The ability to obtain callus cells from a plant and then regenerate new plants from this callus is not easy to do. Some crop lines are genetically more equipped to handle the stress from tissue culture. Unfortunately, these lines are usually older lines or wild-type species, both of which are agronomically inferior to modern, high-yielding hybrids and have a significantly lower yield potential.
The nutrient and environmental requirements of callus can differ between lines. A certain amount of time must be invested up front to determine the optimal conditions for growing a particular callus line. There are so many lines developed each year, it would be impossible for a genetic engineer to develop a tissue culture program for each one. Genetic engineers can make their best progress if they develop methods that work reliably on a small group of lines and continually work with them over several years. The better the agronomic traits of those lines, the shorter the time period will be from identifying a transgenic plant to marketing a genetically engineered variety or hybrid.
Another limitation to tissue culture is the occurence of genetic changes it can induce. Previous to transformation, the original cell is genetically identical to the plant or seed it was sampled from unless a mutation occurs. In most instances, this tissue culture induced variation is not desired. However, it was desirable in the case of ALS herbicide resistant corn and high sucrose soybeans. These plants derived their traits from mutations that arose during tissue culture.
Transformation methods that use callus cells are consequently highly genotype dependent for their successful implementation. For this reason, genetic engineers try to develop transformation systems that introduce genes into cells of the explant that are already programmed to differentiate into a plant.