Is it possible that an F2 population shows genotype like strong parents for stress but their phenotype matches with weak parent for stress tolerance? what could be the possible reasons?
It is completely normal. Depends how dense your genotyping is. If you are using a few markers genome wide then even big recombination events will be missing in your genotyping and you see somethjing like succeptible parent with resistant genotype. Even if you are using GBS you may see thoes but it will be rare.
I observed the similar king of thing in case of background selection, the plant showing distinctly high recovery % over rest of the plants as per the genotype showing no or very less phenotypic similarity to the recurrent parrent. intead plant with average recovery is showing more similarity. so as Farhad said it all depends on how dense and well distributed or genotyping is.
Also you can compare across more than one environment trials for phenotyping F2 Populations using two different plant densities.
