I suggest you have a look at the following papers: 

- Across-line SNP association study of innate and adaptive immune response in laying hens;

- Across-line SNP association study for direct and associative effects on feather damage in laying hens;

The SNP effect is modeled so to capture those effects that are common across populations (i.e. in all populations).

Hope this helps,

Filippo

maybe try meta-analysis or association test adjusting for co-variate, such as PCs