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Hidden-color configurations are a key prediction of QCD with important physical consequences. In this work we examine a QCD color-singlet configuration in nuclei formed by combining six scalar $[u d]$ diquarks in a strongly bound $\rm SU(3)_C$ channel. The resulting hexadiquark state is a charge-2, spin-0, baryon number-4, isospin-0, color-singlet state. It contributes to alpha clustering in light nuclei and to the additional binding energy not saturated by ordinary nuclear forces in \he as well as the alpha-nuclei sequence of interest for nuclear astrophysics. We show that the strongly bound combination of six scalar isospin-0 $[ud]$ diquarks within the nuclear wave function - relative to free nucleons - provides a natural explanation of the EMC effect measured by the CLAS collaboration's comparison of nuclear parton distribution function ratios for a large range of nuclei. These experiments confirmed that the EMC effect; i.e., the distortion of quark distributions within nuclei, is dominantly identified with the dynamics of neutron-proton (``isophobic'') short-range correlations within the nuclear wave function rather than proton-proton or neutron-neutron correlations.