The invention relates to the technical field of animal and
plant breeding and
human disease prediction, and provides an efficient high-accuracy whole-
genome selection method capable of performing parallel operation. The method comprises the following steps: firstly, reading an original
genotype file and a
phenotype file, constructing a new
genotype file and a new
phenotype file, and calculating agenetic relationship matrix of all individuals; then, extracting all individuals in the new phenotypic file as a reference group, and extracting all individuals without phenotypic data in the originalgenotypic file as a prediction group; carrying out
whole genome association analysis by utilizing the reference group data, and extracting result characteristics of the
whole genome association analysis; constructing a model
library with specific characters, sequentially optimizing an optimal fixed effect and an optimal random effect by adopting a
cross validation strategy, and selecting an optimal prediction model from the model
library; and finally, calculating
genome estimated breeding values of the prediction group by utilizing the optimal prediction model. The method can quickly, accurately and stably predict individual
genome breeding values, and thus the accuracy and efficiency of whole genome selection are improved.