I am working on wheat which has long generation time and developing different genetic background with recurrent line takes long time. Please share some ideas about validating QTLs other than different genetic background.
I think it is better to verify the percent phenotypic variance of the QTLs you have detected. If you have low phenotypic variance of the QTLs detected it is recommended that you need to dissect it for the better marker trait association through fine mapping which mostly increases phenotypic variance expressed by the QTL towards the targeted phenotype. Then you may plan for marker validation.
I would suggest you can use different generation genotypes derived from the same parentage as a population for the marker validation. It would be better if you can use backcross generations derived from the same parents.