Propagating plants through cloning is often much more expensive than producing plants from seeds. Plant propagation through cuttings, layering, grafting and division requires more equipment, knowledge and experience than most seed planting does, especially when performed on the mass scale. Cuttings, layers and grafts are usually kept in controlled environments to ensure success, until they are rooted. Tissue culture cloning is a complicated procedure performed in a laboratory by a botanist. Even when performing these tasks in the home garden, cloning is more expensive, harder work and more time consuming than planting seed.
Cloning prevents the natural evolution of plants pollinating and cross breeding with other plants to create new varieties, leading to a loss of diversity among species. Natural evolution helps to create different plants with different traits and characteristics such as leaf shapes, flower colors or plant size. All ecosystems naturally have multiple varieties of the same plant in that location. This prevents the elimination of that variety in the event something, such as a disease or pest, kills out one strain that is susceptible to it, while another variety will live, continuing the plant. By not allowing evolution to happen, entire strains of existing plants could be lost in locations where only cloned plants are used, leading to a lack of diversity in the gene pool.
A cloned plant cannot pollinate another plant from the same clone. To ensure cross-pollination for producing fruit, you must have clones from different unrelated plants. In some plantings, this is not a problem because fruit is not desired, but fruit trees are a popular cloned plant where fruit is wanted. When purchasing fruit trees, buy each fruit tree from a different nursery or ask the nursery if they can guarantee you plants from different clones to ensure cross-pollination and fruit production.
Cloned plants inherit the exact same traits and genes as the parent because cloning produces an identical plant. If the parent plant is susceptible to a disease, pest or type of infection, the clone will also continue to carry these traits and be susceptible to them as well. The result is a weak plant that spreads and perpetuates unwanted traits. Cross-breeding or careful selections of strains that are resistant to the problems helps to eliminate some of these traits and produce plants that are more resistant to the pests, infections or diseases in a particular location but inherited issues still remain a common problem of cloning.