MAS can be useful to select for traits that are difficult or expensive to measure, exhibit low heritability and/or are expressed late in development.
In 1923, Karl Sax first reported association of a simply inherited genetic marker with a quantitative trait in plants when he observed segregation of seed size associated with segregation for a seed coat color marker in beans (Phaseolus vulgaris L.).
The gene of interest directly causes production of protein(s) or RNA that produce a desired trait or phenotype, whereas markers (a DNA sequence or the morphological or biochemical markers produced due to that DNA) are genetically linked to the gene of interest.
For some traits, the gene of interest has been discovered and the presence of desirable alleles can be directly assayed with a high level of confidence.
Numerous markers have been mapped to different chromosomes in several crops including rice, wheat, maize, soybean and several others, and in livestock such as cattle, pigs and chickens.
Those markers have been used in diversity analysis, parentage detection, DNA fingerprinting, and prediction of hybrid performance.
Such characteristics include disease resistance, male sterility,[12] self-incompatibility, and others related to shape, color, and architecture of whole plants and are often of mono- or oligogenic in nature.
Alternatively, in such cases that the target gene of interest differs between two alleles by a difficult-to-detect single nucleotide polymorphism, an external marker (be it another gene or a polymorphism that is easier to detect, such as a short tandem repeat) may present as the most realistic option.
Situations such as: The cost of genotyping (for example, the molecular marker assays needed here) is decreasing thus increasing the attractiveness of MAS as the development of the technology continues.
For example, if two flanking markers are used at same time with an interval between them of approximately 20cM, there is higher probability (99%) for recovery of the target gene.
Linkage between the phenotype and markers which have already been mapped is tested in these populations in order to determine the position of the QTL.
[13][14] In such an approach, in the first few breeding cycles, markers linked to the trait of interest are identified by QTL mapping and later the same information is used in the same population.