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Spectral analysis (via drone, satellite, airplane etc) is good but won't give you the resolution of 1 chip per plant. It does seem labor intensive to implant every plant, but not impossible. Even large farmers trim and take cuttings from individual plants.

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You can get plenty of resolution off an airplane. I have seen aerial imagery of sufficient resolution to do stand count analysis, which is basically counting individual green shoots of corn in the spring.

As another poster mentioned, though, spectral analysis shows problems in the leaves of the plant, where it is too late: if your plant is yellowing due to lack of water or nutrients, you've already decreased the potential yield from that plant. It's better to detect deficiencies in the ground.

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