We prove that the theta correspondence for the dual pair ( SL 2 , P B × ), for B an indefinite quaternion algebra over Q, acting on modular forms of odd square-free level, preserves rationality and p-integrality in both directions. As a consequence, we deduce the rationality of certain period ratios of modular forms and even p-integrality of these ratios under the assumption that p does not divide a certain L-value. The rationality is applied to give a direct construction of isogenies between new quotients of Jacobians of Shimura curves, completely independent of Faltings isogeny theorem.