A new approach fits multivariate genomic prediction models efficiently

Abstract

Background Fast, memory-efficient, and reliable algorithms for estimating genomic estimated breeding values (GEBV) for multiple traits and environments are needed to make timely decisions in breeding. Multivariate genomic prediction exploits genetic correlations between traits and environments to increase accuracy of GEBV compared to univariate methods. These genetic correlations are estimated simultaneously with GEBV, because they are specific to year, environment, and management. However, estimating genetic parameters is computationally demanding with restricted maximum likelihood (REML) and Bayesian samplers, and canonical transformations or orthogonalizations cannot be used for unbalanced experimental designs. Methods We propose a multivariate randomized Gauss–Seidel algorithm for simultaneous estimation of model effects and genetic parameters. Two previously proposed methods for estimating genetic parameters were combined with a Gauss–Seidel (GS) solver, and were called Tilde-Hat-GS (THGS) and Pseudo-Expectation-GS (PEGS). Balanced and unbalanced experimental designs were simulated to compare runtime, bias and accuracy of GEBV, and bias and standard errors of estimates of heritabilities and genetic correlations of THGS, PEGS, and REML. Models with 10 to 400 response variables, 1279 to 42,034 genetic markers, and 5990 to 1.85 million observations were fitted. Results Runtime of PEGS and THGS was a fraction of REML. Accuracies of GEBV were slightly lower than those from REML, but higher than those from the univariate approach, hence THGS and PEGS exploited genetic correlations. For 500 to 600 observations per response variable, biases of estimates of genetic parameters of THGS and PEGS were small, but standard errors of estimates of genetic correlations were higher than for REML. Bias and standard errors decreased as sample size increased. For balanced designs, GEBV and estimates of genetic correlations from THGS were unbiased when only an intercept and eigenvectors of genotype scores were fitted. Conclusions THGS and PEGS are fast and memory-efficient algorithms for multivariate genomic prediction for balanced and unbalanced experimental designs. They are scalable for increasing numbers of environments and genetic markers. Accuracy of GEBV was comparable to REML. Estimates of genetic parameters had little bias, but their standard errors were larger than for REML. More studies are needed to evaluate the proposed methods for datasets that contain selection.

Improving predictive ability in sparse testing designs in soybean populations

“…On the other hand, the results of model M3 (also including the interaction between family and environment) were similar to those obtained by Persa et al, 2020 analyzing information of the SoyNAM experiment comprising 1,358 RILs observed in 18 environments (not all RILs observed in all environments) but considering a conventional fivefold cross-validation predicting tested genotypes in observed environments (CV2) and untested genotypes in observed environments (CV1). In addition, Xavier and Habier (2022), using the SoyNAM population conducted an study to evaluate the effects in predictive ability of models similar to M1 and M2 when considering simulated data for the case where RILs are observed only once across environments for different heritabilities. The results obtained for these authors were higher compared with the results here presented probably due to the fact they considered simulated data as response as opposed to real data and a different cross-validation scheme.…”

Soybean genetics, genomics, and breeding for improving nutritional value and reducing antinutritional traits in food and feed

“…Although promising, the applicability of genomic prediction for seed oil content is still negligible for many soybean breeding programs given the relatively low cost and high‐throughput assessment of seed composition through near‐infrared reflectance spectroscopy (NIRS) compared to genotyping costs. Nevertheless, multivariate genomic prediction models leveraging the genetic correlations among traits of interest (Xavier & Habier, 2022) can be explored to improve the identification and selection of genotypes with desirable oil content and/or fatty acid profile and grain yield simultaneously.…”