Thanks to the DWin suggestion, I used ave to find xmin and xmax for each group separately and included them directly in the chart command.
There may be a more elegant way to do this (and suggestions are welcome), but it works.
qplot(prevRT, RT, group=ss, color = prim, geom = c("smooth"), method="lm", data =ss) + facet_grid(~ Groupe) + geom_rect(data=ss, aes(xmin=ave(ss$RT, ss$Groupe, FUN = function(x)quantile(x,c(0.05))), xmax=ave(ss$RT, ss$Groupe, FUN = function(x)quantile(x,c(0.95))), ymin=-Inf,ymax=Inf), color="green", alpha=1/280, inherit.aes = FALSE)

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