It is possible that higher casts selected for intelligence over the years. Since in India arranged marriage is the norm, parents can select for intelligence if that is a trait they care about. If there is a genetic portion of intelligence that can be selected for.

Note the above uses words like "possible" and "if". I find it unlikely this is what was done. More likely - like every other society - they selected for politically powerful.

Note too that it is highly likely that in the past rape of lower casts was accepted in some form, which would bring any selected IQ genes to the lower casts.