Interpretive Summary: Efficient approximation of reliabilities for single-step genomic best linear unbiased predictor models with the Algorithm for Proven and Young
By: Matias Bermann
The estimated breeding value (EBV) of an animal measures its genetic merit. For calculating EBVs, pedigree and genomic information are jointly used in a procedure called single-step genomic best linear unbiased prediction (ssGBLUP). Genetic evaluations report each EBV with its reliability, which measures how accurate the breeding value estimation was. Calculating EBV with ssGBLUP for large datasets is computationally expensive; Therefore, the Algorithm for Proven and Young (APY) was developed to reduce its computational cost. However, the procedure for obtaining the reliabilities of EBV is still computationally unfeasible to apply. Thus, this study aimed to develop a new method for approximating reliabilities for ssGBLUP with APY for large datasets. We required this new method to be accurate and with fewer computational requirements than the estimation of breeding values by itself. The method that we develop consists of accumulating pedigree and genomic information in successive steps, allowing for computational efficiency. Using a dataset with more than 300,000 genotypes in a pedigree of 10,000,000 animals provided by the American Angus Association, we showed that our proposed method is accurate and computationally efficient, with a correlation of 0.98 between the approximated and target values running in less than 12 min.
This article is available in the Journal of Animal Science.