Although apples reproduce in nature by seed, many commercial apple trees are produced using asexual cloning techniques to ensure consistency and quality in the fruit. The appropriate method depends on a number of things including whether consistency among various apple trees--- such as in an orchard producing Fuji apples ---is necessary.
Apples have been a part of culinary traditions since prehistoric times. Although known since antiquity in Asia, they were commonly cultivated in Europe by the time of the Roman empire, according to Purdue University's Midwest Apple Improvement Association. Early apples were likely grown from seed, with asexual reproduction via grafting and rooting becoming common in later times.
Flowers & Seeds
In nature, apples reproduce in the same way as other flowering plants. Pollen from the male parts of the flower makes its way to the stigmas; the female parts of the flower. Fertilized flowers eventually die, leaving a bud that grows into an apple. Animals or people take the apple and consume the outer layer of fruit, often dropping or intentionally discarding the seeds. Those seeds can eventually take root and grow into a new apple tree.
One of two types of asexual cloning that is used in commercial apple tree reproduction is grafting. In a grafted tree, a living branch is cut from a known cultivar, like a Fuji, Granny Smith, or Red Delicious. That branch is grafted to a compatible root stock where it attaches itself and begins to draw nutrients from the roots. Grafting is a way of ensuring that the apples produced by the new tree will be identical to apples that grow on the parent tree. By selecting a cold, tolerant root stock, varieties of apples can sometimes grow in colder areas.
In areas where particular varieties of apples will grow on their natural root stocks, cloned apple trees can be made by rooting cuttings taken from young growth. Rooting has many of the same advantages as grafting. Because the trees are genetically identical to the parent trees, the apples will also be identical. In most cases, rooted trees will need to be grown for several years in a greenhouse or protected environment before being transplanted outside.
New varieties of apples are often created by cross pollinating two existing varieties. When creating a new variety, growers take pollen from one variety and place it in the stigma of a different variety. In this way, genetic aspects of the two varieties merge to create a new variety. Once a new tree with the desired characteristics begins to grow, it can be cloned using grafting or rooting to create more trees with the new variety of apples.