Misztal I, Legarra A, Aguilar I
Department of Animal and Dairy Science, University of Georgia, Athens 30602-2771.
INRA, UR631-SAGA, BP 52627, 31326 Castanet-Tolosan Cedex, France.
J Dairy Sci. 2014;97(6):3943-52. doi: 10.3168/jds.2013-7752. Epub 2014 Mar 27.
Computing the inverse of the genomic relationship matrix using recursion was investigated. A traditional algorithm to invert the numerator relationship matrix is based on the observation that the conditional expectation for an additive effect of 1 animal given the effects of all other animals depends on the effects of its sire and dam only, each with a coefficient of 0.5. With genomic relationships, such an expectation depends on all other genotyped animals, and the coefficients do not have any set value. For each animal, the coefficients plus the conditional variance can be called a genomic recursion. If such recursions are known, the mixed model equations can be solved without explicitly creating the inverse of the genomic relationship matrix. Several algorithms were developed to create genomic recursions. In an algorithm with sequential updates, genomic recursions are created animal by animal. That algorithm can also be used to update a known inverse of a genomic relationship matrix for additional genotypes. In an algorithm with forward updates, a newly computed recursion is immediately applied to update recursions for remaining animals. The computing costs for both algorithms depend on the sparsity pattern of the genomic recursions, but are lower or equal than for regular inversion. An algorithm for proven and young animals assumes that the genomic recursions for young animals contain coefficients only for proven animals. Such an algorithm generates exact genomic EBV in genomic BLUP and is an approximation in single-step genomic BLUP. That algorithm has a cubic cost for the number of proven animals and a linear cost for the number of young animals. The genomic recursions can provide new insight into genomic evaluation and possibly reduce costs of genetic predictions with extremely large numbers of genotypes.
研究了使用递归计算基因组关系矩阵的逆矩阵。一种传统的求分子关系矩阵逆矩阵的算法基于这样的观察:在已知所有其他动物效应的情况下,某一动物加性效应的条件期望仅取决于其父系和母系的效应,且系数均为0.5。对于基因组关系,这种期望取决于所有其他已分型的动物,且系数没有固定值。对于每只动物,这些系数加上条件方差可称为基因组递归。如果已知这样的递归,就可以在不明确创建基因组关系矩阵逆矩阵的情况下求解混合模型方程。开发了几种算法来创建基因组递归。在一种顺序更新算法中,逐个动物地创建基因组递归。该算法也可用于为额外的基因型更新已知的基因组关系矩阵逆矩阵。在一种前向更新算法中,新计算的递归会立即用于更新其余动物的递归。这两种算法的计算成本都取决于基因组递归的稀疏模式,但低于或等于常规求逆的成本。一种针对经产动物和幼年动物的算法假设幼年动物的基因组递归仅包含经产动物的系数。这种算法在基因组最佳线性无偏预测(genomic BLUP)中生成精确的基因组估计育种值(genomic EBV),在单步基因组最佳线性无偏预测中是一种近似值。该算法对于经产动物数量的计算成本是三次方的,对于幼年动物数量的计算成本是线性的。基因组递归可为基因组评估提供新的见解,并可能降低在具有极大量基因型时进行遗传预测的成本。