For this purpose, there are elaborated kits available. However, it would probably be helpful to know your flow cytometry setup. An exemplary solution from BD Biosciences is available here:
Run a PBMC sample and note the channel number( X) for G0/G1 which is equivalent to 2n population. Keeping the same acquisition settings now run the sample for which you want ploidy level. Note the channel number for G0/G1 (Y). Now do Y/X. will give you ploidy number.
PBMC are taken as 2n control they are Peripheral blood mononuclear cells. But they are taken for human cell ploidy determination as DNA content per chromosome can vary between different organisms. To my knowledge you can not use PBMC but look for some growth arrested diploid cells from same plant. otherwise look for some diploid control reagents for plants from any company.
http://www.flowingsoftware.com/ this flow cytometry software is free and, tutorials and automation tools are very helpful to use DNA peaks to make estimation for ploidy levels