Functional Breeding - Genetik und züchterische Verbesserung funktionaler Merkmale, GAU, Göttingen, Germany.
Biometrie, Vereinigte Informationssysteme Tierhaltung w.V., Verden, Germany.
J Anim Breed Genet. 2023 Sep;140(5):496-507. doi: 10.1111/jbg.12774. Epub 2023 Apr 16.
The implementation of genomic selection for six German beef cattle populations was evaluated. Although the multiple-step implementation of genomic selection is the status quo in most national dairy cattle evaluations, the breeding structure of German beef cattle, coupled with the shortcoming and complexity of the multiple-step method, makes single step a more attractive option to implement genomic selection in German beef cattle populations. Our objective was to develop a national beef cattle single-step genomic evaluation in five economically important traits in six German beef cattle populations and investigate its impact on the accuracy and bias of genomic evaluations relative to the current pedigree-based evaluation. Across the six breeds in our study, 461,929 phenotyped and 14,321 genotyped animals were evaluated with a multi-trait single-step model. To validate the single-step model, phenotype data in the last 2 years were removed in a forward validation study. For the conventional and single-step approaches, the genomic estimated breeding values of validation animals and other animals were compared between the truncated and the full evaluations. The correlation of the GEBVs between the full and truncated evaluations in the validation animals was slightly higher in the single-step evaluation. The regression of the full GEBVs on truncated GEBVs was close to the optimal value of 1 for both the pedigree-based and the single-step evaluations. The SNP effect estimates from the truncated evaluation were highly correlated with those from the full evaluation, with values ranging from 0.79 to 0.94. The correlation of the SNP effect was influenced by the number of genotyped animals shared between the full and truncated evaluations. The regression coefficients of the SNP effect of the full evaluation on the truncated evaluation were all close to the expected value of 1, indicating unbiased estimates of the SNP markers for the production traits. The Manhattan plot of the SNP effect estimates identified chromosomal regions harbouring major genes for muscling and body weight in breeds of French origin. Based on the regression intercept and slope of the GEBVs of validation animals, the single-step evaluation was neither inflated nor deflated across the six breeds. Overall, the single-step model resulted in a more accurate and stable evaluation. However, due to the small number of genotyped individuals, the single-step method only provided slightly better results when compared to the pedigree-based method.
评估了 6 个德国肉牛群体中基因组选择的实施情况。尽管在大多数国家的奶牛评估中,多步骤实施基因组选择是现状,但德国肉牛的育种结构,加上多步骤方法的缺点和复杂性,使得单步更具吸引力,可用于德国肉牛群体中的基因组选择。我们的目标是在六个德国肉牛群体的五个重要经济性状中建立一个全国性的肉牛单步基因组评估,并研究其相对于当前基于系谱的评估对基因组评估的准确性和偏差的影响。在我们的研究中,六个品种的 461929 头表型和 14321 头基因型动物用多性状单步模型进行了评估。为了验证单步模型,在前向验证研究中去除了最后 2 年的表型数据。对于常规和单步方法,在截断和完整评估中比较了验证动物和其他动物的基因组估计育种值。在验证动物中,完整和截断评估之间 GEBV 的相关性在单步评估中略高。基于系谱的和单步的评估中,全 GEBV 对截断 GEBV 的回归接近 1 的最优值。从截断评估中获得的 SNP 效应估计值与全评估中获得的 SNP 效应估计值高度相关,相关系数范围为 0.79 至 0.94。SNP 效应的相关性受全评估和截断评估中共享的基因型动物数量的影响。全评估中 SNP 效应的回归系数都接近 1,表明 SNP 标记对生产性状的估计是无偏的。SNP 效应估计的曼哈顿图确定了起源于法国的品种中肌肉和体重的主要基因所在的染色体区域。基于验证动物 GEBV 的回归截距和斜率,单步评估在六个品种中既不膨胀也不收缩。总体而言,单步模型产生了更准确和稳定的评估。然而,由于基因型个体数量较少,与基于系谱的方法相比,单步方法仅提供了略好的结果。