Einstein showed that mass has energy, and energy has apparent mass (mass energy equivalence, or E = mc^(2)). They’re two sides of the same coin, proverbially speaking.
A system of quarks held together by the strong force have potential energy, just as an atomic nucleus held together by the strong force has potential energy: if you were to overcome the strong force, you would release the electromagnetic potential energy that wants to push those nucleons apart, just as if you were to overcome the static friction keeping a ball on top of a hill still to push it over the edge, you would release the gravitational potential energy contained in the ball-earth system.
That’s simplifying a lot, but the energy present in the quark system that comprises a composite particle like a proton bends spacetime and gives rise to apparent mass.
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