The disadvantages of cross-pollination include:
Decrease in quality of the fruits produced from the self-pollinated plants.
Lower crop yields because some of the seeds have not been fertilized.
Increased production costs and reduced efficiency because more resources are required for the pollination process.
Changes in plant morphology (e.g., altered flowering time or flower structure) as a result of interplant pollination.
Loss of genetic diversity.
Altered gene expression.
Possible disease transmission.
Alteration of plant physiology.