Molecular Breeding

, Volume 2, Issue 3, pp 225–238

The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis

Authors

  • Wayne Powell
    • Biotechnology Research, Agricultural Products DepartmentE.I. du Pont de Nemours and Co (Inc.)
  • Michele Morgante
    • Biotechnology Research, Agricultural Products DepartmentE.I. du Pont de Nemours and Co (Inc.)
  • Chaz Andre
    • Biotechnology Research, Agricultural Products DepartmentE.I. du Pont de Nemours and Co (Inc.)
  • Michael Hanafey
    • Biotechnology Research, Agricultural Products DepartmentE.I. du Pont de Nemours and Co (Inc.)
  • Julie Vogel
    • Biotechnology Research, Agricultural Products DepartmentE.I. du Pont de Nemours and Co (Inc.)
  • Scott Tingey
    • Biotechnology Research, Agricultural Products DepartmentE.I. du Pont de Nemours and Co (Inc.)
  • Antoni Rafalski
    • Biotechnology Research, Agricultural Products DepartmentE.I. du Pont de Nemours and Co (Inc.)
Research Paper

DOI: 10.1007/BF00564200

Cite this article as:
Powell, W., Morgante, M., Andre, C. et al. Mol Breeding (1996) 2: 225. doi:10.1007/BF00564200

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.

Key words

AFLPSSRsimple sequence repeat polymorphismgermplasmmicrosatellitepolymorphismRAPDRFLPsoybeanGlycine

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

Copyright information

© Kluwer Academic Publishers 1996