If you want to evaluate the parent and tjeir offsprings, you can analyze your data using Colony software, to determine whether the progeny is actually descended from the hybrid parents. Colony software will help you determine whether your offsprings are legitimate progenies derived from the specific parents (pure hybrids) or there are some illegitimate progenies, having pollen contributors different to the hybrid parents (there are hybrid impurities).
In my opinion, even the single polymorphic SSR marker can be used to differentiate nucellar and zygotic seedlings in citrus. Two or more SSR markers (Polymorphic) may not give the replicated results. So we can say that one SSR marker is highly informative while the other may not.