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May 11, 2016 at 2:25 comment added Jorge Vitório Pereira I think it works. After base change we get a map to an appropriate Hilbert scheme of a certain projective space. On the Hilbert scheme we consider the foliation induced by automorphism of the ambient projective space. We pullback this foliation to the relative Picard. It is a foliation by algebraic leaves. Since its leaves dominates the leaves of the original foliation on $Y$ we have that its leaves cannot be Zariski dense unless the fibration is isotrivial.
May 11, 2016 at 0:09 comment added Jason Starr I am still checking the details . . .
May 10, 2016 at 20:26 comment added Jason Starr This should be true. Here is a sketch. First, let $\widetilde{X}\to \text{Pic}^0_{X/Y}$ be the pullback of $X$ to the relative Picard scheme. Now pullback $\mathcal{O}_X(1)$ to $\widetilde{X}$, then twist that by the Poincare bundle. Now, instead of considering isomorphisms of "bare" varieties, consider isomorphisms of the polarized varieties coming from this invertible sheaf. For a fixed pair $(X_0,\mathcal{L}_0)$, the corresponding subset $\widetilde{Z}(X_0,\mathcal{L}_0) \subset \text{Pic}^0_{X/Y}$ is "constructible". Using connectedness, $\widetilde{Z}\to Z$ should be surjective.
May 10, 2016 at 13:50 comment added Jorge Vitório Pereira Thanks Jason. You are of course right. The key hypothesis is connectedness. The real question is about the nature of the leaves of the foliation defined by the saturation inside $TY$ of the image of the natural map $\pi_* TX \to TY$.
May 10, 2016 at 13:45 history edited Jorge Vitório Pereira CC BY-SA 3.0
Corrected grammar.
May 10, 2016 at 13:44 comment added Jason Starr Silly observation: I think I can choose a countable subset of the Zariski dense subset above so that the only accumulation point is $(0,0)$, and of course we removed this from $X_0$ to form $Y$. So that countable subset of $Y$ would be an analytic subvariety. So probably the important hypothesis is connectedness.
May 10, 2016 at 13:34 comment added Jason Starr If you drop the connectedness and analyticity hypotheses, it is false (as you probably already know). You can begin with $X_0=E\times E$, for $E$ an elliptic curve, you let $Y=X_0\setminus\{(0,0)\}$, and you let $X$ be the blowing up of $X_0\times Y$ along the union of $\{(0,0)\}\times Y$ and the diagonal. Fixing a general point $(y,z)\in Y$, the Zariski dense subset $\{(ay+bz,cy+dz)\in Y: (a,b,c,d)\in \mathbb{Z}^4, ad-bc=1\}$ has your property, but it is neither connected nor analytic (since it accumulates).
May 10, 2016 at 13:17 history asked Jorge Vitório Pereira CC BY-SA 3.0