HiPerBreedSim: High-Performance breeding simulations with complex genomes & phenotypes

Summary

With the HiPerBreedSim project, we are going to enhance the agrigenetic simulation ecosystem. This will supercharge theoretical and applied studies in selective breeding and the adoption of their results in practice. As in other branches of science, simulations are pivotal to research in modern data-driven selective breeding of agricultural populations. In this context, simulations are essential to decision making about how to deploy new data generation processes and associated analysis methods to increase the efficiency and return on investment. These uses of simulations have a significant academic, industrial, and societal impact by advancing the fundamental role of agriculture – food production. There is now a vibrant and complementary ecosystem of high-quality simulation software packages. Further developments are required to increase interoperability and to fully leverage their distinct strengths.

More specifically, we aim to deliver three key innovations to improve the agrigenetic simulation ecosystem. First, we will increase interoperability between population genomics and selective breeding simulation software packages by leveraging the succinct tree sequence encoding of ancestral recombination graphs, including support for the common diploid genomes and complex polyploid genomes. Second, we will increase flexibility of agrigenetic simulation software to generate complex phenotypes as a function of a range of effects with user-defined relationships to account for the nature of agriculturally important traits and concepts such as adaptability, resilience and genotype-by-environment interactions. Third, we will increase the use of vast amounts of publicly available genomic data in an easy-to-use and affordable way.