Do you have a question that you want to answer or a product that you want to produce?

Otherwise, it sounds like you have a solution in search of a problem.

Hi Malka,

1. GWAS (Genome Wide Association Study) enables associating markers (ex. SNP) on chromosomes to a specific trait (attached picture). This approach has first successfully used in detecting genes involving in human diseases. However, you have to remember that while the associated genetic variations can serve as good pointers to a specific REGION of a chromosome where the trait gene resides, the associated variants themselves may not directly cause the trait. Researchers often need extra experiments to identify the exact locus involve the traits [ https://www.genome.gov/20019523#gwas-1 ].

2. For that, you may have many things you can do: (a) you can use your 'variation data' to search for the exact locations of the genes involved in your target traits. This will take a while. Especially a QTL trait. (b) Once you have the genes located, you can clone it (them) and verify them, (c) you can search and compare similar genes in other species, (d) overexpressing these genes (ex. drought tolerant gene) in model plants such as Arabidopsis for study, (e) if your trait is controlled by QTL, you can even pyramid them into a regional variety to improved a variety, or to develop broad-spectrum resistance to a disease as that mentioned in the paper below (see attachment):

"Genome-Wide Association Study Reveals Novel Quantitative Trait Loci Associated with Resistance to Multiple Leaf Spot Diseases of Spring Wheat (2014)"