In theory, every time one plants a seed of an apple or peach, the ensuing seedling is a new variety. The only way of duplicating the parent fruit tree is by asexual means -- budding or grafting. Most Virginia "Farm Orchards" were planted with seedling trees, partly because it was simpler, partly because any fruit would suffice when apples were harvested for cider or peaches were picked for brandy. The planting of seedling orchards was a significant development in that the seedling trees would sometimes produce exceptional fruit, a tasty apple or a hardy peach, which would be named and then preserved by budding or grafting.
Although Jefferson believed most stone fruits (peaches, nectarines, etc.) could be propagated from seed and that seedling trees were healthier, he usually grafted or budded the trees he planted in the South Orchard in order to preserve the dessert qualities of a Newtown (Albemarle) Pippin apple or Carnation cherry. Outside specialists, or else his Scottish gardener Robert Bailey, were often contracted to graft apples and pears and "inoculate" or bud cherries.
Jefferson had at least two nurseries: the "old nursery" below the garden wall and the terraced "new nursery," which was an extension of the northeast end of the vegetable garden. Here he propagated seeds and cuttings from friends and neighbors. Jefferson occasionally purchased fruit from commercial sources, such as the William Prince nursery on Long Island, yet his home nurseries provided most of the plants for the Fruitery. The list of plants Jefferson grew in them included his favorite species: plants discovered by the Lewis and Clark Expedition, a sampling of his "pet" ornamental trees, and potentially significant economic species like the sugar maple and sesame. Jefferson propagated thirteen kinds of shrubs, forty-one species of ornamental trees, twenty-six vegetable varieties, six kinds of grasses, eleven nut trees, and fifty-three fruit tree varieties in his nurseries. They were the heart of his pomological, perhaps even his horticultural, world.