A low-cost, high-throughput polyacrylamide gel electrophoresis system for genotyping with microsatellite DNA markers

Microsatellite DNA markers are widely used in genetic research. Their use, however, can be costly and throughput is sometimes limited. The objective of this paper is to introduce a simple, low-cost, high-throughput system that detects amplification products from microsatellite markers by nondenaturing polyacrylamide gel electrophoresis. This system is capable of separating DNA fragments that differ by as little as two base pairs. The electrophoresis unit holds two vertical 100-sample gels allowing standards and samples from a 96-well plate to be analyzed on a single gel. DNA samples are stained during electrophoresis by ethidium bromide in the running buffer. In addition, one of the gel plates is UV-transparent so that gels can be photographed immediately after electrophoresis without disassembling the gel-plate sandwich. Electrophoresis runs are generally less than two hours. The cost per gel, excluding PCR cost, is currently estimated at about $2.60, or less than $0.03 per data point. This system has been used successfully with soybean [Glycine mar (L.) Merr.] and wheat (Triticum aestivum L.) microsatellite markers and could be a valuable tool for researchers employing markers in other species.