Not all genetically modified organisms (GMO) that are used for food increase the food quality. Some GMOs are manipulated so as to be easier to grow. For example, genes may be inserted into plants to make them more resistant to disease. Genes are taken from a plant or other source that can resist a disease and are inserted into another plant to give it more resistance or other feature such as expressing its own pesticide.
GMO foods can be made to be higher quality through the same sort of mechanism. Let us imagine, for instance, that a certain kind of food (like a certain nut) has fatty acids in it that are good for heart health. If the genes that give the plant that attribute can be isolated, they might be inserted into another plant (like wheat) that lacks such acids. If this can be done, the wheat will be more “heart healthy” than it previously was. There are efforts currently underway to genetically engineer tomatoes that will be able to raise levels of “good cholesterol” and otherwise enhance heart health.
In short, GMO foods can be modified to give them new properties that do more to promote health. This increases their “food quality.”