Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE.
DNA Genetics, Columbus, NE.
J Anim Sci. 2018 Nov 21;96(11):4532-4542. doi: 10.1093/jas/sky330.
Across the majority livestock species, routinely collected genomic and pedigree information has been incorporated into evaluations using single-step methods. As a result, strategies that reduce genotyping costs without reducing the response to selection are important as they could have substantial economic impacts on breeding programs. Therefore, the objective of the current study was to investigate the impact of selectively genotyping selection candidates on the selection response using simulation. Populations were simulated to mimic the genome and population structure of a swine and cattle population undergoing selection on an index comprised of the estimated breeding values (EBV) for 2 genetically correlated quantitative traits. Ten generations were generated and genotyping began generation 7. Two phenotyping scenarios were simulated that assumed the first trait was recorded early in life on all individuals and the second trait was recorded on all versus a random subset of the individuals. The EBV were generated from a bivariate animal model. Multiple genotyping scenarios were generated that ranged from not genotyping any selection candidates, a proportion of the selection candidates based on either their index value or chosen at random, and genotyping all selection candidates. An interim index value was utilized to decide who to genotype for the selective genotype strategy. The interim value assumed only the first trait was observed and the only genotypic information available was on animals in previous generations. Within each genotyping scenario 25 replicates were generated. Within each genotyping scenario the mean response per generation and the degree to which EBV were inflated/deflated was calculated. Across both species and phenotyping strategies, the plateau of diminishing returns was observed when 60% of the selection candidates with the largest index values were genotyped. When randomly genotyping selection candidates, either 80 or 100% of the selection candidates needed to be genotyped for there not to be a reduction in the index response. Across both populations, no differences in the degree that EBV were inflated/deflated for either trait 1 or 2 were observed between nongenotyped and genotyped animals. The current study has shown that animals can be selectively genotyped in order to optimize the response to selection as a function of the cost to conduct a breeding program using single-step genomic best linear unbiased prediction.
在大多数牲畜品种中，常规收集的基因组和系谱信息已被纳入使用单步方法进行的评估中。因此，降低基因分型成本而不降低选择反应的策略非常重要，因为它们可能对育种计划产生重大的经济影响。因此，本研究的目的是通过模拟研究有选择地对候选者进行基因分型对选择反应的影响。模拟种群以模拟猪和牛种群的基因组和群体结构，该种群在由两个遗传相关的数量性状的估计育种值 (EBV) 组成的指数上进行选择。生成了十代，从第 7 代开始进行基因分型。模拟了两种表型情况，假设第一个性状在所有个体的生命早期被记录，第二个性状在所有个体上或在个体的随机子集中被记录。EBV 是从双变量动物模型生成的。生成了多种基因分型方案，范围从不对任何选择候选者进行基因分型，基于候选者的指数值或随机选择的一部分进行基因分型，以及对所有选择候选者进行基因分型。使用中间指数值来决定对选择性基因分型策略进行基因分型的对象。中间值仅假设观察到第一个性状，并且可用的唯一基因型信息是前几代的动物。在每个基因分型方案中生成了 25 个重复。在每个基因分型方案中，计算了每代的平均响应以及 EBV 膨胀/缩小的程度。在两种物种和表型策略中，当最大指数值的 60%的选择候选者被基因分型时，观察到收益递减的平台。当随机对选择候选者进行基因分型时，需要对 80%或 100%的选择候选者进行基因分型，才能不降低指数反应。在两个群体中，对于第一个或第二个性状，未基因分型的动物和基因分型的动物之间，EBV 膨胀/缩小的程度没有差异。本研究表明，可以有选择地对动物进行基因分型，以优化选择反应，作为使用单步基因组最佳线性无偏预测进行育种计划的成本的函数。
