Essentially, conventional breeding is always based on a wide range of genetic and biological diversity found in natural populations, as well as in all previously bred plant and animal varieties and breeds. In addition, new mutations happen continually and specific triggers can speed up the occurrence of mutations. Not all of these mutations are considered beneficial. In order to achieve the desired results, breeders screen natural populations and previously bred varieties for specific traits. Subsequently, plants are chosen and then grown and crossed to achieve an optimal combination of genetic information. The natural mechanisms of inheritance and gene regulation cannot be bypassed with this method.
Genetic engineering on the other hand uses direct technical and targeted intervention to establish new traits. These technical interventions bypass natural biological mechanisms governed by evolution, inheritance and gene regulation, and can therefore be much faster than conventional breeding. Since genetic engineering intervenes directly in the genome, the resulting plants and animals can be very different to those from conventional breeding. Therefore, it is necessary to treat these organisms with caution before any environmental releases take place or they are approved for use in food production. [Source]