Initially this was accomplished by selecting plants, fruits, seeds, or other plant parts for producing new plants with desirable traits such as higher yields, and improved flavors.

A notable example of this is corn. Between 6,000 and 10,000 years ago, Meso-American farmers in Mexico and Central America cultivated teosinte, a grass species. By means of selection, the teosinte was changed from a plant with numerous stalks and cobs with 5-12 encapsulated kernels with a hard indigestible seed coats to a plant with a single stalk and a cob with dozens if not hundreds of highly digestible large seeds. Ancient farmers did not realize that they were changing the genes of the plants when selecting for these positive mutations.