Characteristics of genetic markers: Operational costs

Wages, laboratory facilities, technical equipment and consumables all contribute to the operational costs of the technologies. Relatively expensive consumables include Taq-polymerase needed for all PCR-based marker types, restriction enzymes (for RFLPs, minisatellites and CAPS, and particularly the restriction enzyme MseI often used in AFLPs) and isotopes where polymorphisms are visualized by means of radioactive labelling. Polyacrylamide gels are more expensive to run than agarose gels and require visualization of polymorphisms by autoradiography or silver staining procedures, which are more costly compared to ethidium-bromide staining. Laborious and technically demanding markers, such as RFLPs, minisatellites, PCR sequencing, and those techniques being performed by automated equipment, are quite expensive. Costs of performing RAPD analyses are usually considered low. However, if measures to ensure reproducibility and low numbers of markers per primer are taken into account, costs may increase to the level of the more complex technologies. In general, operational costs of markers will vary depending on the methodology. Regarding automated procedures and technologies, while purchasing the equipment is usually very expensive and the technical expertise required is high, a significant increase in throughput may be obtained through multiplexing. An additional consideration is the emergence of cost effective “outsourcing” companies to generate marker-based and DNA sequencing data, as service laboratories keep up with efficient equipment developments. Outsourcing allows researchers to concentrate on defining questions, experimental design, data analysis and interpretation. The relative costs/benefits of outsourcing will vary in different labs according to local labour and supply costs, availability of equipment, the benefit of generating your own data for quality control or educational purposes, and the legal requirements to ship crop germplasm DNA out of a country.