Incorporating Prior Knowledge of Principal Components in Genomic Prediction

Abstract

Genomic prediction using a large number of markers is challenging, due to the curse of dimensionality as well as multicollinearity arising from linkage disequilibrium between markers. Several methods have been proposed to solve these problems such as Principal Component Analysis (PCA) that is commonly used to reduce the dimension of predictor variables by generating orthogonal variables. Usually, the knowledge from PCA is incorporated in genomic prediction, assuming equal variance for the PCs or a variance proportional to the eigenvalues, both treat variances as fixed. Here, three prior distributions including normal, scaled-t and double exponential were assumed for PC effects in a Bayesian framework with a subset of PCs. These developed PCR models (dPCRm) were compared to routine genomic prediction models (RGPM) i.e., ridge and Bayesian ridge regression, BayesA, BayesB, and PC regression with a subset of PCs but PC variances predefined as proportional to the eigenvalues (PCR-Eigen). The performance of methods was compared by simulating a single trait with heritability of 0.25 on a genome consisted of 3,000 SNPs on three chromosomes and QTL numbers of 15, 60, and 105. After 500 generations of random mating as the historical population, a population was isolated and mated for another 15 generations. The generations 8 and 9 of recent population were used as the reference population and the next six generations as validation populations. The accuracy and bias of predictions were evaluated within the reference population, and each of validation populations. The accuracies of dPCRm were similar to RGPM (0.536 to 0.664 vs. 0.542 to 0.671), and higher than the accuracies of PCR-Eigen (0.504 to 0.641) within reference population over different QTL numbers. Decline in accuracies in validation populations were from 0.633 to 0.310, 0.639 to 0.313, and 0.617 to 0.298 using dPCRm, RGPM and PCR-Eigen, respectively. Prediction biases of dPCRm and RGPM were similar and always much less than biases of PCR-Eigen. In conclusion assuming PC variances as random variables via prior specification yielded higher accuracy than PCR-Eigen and same accuracy as RGPM, while fewer predictors were used.