Transposable elements are an important source of genome variability. Here, we analyze their contribution to gene expression variability in crops by performing a TE insertion polymorphism (TIP)-eQTL mapping using expression data from rice varieties from the O. sativa ssp. indica and O. sativa ssp. japonica subspecies. Our data shows that TE insertions are associated with changes of expression of many genes known to be targets of rice domestication and breeding. An important fraction of these insertions were already present in the rice wild ancestors, and have been differentially selected in indica and japonica rice populations. Taken together, these data show that small changes of expression in signal transduction genes induced by TE insertions accompany the domestication and adaptation of rice populations.