On a recent Tuesday afternoon, Matt Barnard, the CEO of the indoor farming company Plenty, stood at the entrance of a Whole Foods in midtown Manhattan, surveying a mountain of berries.

Inbound shoppers wove around the display — a ziggurat of strawberry cartons, flanked by smaller piles of blueberries, raspberries, and cherries — stopping every so often to peel a container off the stack. In early summer, the strawberries sold here are local, sourced from farms in New York and New…