Quantitative genetics: genomic prediction
We'll start today's lecture by going over a little two-locus population genetics. Specifically, we'll get an introduction to gametic disequilibrium (which is the term I prefer to "linkage disequilibrium" for reasons that will become apparent), and we'll see that there's a two-locus analog of the Wahlund effect that can lead to statistical associations between alleles at different loci even when they're unlinked.
With that out of the way we'll explore the ideas behind genomic prediction using a simple simulation model to produce the data. You'll find the simulation model and the analysis in the R notebook linked to below. I encourage you to download it and try it yourself. If you're ambitious, you'll get even more out of it by generating some new data sets, either by commenting out the set.seed() or by changing effect, s_dev, or n_loci_total when calling generate_data().