Exploring the Potential of Polyploid Forages through Computer Simulation

Polyploidy, a result of whole genome duplications, is a major evolutionary process contributing to the diversity of the grasses. The population genetics and evolutionary consequences of polyploidy are not well understood when compared to diploids. Computer simulation offers an alternative tool to understand complex systems that cannot be easily studied empirically. Most current genome simulation software are restricted to diploid organisms and their features do not account for the special inheritance and evolutionary nature of polyploids. We developed the first simulator “PolySim” that takes into account the evolution of polyploids from diploid ancestors, polysomic inheritance, inbreeding, and other evolutionary features. Running a large scale simulation study to examine the effect of different parameters on the evolution of the final polyploid population revealed novel insights. In general, autopolyploid populations showed significantly higher heterozygosity, relatedness and extended linkage disequilibrium at different inbreeding levels. Allopolyploid populations showed no difference from their ancestral diploids in any statistic considering constant population size, while autopolyploid populations show significant differences from their ancestors. Autopolyploids diverged faster than allopolyploids from their ancestral populations with at least 0.2 increase in Fst value after 14,000 generations of polyploidy emergence. A small rate of multivalent formation can homogenize allopolyploid sub-genomes, while complete disomic inheritance shapes allopolyploids as a population of two independent diploid organisms. A very small rate of gene flow from diploids to polyploids can significantly increase the polyploid effective population size. Understanding the dynamics of polyploid population genetics can be considered as the first building block to effectively utilize orphan polyploid grasses in forage breeding and develop refined statistical procedures that fit polyploid genomes. This research articulated the effect of different parameters on the evolution of polyploid populations under complex evolutionary scenarios. Moreover, PolySim has several applications such as the creation of genomes of polyploid populations to investigate the power of genome-wide association and genomic prediction studies, as well as genomic breeding program design.