New crop varieties are developed by applying traditional breeding methods that rely on random genome modifications. These varieties combine multiple traits that support farm efficiency and acceptable yields but also contain genes associated with the production of toxins, allergens, and/or antinutritional compounds that were not considered during the selection process. Furthermore, existing cultivars frequently lack the functional genes required for specific sensory traits and the formation of health-promoting antioxidants. One new method efficiently addresses some of these issues by either silencing undesirable genes or enhancing the expression of genes that are linked to dormant beneficial traits. Rather than incorporating foreign DNA into the plant's genome, these methods transform crops with plant-derived transfer (P-) DNAs that consist of only native genetic elements. The genetic modification can be characterized molecularly so that any inadvertent transfer of undesirable DNA, as may be the case with traditional methods, is excluded. A recently developed intragenic potato plant is silenced for the polyphenol oxidase, dikinase R1, and phosphorylase-L genes in a tuber-specific manner. French fries derived from these tubers lack discolorations, display an enhanced potato flavor, and produce greatly reduced amounts of the suspected carcinogen acrylamide. It is argued that intragenic modification is unlikely to trigger phenotypic, biochemical, or physiological variation that is new to the species. Similarly, the targeted traits are similar to those that breeders select for and often have a history of domestication and reduced fitness. For these reasons, an updated regulatory system is proposed whereby intragenic crops are considered as low risk and should be cleared for commercial release in a timely and cost-effective manner. By using modern techniques to modify the same genetic material that is used by breeders, intragenic approaches may be perceived as an acceptable extension of traditional methods in crop improvement.