Due to local adaptation and population structure, genomes of different individuals can vary to a great extent. To represent this variation, we utilize the concept of variation graphs, which provide a powerful toolkit. I am working to combine these genome graphs with genome-wide-association (GWA) approaches to connect complex genomic variation with organism traits. Beginning with multiple whole-genome assemblies, I will first tackle the problem of graph construction, providing an accurate representation of genomic variation and the basis of the analysis.