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The comparison of RFLP,RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis
Authors:Wayne Powell  Michele Morgante  Chaz Andre  Michael Hanafey  Julie Vogel  Scott Tingey  Antoni Rafalski
Institution:(1) Biotechnology Research, Agricultural Products Department, E.I. du Pont de Nemours and Co (Inc.), Experimental Station, P.O.Box 80402, 19880-0402 Wilmington, DE, USA;(2) Present address: Scottish Crop Research Institute, Invergowrie, DD2 5DA Dundee, UK;(3) Present address: Dipartimento di Produzione Vegetale e Tecnologie Agrarie, Universita de Udine, Via della Scienze 208, I-33100 Udine, Italy;(4) Present address: Applied Biosystems Division, Perkin Elmer, 850 Lincoln Centre Drive, 94404 Foster City, CA, USA
Abstract:The utility of RFLP (restriction fragment length polymorphism), RAPD (random-amplified polymorphic DNA), AFLP (amplified fragment length polymorphism) and SSR (simple sequence repeat, microsatellite) markers in soybean germplasm analysis was determined by evaluating information content (expected heterozygosity), number of loci simultaneously analyzed per experiment (multiplex ratio) and effectiveness in assessing relationships between accessions. SSR markers have the highest expected heterozygosity (0.60), while AFLP markers have the highest effective multiplex ratio (19). A single parameter, defined as the marker index, which is the product of expected heterozygosity and multiplex ratio, may be used to evaluate overall utility of a marker system. A comparison of genetic similarity matrices revealed that, if the comparison involved both cultivated (Glycine max) and wild soybean (Glycine soja) accessions, estimates based on RFLPs, AFLPs and SSRs are highly correlated, indicating congruence between these assays. However, correlations of RAPD marker data with those obtained using other marker systems were lower. This is because RAPDs produce higher estimates of interspecific similarities. If the comparisons involvedG. max only, then overall correlations between marker systems are significantly lower. WithinG. max, RAPD and AFLP similarity estimates are more closely correlated than those involving other marker systems.Abbreviations RFLP restriction fragment length plymorphism - RAPD random-amplified polymorphic DNA - AFLP amplified fragment length polymorphism - SSR simple sequence repeat - PCR polymerase chain reaction - TBE Tris-borate-EDTA buffer - MI marker index - SENA sum of effective numbers of alleles
Keywords:AFLP  SSR  simple sequence repeat polymorphism  germplasm  microsatellite  polymorphism  RAPD  RFLP  soybean  Glycine
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