22 Accuracy of indirect predictions for large datasets based on prediction error covariance of SNP effects from single-step GBLUP

Abstract

Abstract With an ever-increasing number of genotyped animals, there is a question of whether to include all genotypes into single-step GBLUP (ssGBLUP) evaluations or to include only genotyped animals with phenotypes and use indirect predictions (IP) for the remaining young genotyped animals. Under ssGBLUP, SNP effects can be backsolved from GEBV, and IP can be calculated as the sum of SNP effects weighted by the gene content. To publish IP, a measure of accuracy that reflects the standard error of prediction, and that is comparable to GEBV accuracy, is needed. Our first objective was to test formulas to compute accuracy of IP by backsolving prediction error covariance (PEC) of GEBV into PEC of SNP effects. The second objective was to investigate the number of genotyped animals needed to obtain robust IP accuracy. Data were provided by the American Angus Association, with 38,000 post-weaning gain phenotypes and 60,000 genotyped animals. Correlations between GEBV and IP were ≥0.99. When all genotyped animals were used for PEC computations, accuracy correlations were also ≥0.99. Additionally, GEBV and IP accuracies were compatible, with both direct inversion of the genomic relationship matrix (G) or using the algorithm for proven and young (APY) to obtain G inverse. As the number of genotyped animals in PEC computations decreased to 15,000, accuracy correlations were still high (≥0.96), but IP accuracies were biased downwards. Indirect prediction accuracy can be successfully obtained from ssGBLUP without running an extra SNP-BLUP evaluation to compute SNP PEC. It is possible to reduce the number of genotyped animals in PEC computations, but accuracies may be slightly underestimated. When the amount of genomic and phenotypic data is large, the polygenic part of GEBV becomes small and IP can be very accurate. Further research is needed to approximate SNP PEC with a large number of genotyped animals.