What is the minimal supersymmetric Standard Model from F-theory?

We construct gauge theory of SU(3)×SU(2)×U(1) by spectral cover from F-theory and ask how the Standard Model is extended under minimal assumptions on Higgs sector. For the requirement on different numbers between Higgs pairs and matter generations (respectively one and three) distinguished by R-parity, we choose a universal G-flux obeying SO(10) but slightly breaking E6 unification relation. This condition forces distinction between up and down Higgs fields, suppression of proton decay operators up to dimension five, and existence and dynamics of a singlet related to μ-parameter.