Fragomeni B O, Lourenco D A L, Tsuruta S, Masuda Y, Aguilar I, Misztal I
Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.
Instituto Nacional de Investigacion Agropecuaria, Canelones, Uruguay.
J Anim Breed Genet. 2015 Oct;132(5):340-5. doi: 10.1111/jbg.12161. Epub 2015 Apr 10.
The purpose of this study was to examine accuracy of genomic selection via single-step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix (G) is replaced by an approximation of G(-1) based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively. When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G(-1) and the approximated G(-1) via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively) were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G(-1) and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was reduced from 227 to 206 in the first scenario and from 232 to 209 in the second scenario. Cows can be treated as young animals in APY without reducing the accuracy. The proposed algorithm can be implemented to reduce computing costs and to overcome current limitations on the number of genotyped animals in the ssGBLUP method.
本研究的目的是,当基因组关系矩阵(G)的直接逆矩阵被基于以经证实动物的一个子集为条件的年轻基因型动物递归的G(-1)近似值所取代时,检验通过单步基因组最佳线性无偏预测(ssGBLUP)进行基因组选择的准确性,该近似值称为经证实和年轻动物算法(APY)。通过高效实施,该算法对经证实动物的计算成本为三次方,对年轻动物为线性。模拟了十个模仿奶牛群体的重复数据集。在第一种情况下,为每个重复生成了20k基因型公牛的基因组信息,分为7k经证实公牛和13k年轻公牛。在第二种情况下,将5k有表型的基因型母牛作为年轻动物纳入分析。在常规估计育种值(EBV)中,经证实和年轻动物的准确性(10次重复的平均值)分别为0.72和0.34。当纳入基因组信息时,它们分别提高到0.75和0.50。未观察到通过常规G(-1)获得的基因组估计育种值(GEBV)与通过递归方法获得的近似G(-1)之间存在差异。在第二种情况下,GEBV的准确性(经证实公牛、年轻雄性和年轻雌性分别为0.76、0.51和0.59)也高于EBV(0.72、0.35和0.49)。同样,未观察到常规G(-1)和递归的GEBV之间存在差异。使用递归算法,在第一种情况下达到收敛的迭代次数从227减少到206,在第二种情况下从232减少到209。在APY中,母牛可被视为年轻动物而不降低准确性。所提出的算法可用于降低计算成本,并克服ssGBLUP方法中当前对基因型动物数量的限制。