you can look for restriction sites on the genome

Rajib,

Your question is not really clear to me what is your parameter for checking the inter-varietal difference through MAS. I think you want to check different cultivar variety of a specific species on the basis of a particular gene expression..if it is you should go for Marker Assisted Selection procedure (MAS) using cDNA of those cultivar varieties. It is suggested to design your PCR primers from the minisatellite & microsatellite region of the specific gene sequence of that particular species. After getting the PCR product gel have to be analysed through AHC. From the dendrogram you will get the result. I hope it will help you.

Or is possible to use a RT-qPCR and quantify the gene expression.