Comparison of Fluorescence and Silver-staining Detection Systems of Microsatellite Markers

Four-hundred and fifty-one wheat cultivars from Northern Winter Wheat Region were analyzed by fluorescence based genescan with multiple PCR microsatellite markers and SSR marker technology based on silver staining. In the same cultivars and the same set of SSR primers, the detection efficiency of the two systems was compared. At 24 loci among 451 accessions, total 235 alleles were obtained and average 9.8 alleles (from 3 to 20) were detected for every pairs of primers with silver staining system. However, average 13.0 alleles were detected by fluorescent system. Three more alleles were detected averagely by fluorescent system than silver-staining at one locus. With almost equal cost, the efficiency of fluorescent system was 7.8 times of silver staining system without consideration of instrument investment. Some other strategies, such as building low-cost and high-throughout multiple PCR system and data analysis using Genescan and Genotyper procedure were also discussed.