I just uploaded the final set of notes on genomic prediction. As you’ll see, there are some things you’ll need to be careful of if you want to use genomic prediction in your own work. Although I don’t mention this explicitly in the notes, the implication of the last caveat about genomic prediction is that GWAS may not be very useful in understanding the genetic basis of variation in a complicated trait beyond the population in which the analysis was done. A further leap is that even a traditional quantitative genetic analysis may not extrapolate well to other populations, even if the environmental conditions are similar.
In short, quantitative genetics provides some very powerful tools, but powerful tool can also cause a lot of damage. Be careful when you wield this one.