In order to compare enzyme activities from different stages of plant (fruit) development at the same time, the authors described in their paper: "Each sample was ground to a ne powder under liquid nitrogen and stored at -80C until use." They analyzed >22 enzymes from tomato (see attached paper).
You can simply grow a sufficient number of plants and replicates in the same conditions..And collect them at different stages.. separate the shoots from the roots if you want to analyse them separately.. soak immediately in liquid nitrogen and store them in -80°C untill use...