the plants are cross bred for generations. Each time the seeds of the plants with the best desired properties are kept.

the seeds can also be treated (see "feminizing marijuana seeds) with chemicals to produce certain traits.

the producers of these seeds (like monsanto, bayer, basf, ...) have large R&D groups where the dna of the seeds can be further tracked and modified if required.

these producers have large green houses just for breeding the plants and collecting the desired seeds.

these seeds are patented. The plants produce fruits to specifications. To protect the intellectual property, patents and business, they are made not to produce further offspring, so the farmer needs to buy the seeds year after year.

another trait that's being developped in the plants, for example, is making the plant immune to glyphosate, allowing the farmer to wastefully spray the herbicide on the field. It will kill all plants except for the desired crops.

source: used to work in for one of the above mentioned companies in the cropscience division.

It depends on the fruit in question, really.

Seedless Watermelon, for example, was developed by hybridizing diploid plants (has 2 chromosomes,) with tetraploid plants (they have 4 chromosomes,). Incidentally, this creates a triploid that happens to be sterile.

the way this is done is taking the pollen from a male diploid watermelon and pollinating female tetraploids. the fruit grows as you would expect and develop seeds that are themselves sterile (they can grow into plants, but don't generate seeds.) (we still commonly grow seeded water melons because inorder to trigger fruit development, the seedless variety needs to be pollinated; it just doesn't develop the mature seeds, and instead, has 'seed casings'- the white things.)

many seedles variets of grapes can be propagated from cuttings; though they too were originally developed the same as watermelons.

Bananas are all clones; by the way. The only kinds of banana that are also edible are sterile. (this is actually potentially a huge problem.) Banana trees will send up new shoots every so often coming up along side the main stem/trunk, these stalks are what produce the fruit, but they can be cut off at the base (with some roots,) and then replanted.

Tree fruits are generally hybridized and grafted onto root stock. (apples commonly are grafted because it's faster and you can use a more hardy rootstock with better varieties of apples. The roots are genetically one variety of tree, while everything else is another.) this would include otherwise sterile varieties.

My guess would be from cloned cuttings, but I don't know for certain.

Seedless watermelons, at least, still have seeds. They're just not as numerous, or as big (and often just white instead of black). Also, many plants can be cloned by planting a cutting from the stem.

From cuttings.

It's not even new. We had it from centuries.

Genetic Modification