• With advancements in our understanding of the genetic basis of plant diseases, genetic engineering has been effectively utilized for developing plants resistant to various plant pests and thus diseases.
• Also plants resistant to newer herbicides used to control weed growth have become a possibility due to strategies such as over producing the enzyme that confers herbicide resistance to the plant.
• Plant cells transformed by bacterial genes from a bacterium lethal to insects have produced transgenic plants resistant to insect pests, for example, Boll worm–resistant cotton plants. Many such genetically transformed economically important plants are now insect resistant. This reduces cost spent on pesticides and enhances the yield, as plants are healthy and also act as biopesticides.
• Milder forms of viral strains may be used to transfect host plants to develop resistance to more virulent strains of virus much similar to vaccination to protect it, for example, papaya against papaya ring spot disease.
• Genes responsible for plant pathogen defense mechanisms are identified and made to over express in plants making them resistant to a range of bacterial and fungal pathogens.
• Similar over expression of genes coding for compounds released in response to abiotic stress such as drought, temperature extremes, and nutrient deficiency are used to develop transgenic plants that can better tolerate such adverse conditions.
• Fruit ripening may be delayed to enable the intact transfer of fruits to distant locations over a longer duration. This can be done by transgenic plants whose ethylene-producing genes have in-built trigger genes that slow down natural ethylene production by the fruits.
• By manipulating enzymes involved in the biosynthesis of several phytochemicals, plant yield with respect to these economically important compounds may be greatly increased. Such experiments have been tried on Taxus species to enhance taxol yield.
• Transgenic tobacco plants bearing gene coding for mannitol dehydrogenase from E. coli produce high levels of mannitol. Transgenic potato bearing the gene coding for cyclodextrin glucosyl transferase from Klebsiella produces tubers rich in α- and β-cyclodextrin, which is used as a drug solubilizing agent in pharmaceutical dosage forms.
• Transgenic rice able to generate vitamin A as a result of having three additional genes that code for enzymes controlling carotenoid biosynthesis has been developed.
• Genes coding for many therapeutic and diagnostic proteins having been identified, transgenic plants with such genes may be used as sources of monoclonal antibodies, blood plasma proteins, growth hormones, cytokinins, etc.
• Likewise, if antigenic proteins can be produced in plants, they will become sources of vaccines as well.

These modifications may be possible when few genes have to be manipulated. However, plant secondary metabolite biogenesis happens due to a complex and multiple cascade of metabolic reactions, controlled by multiple enzymes. It may still be a long time before we have transgenic plants acting as biochemical factories generating the needed quantity of secondary metabolites.