No, JI is for animals. For plants, you should use other methods such as ordination, in which differences in vegetation among patch types are related in part to environmental variables such as soil moisture and light availability.
The paper recommended by Arvind above, although interesting, does not mention JI.
I hope the following helps:
Habitat Selection in Plants
F. A. Bazzaz
The American Naturalist
Vol. 137, Supplement: Habitat Selection (Jun., 1991), pp. S116–S130.
Climate envelope habitat and niche are scales of ranges thst themselves are defined by specific occupances. Species distribution models are used to define these ranges. An intro to stats can be https://cran.r-project.org/web/packages/dismo/vignettes/sdm.pdf