Xilon-Diguus

It seems like the highly inbred nature of domesticated dogs would lead to huge issues with linkage disequilibrium on your markers (though I have never tried to do any sort of GWAS analysis on inbred populations). How are you disentangling markers resulting from extreme bottlenecks from markers that are truly predictive of phenotypic variation?

That makes sense to me, all of the natural crosses could come in very handy given the limited pool they can originate from. Are you guys actually going for causal mutations? That seems extraordinarily difficult. Are you making inferences from polymorphisms within genic regions near a marker or do you just have such extreme resolution that you can spot conserved features in a very small window? Do you tend to find that phenotypic differences in dogs are due to changes in protein-coding regions, cis-regulatory regions, or even something like noncoding RNA?