracies based on varying proportions of genotyping and phenotype- and pedigree-based selection as well as genomic breeding values are compared.
Selection of hens based on estimated breeding values, either pedigree-based or genomic, increased genetic gain compared to selection based on phenotypes only. The use of two time-shifted subpopulations with exchange of males between subpopulations to reduce the generation interval on the male side led to significantly higher genetic gains. Reducing the generation interval for both males and females was only efficient when population sizes were maintained, which result in doubling of the number of females to genotype and phenotype within the same time frame compared to the scenarios with the longer generation intervals. Although substantially higher gains were obtained by in particular pedigree-based selection of females and a reduction of generation intervals this led to substantially greater rates of inbreeding per year. The use of a genomic relationship matrix in breeding value estimation instead of a pedigree-based relationship matrix not only increased genetic gains but also reduced inbreeding rates. The use of optimum contribution selection led to basically the same genetic gains as without it but reduced inbreeding rates. However, overall differences obtained with optimal contribution selection were small compared to differences caused by the other effects that were considered.
The reduction of the generation interval on the male side by the use of genomic estimated breeding values was highly beneficial. Reduction of the generation interval on the female side was only beneficial when a high proportion of hens was genotyped and housing capacities were increased. On the female side of a layer breeding program, selection based on pedigree-based estimated breeding values was inferior to phenotypic selection, as it resulted in a substantial increase in inbreeding rates.
基因组选择已成为现代动物育种计划的一个组成部分，它有可能通过获得更高的预测准确性和缩短世代间隔来提高蛋鸡育种计划的效率，特别是对于雄性而言，因为它们无法针对产蛋性能等限性性状进行表型测定。在本研究中，我们使用软件MoBPS基于随机模拟研究了不同的策略，以缩短两性或仅育种方案中雄性一方的世代间隔。此外，还比较了基于不同比例的基因分型、基于表型和系谱的选择以及基因组育种值的预测准确性。
与仅基于表型的选择相比，基于系谱或基因组的估计育种值对母鸡进行选择可提高遗传进展。使用两个时间错开的亚群体并在亚群体之间交换雄性以缩短雄性一方的世代间隔，可显著提高遗传进展。只有在保持群体规模的情况下，缩短雌雄两性的世代间隔才有效，这导致与世代间隔较长的情况相比，在相同时间框架内需要进行基因分型和表型测定的雌性数量增加一倍。尽管特别是基于系谱的雌性选择和世代间隔的缩短获得了更高的进展，但这导致每年的近亲繁殖率大幅提高。在育种值估计中使用基因组关系矩阵而非基于系谱的关系矩阵，不仅提高了遗传进展，还降低了近亲繁殖率。使用最优贡献选择导致的遗传进展与不使用时基本相同，但降低了近亲繁殖率。然而，与所考虑的其他效应所导致的差异相比，最优贡献选择所获得的总体差异较小。
通过使用基因组估计育种值来缩短雄性一方的世代间隔非常有益。只有在对高比例的母鸡进行基因分型且饲养能力增加的情况下，缩短雌性一方的世代间隔才有益。在蛋鸡育种计划的雌性一方，基于系谱的估计育种值的选择不如表型选择，因为它导致近亲繁殖率大幅增加。
