Fragomeni B O, Lourenco D A L, Tsuruta S, Masuda Y, Aguilar I, Legarra A, Lawlor T J, Misztal I
Department of Animal and Dairy Science, University of Georgia, Athens 30602.
Department of Animal and Dairy Science, University of Georgia, Athens 30602.
J Dairy Sci. 2015 Jun;98(6):4090-4. doi: 10.3168/jds.2014-9125. Epub 2015 Apr 8.
The purpose of this study was to evaluate the accuracy of genomic selection in single-step genomic BLUP (ssGBLUP) when the inverse of the genomic relationship matrix (G) is derived by the "algorithm for proven and young animals" (APY). This algorithm implements genomic recursions on a subset of "proven" animals. Only a relationship matrix for animals treated as "proven" needs to be inverted, and the extra costs of adding animals treated as "young" are linear. Analyses involved 10,102,702 final scores on 6,930,618 Holstein cows. Final score, which is a composite of type traits, is popular trait in the United States and was easily available for this study. A total of 100,000 animals with genotypes were used in the analyses and included 23,000 sires (16,000 with >5 progeny), 27,000 cows, and 50,000 young animals. Genomic EBV (GEBV) were calculated with a regular inverse of G, and with the G inverse approximated by APY. Animals in the proven subset included only sires (23,000), sires+cows (50,000), only cows (27,000), or sires with >5 progeny (16,000). The correlations of GEBV with APY and regular GEBV for young genotyped animals were 0.994, 0.995, 0.992, and 0.992, respectively Later, animals in the proven subset were randomly sampled from all genotyped animals in sets of 2,000, 5,000, 10,000, 15,000, and 20,000; each sample was replicated 4 times. Respective correlations were 0.97 (5,000 sample), 0.98 (10,000 sample), and 0.99 (20,000 sample), with minimal difference between samples of the same size. Genomic EBV with APY were accurate when the number of animals used in the subset is between 10,000 and 20,000, with little difference between the ways of creating the subset. Due to the approximately linear cost of APY, ssGBLUP with APY could support any number of genotyped animals without affecting accuracy.
本研究的目的是评估当通过“经产和青年动物算法”（APY）推导基因组关系矩阵（G）的逆矩阵时，单步基因组最佳线性无偏预测（ssGBLUP）中基因组选择的准确性。该算法在一部分“经产”动物上实施基因组递归。只需要求逆处理为“经产”动物的关系矩阵，而添加被视为“青年”动物的额外成本是线性的。分析涉及6,930,618头荷斯坦奶牛的10,102,702个最终评分。最终评分是体型性状的综合指标，在美国是一个常见性状，且本研究很容易获取该数据。分析中总共使用了100,000头有基因型的动物，包括23,000头公牛（其中16,000头有超过5头后代）、27,000头母牛和50,000头青年动物。基因组估计育种值（GEBV）分别用常规的G逆矩阵和APY近似的G逆矩阵进行计算。经产子集中的动物包括仅公牛（23,000头）、公牛 + 母牛（50,000头）仅母牛（27,000头）或有超过5头后代的公牛（16,000头）。对于有基因型的青年动物，APY计算的GEBV与常规GEBV的相关性分别为0.994、0.995、0.992和0.992。之后，从所有有基因型的动物中随机抽取经产子集中的动物，样本量分别为2,000、5,000、10,000、15,000和20,000；每个样本重复4次。相应的相关性分别为0.97（样本量5,000）、0.98（样本量10,000）和0.99（样本量20,000），相同样本量的样本之间差异极小。当子集中使用的动物数量在10,000到20,000之间时，APY计算的基因组EBV是准确的，创建子集的方式之间差异很小。由于APY成本近似呈线性，使用APY的ssGBLUP可以支持任意数量的有基因型动物，而不影响准确性。
