Plieschke Laura, Edel Christian, Pimentel Eduardo C G, Emmerling Reiner, Bennewitz Jörn, Götz Kay-Uwe
Bavarian State Research Center for Agriculture, Institute of Animal Breeding, Prof.-Dürrwaechter-Platz 1, 85586, Poing-Grub, Germany.
Institute of Animal Science, University Hohenheim, Garbenstraße 17, 70599, Stuttgart, Germany.
Genet Sel Evol. 2016 Sep 28;48(1):73. doi: 10.1186/s12711-016-0250-9.
Extending the reference set for genomic predictions in dairy cattle by adding large numbers of cows with genotypes and phenotypes has been proposed as a means to increase reliability of selection decisions for candidates.
In this study, we explored the potential of increasing the reliability of breeding values of young selection candidates by genotyping a fixed number of first-crop daughters of each sire from one or two generations in a balanced and regular system of genotyping. Using stochastic simulation, we developed a basic population scenario that mimics the situation in dual-purpose Fleckvieh cattle with respect to important key parameters. Starting with a reference set consisting of only genotyped bulls, we extended this reference set by including increasing numbers of daughter genotypes and phenotypes. We studied the effects on model-derived reliabilities, validation reliabilities and unbiasedness of predicted values for selection candidates. We also illustrate and discuss the effects of a selected sample and an unbalanced sampling of daughters. Furthermore, we quantified the role of selection with respect to the influence on validation reliabilities and contrasted these to model-derived reliabilities.
In the most extended design, with 200 daughters per sire genotyped from two generations, single nucleotide polymorphism (SNP) effects were estimated from a reference set of 420,000 cows and 4200 bulls. For this design, the validation reliabilities for candidates reached 80 % or more, thereby exceeding the reliabilities that were achieved in traditional progeny-testing designs for a trait with moderate to high heritability. We demonstrate that even a moderate number of 25 genotyped daughters per sire will lead to considerable improvement in the reliability of predicted breeding values for selection candidates. Our results illustrate that the strategy applied to sample females for genotyping has a large impact on the benefits that can be achieved.
通过添加大量具有基因型和表型的奶牛来扩展奶牛基因组预测的参考集，已被提议作为提高候选个体选择决策可靠性的一种方法。
在本研究中，我们探索了通过在平衡且规则的基因分型系统中对一代或两代中每个父系的固定数量的头胎女儿进行基因分型，来提高年轻选择候选个体育种值可靠性的潜力。使用随机模拟，我们开发了一个基本群体情景，该情景在重要关键参数方面模拟了兼用型弗莱维赫牛的情况。从仅由基因分型公牛组成的参考集开始，我们通过纳入越来越多的女儿基因型和表型来扩展这个参考集。我们研究了对模型推导的可靠性、验证可靠性以及选择候选个体预测值的无偏性的影响。我们还举例说明了并讨论了所选样本和女儿的不平衡抽样的影响。此外，我们量化了选择在对验证可靠性的影响方面的作用，并将其与模型推导的可靠性进行对比。
在最扩展的设计中，每个父系有来自两代的200个女儿进行基因分型，单核苷酸多态性（SNP）效应是从420,000头母牛和4200头公牛的参考集中估计出来的。对于这种设计，候选个体的验证可靠性达到80%或更高，从而超过了传统后裔测试设计中对于中等到高遗传力性状所达到的可靠性。我们证明，即使每个父系有适度数量的25个基因分型女儿，也将导致选择候选个体预测育种值的可靠性有相当大的提高。我们的结果表明，应用于对雌性进行基因分型抽样策略对所能实现的效益有很大影响。
