Partial Fourier--Mukai transform for integrable systems with applications to Hitchin fibration

Let X be an abelian scheme over a scheme B. The Fourier--Mukai transform gives an equivalence between the derived category of X and the derived category of the dual abelian scheme. We partially extend this to certain schemes X over B (which we call degenerate abelian schemes) whose generic fiber is an abelian variety, while special fibers are singular. Our main result provides a fully faithful functor from a twist of the derived category of Pic$^\tau$(X/B) to the derived category of X. Here Pic$^\tau$(X/B) is the algebraic space classifying fiberwise numerically trivial line bundles. Next, we show that every algebraically integrable system gives rise to a degenerate abelian scheme and discuss applications to Hitchin systems.