Molecular markers and MAS used

Molecular markers are identifiable DNA sequences, found at specific locations of the genome and associated with the inheritance of a trait or linked gene.

Molecular markers can be used for
(a) marker-assisted breeding,
(b) understanding and conserving genetic resources and
(c) genotype verification.

Genetic linkage maps can be used to locate and select for genes affecting traits of economic importance in plants or animals. The potential benefits of marker-assisted selection (MAS) are greatest for traits that are controlled by many genes.

Markers can also be used to increase the speed or efficiency of introducing new genes from one population to another, for example when wishing to introduce genes from wild relatives into modern plant varieties. When the desired trait is found within the same species, it may be transferred with traditional breeding methods, with molecular markers being used to track the desired gene.

Genetic engineering can be used when insufficient natural variation in the desired nutrient exists within a species. Biofortification (the development of nutritionally enhanced foods) can be advanced through the application of several biotechnologies in combination. Genomic analysis and genetic linkage mapping are needed to identify the genes responsible for natural variation in nutrient levels of common foods. These genes can then be transferred into familiar cultivars through conventional breeding and MAS or, if sufficient natural variation does not occur within a single species, through genetic engineering. Non-transgenic approaches are being used, for example, to enhance the protein content in maize, iron in rice, and carotene in sweet potato.

References: http://www.greenfacts.org/en/gmo/index.htm#4
The State of Food and Agriculture 2003-2004