Just to learn the procedure (if possible) and to prepare the GD and GM data files. If anyone done GWAS in GAPIT using SSR marker data, please share (or help me to prepare) GD and GM files.
A marker is a marker! I see no reason why you can't. Go to the GAPIT forum though. Dr. Lipka who made GAPIT is very responsive if you have questions https://groups.google.com/g/gapit-forum