Characteristics of genetic markers: Development costs
Marker development may be very time-consuming and costly when suitable probes or sequence data for primer construction are unavailable. Development of suitable probes for Southern blot hybridizations (e.g. for RFLP analysis) requires the construction of either genomic or cDNA libraries and the examination of various probe/restriction enzyme combinations for their ability to detect polymorphisms. The development of site-specific PCR primers (e.g. for microsatellite analysis) also requires the construction of libraries, which then need to be screened to identify the fragments of interest. Subsequently, the identified fragments need to be sequenced to verify their suitability and to design primers. Therefore, the investment required for marker development should be evaluated in relation to the intended range of application of the technique. Alternatively, new genomic tools are allowing probes, primers and sequence data to be obtained from genome databases of other species, with the understanding, as in all DNA tools, that their usefulness may decrease with increasing evolutionary distance between the species.