Improved genomic prediction using machine learning with Variational Bayesian sparsity

Abstract

Abstract Background Genomic prediction has become a powerful modelling tool for assessing line performance in plant and livestock breeding programmes. Among the genomic prediction modelling approaches, linear based models have proven to provide accurate predictions even when the number of genetic markers exceeds the number of data samples. However, breeding programmes are now compiling data from large numbers of lines and test environments for analyses, rendering these approaches computationally prohibitive. Machine learning (ML) now offers a solution to this problem through the construction of fully connected deep learning architectures and high parallelisation of the predictive task. However, the fully connected nature of these architectures immediately generates an over-parameterisation of the network that needs addressing for efficient and accurate predictions. Results In this research we explore the use of an ML architecture governed by variational Bayesian sparsity in its initial layers that we have called VBS-ML. The use of VBS-ML provides a mechanism for feature selection of important markers linked to the trait, immediately reducing the network over-parameterisation. Selected markers then propagate to the remaining fully connected feed-forward components of the ML network to form the final genomic prediction. We illustrated the approach with four large Australian wheat breeding data sets that range from 2665 lines to 10375 lines genotyped across a large set of markers. For all data sets, the use of the VBS-ML architecture improved genomic prediction accuracy over legacy linear based modelling approaches. Conclusions An ML architecture governed under a variational Bayesian paradigm was shown to improve genomic prediction accuracy over legacy modelling approaches. This VBS-ML approach can be used to dramatically decrease the parameter burden on the network and provide a computationally feasible approach for improving genomic prediction conducted with large breeding population numbers and genetic markers.