To be a bit more specific, agriculture developed in the Mississippi and Ohio Valleys independently from the development of agriculture in Mesoamerica. We see the initial signs of domestication in local varieties of squash around 5000 years ago (at the very latest). By 3000 years ago, the people of the region had domesticated a suite of unique plants known today as the Eastern Agricultural Complex (EAC). This included squash, sunflower, sunchoke, goosefoot, marshelder, erect knotweed, little barley, and maygrass.

Maize makes its first appearance in the Eastern Woodlands sometime between 2000 and 1600 years ago, but it was southern curiosity at that time. Only a handful of scattered cobs have been found dating to that period; it doesn't seem to have been adopted as a staple crop yet. It's not until about 1000 years ago, or a little before, that maize really takes off throughout the Eastern Woodlands, with another Mesoamerican crop - beans - following shortly thereafter, along with some southern varieties of squash like pumpkins. Many of the EAC crops were pushed to the sidelines, if not abandoned entirely, during this transition. Local squashes, sunflowers, and to a lesser extent goosefoot remained popular plants to grow in the region up to and beyond contact with Europeans, at which point more crops from the south as well as from Eurasia and Africa were added to the ever growing list of crops planted in the Eastern Woodlands.

In addition to the true domesticates, there were also psuedo-domesticates too. This category includes plants whose lifecycles were not control by humans in ways that produce the typical selective pressures associated with domestication. The two most common were groundnuts and wild rice. Groundnuts germinate in the wild, but are transplanted to fields for further care and later harvesting. Wild rice grows in the marshes of the Great Lakes; it's harvested by shaking its grains free from the stalk, which simultaneously sows seeds for next year's harvest.