Usually, scientists do not test for the genes themselves, since many of the genes are still not known. Instead, they look for markers along the chromosome that are near the gene and therefore tend to travel with the gene from one generation to the next. The advantage of this technique is that the markers can be used even if the breeders have not identified the gene. Genetic engineering can be done only if the gene is known and isolated. It is also possible to use markers to follow numerous traits through the breeding process.
Genetic engineering is at present limited to transferring only one or a few genes.
Yet many traits, like the yield of a crop, are governed by multiple genes. But marker-assisted selection can be extremely difficult and has not lived up to the expectations scientists had when the technique was first developed in the late 1980's, said Nevin D. Young, professor of plant pathology and biology at the University of Minnesota. Markers are like loaded dice, but they're hardly precise surgical instruments. It can take years to find the associations between markers and traits, and sometimes links cannot be found at all, he said. Still the costs of such genetic analysis are expected to drop rapidly with the advancement of new DNA testing methods that are also being developed for medical diagnosis.