Wang Chunkao, Da Yang
Department of Animal Science, University of Minnesota, St. Paul, Minnesota, United States of America.
PLoS One. 2014 Dec 17;9(12):e114484. doi: 10.1371/journal.pone.0114484. eCollection 2014.
The traditional quantitative genetics model was used as the unifying approach to derive six existing and new definitions of genomic additive and dominance relationships. The theoretical differences of these definitions were in the assumptions of equal SNP effects (equivalent to across-SNP standardization), equal SNP variances (equivalent to within-SNP standardization), and expected or sample SNP additive and dominance variances. The six definitions of genomic additive and dominance relationships on average were consistent with the pedigree relationships, but had individual genomic specificity and large variations not observed from pedigree relationships. These large variations may allow finding least related genomes even within the same family for minimizing genomic relatedness among breeding individuals. The six definitions of genomic relationships generally had similar numerical results in genomic best linear unbiased predictions of additive effects (GBLUP) and similar genomic REML (GREML) estimates of additive heritability. Predicted SNP dominance effects and GREML estimates of dominance heritability were similar within definitions assuming equal SNP effects or within definitions assuming equal SNP variance, but had differences between these two groups of definitions. We proposed a new measure of genomic inbreeding coefficient based on parental genomic co-ancestry coefficient and genomic additive correlation as a genomic approach for predicting offspring inbreeding level. This genomic inbreeding coefficient had the highest correlation with pedigree inbreeding coefficient among the four methods evaluated for calculating genomic inbreeding coefficient in a Holstein sample and a swine sample.
传统的数量遗传学模型被用作统一方法，以推导基因组加性和显性关系的六个现有及新定义。这些定义的理论差异在于对等位基因效应相等（等同于跨SNP标准化）、等位基因方差相等（等同于SNP内标准化）以及预期或样本SNP加性和显性方差的假设。基因组加性和显性关系的六个定义平均而言与系谱关系一致，但具有个体基因组特异性和系谱关系中未观察到的较大变异。这些大的变异可能允许在同一家庭中找到亲缘关系最小的基因组，以最小化育种个体间的基因组相关性。基因组关系的六个定义在加性效应的基因组最佳线性无偏预测（GBLUP）中通常具有相似的数值结果，以及在加性遗传力的基因组REML（GREML）估计中也相似。在假设等位基因效应相等的定义内或假设等位基因方差相等的定义内，预测的SNP显性效应和显性遗传力的GREML估计相似，但这两组定义之间存在差异。我们基于亲本基因组共祖系数和基因组加性相关性提出了一种新的基因组近交系数测量方法，作为预测后代近交水平的基因组方法。在荷斯坦样本和猪样本中评估的四种计算基因组近交系数的方法中，这种基因组近交系数与系谱近交系数的相关性最高。
