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

Molecular Breeding

Volumn 2, Issue 3, 1996, Pages 225-238

  Powell, Wayne ^b   Morgante, Michele ^c   Andre, Chaz ^d   Hanafey, Michael ^a   Vogel, Julie ^a   Tingey, Scott ^a   Rafalski, Antoni ^a  

^a DUPONT COMPANY   (United States)

^b SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^c UNIVERSITY OF UDINE   (Italy)

^d PERKINELMER INC   (United States)

Author keywords

AFLP; Germplasm; Glycine; Microsatellite; Polymorphism; RAPD; RFLP; Simple sequence repeat polymorphism; Soybean; SSR

Indexed keywords

EID: 7844227430     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF00564200     Document Type: Review

References (57)

1. Akkaya MS, Bhagwat AA, Cregan PB: Length polymorphism of simple sequence repeat DNA in soybean. Genetics 132: 1131-1139 (1992).
2. Beckmann JS, Soller M: Restriction fragment length polymorphisms in genetic improvement: methodologies, mapping and costs. Theor Appl Genet 67: 35-43 (1983).
3. Bell CJ, Ecker JR: Assignment of thirty microsatellite loci to the linkage map of Arabidopsis. Genomics 19: 137-144 (1994).
4. Botstein D, White RL, Skolnick MH, Davis RW: Construction of a genetic map in man using restriction fragment length polymorphisms. Am J Hum Genet 32: 314-331 (1980).
5. Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL: High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455-457 (1994).
6. Caetano-Anolles G, Bassam BJ, Gresshoff PM: High resolution DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Bio/technology 9: 553-557 (1991).
7. Coe J E.H., Neuffer MG, Hoisington DA: The genetics of corn. In: Sprague GF, Dudley JW (eds) Corn and Corn Improvement, pp. 81-258. American Society of Agronomy, Madison, WI (1988).
8. Cornall RJ, Aitman TJ, Hearne CM, Todd JA: The generation of a library of PCR-analyzed microsatellite variants for genetic mapping of the mouse genome. Genomics 10: 874-881 (1991).
9. Delanney X, Rodgers DM, Palmer RG: Relative genetic contributions among ancestral lines to North-American soybean cultivars. Crop Sci 23: 944-949 (1983).
10. Dietrich W, Katz H, Lincoln SE, Shin H-S, Friedman J, Dracopoli NC, Lander ES: A genetic map of the mouse suitable for typing intraspecific crosses. Genetics 131: 423-447 (1992).
11. dos Santos JB, Nienhuis J, Skroch P, Tivang J, Slocum MK: Comparison of RAPD and RFLP genetic markers in determining genetic similarity among Brassica oleracea L. genotypes. Theor Appl Genet 87: 909-915 (1994).
12. Gregorius HR: The relationship between the concepts of genetic diversity and differentiation. Theor Appl Genet 74: 397-401 (1987).
13. Hallden C, Nilsson N-O, Rading IM. Saell T: Evaluation of RFLP and RAPD markers in comparison of Brassica napus breeding lines. Theor Appl Genet 88: 123-128 (1994).
14. Hymowitz T, Bernard RL: Origin of the soybean and germplasm introduction and development in North America. In: Use of Plant Introductions in Cultivar Development, Part I CSSA Special Publication 17, pp. 147-164. Crop Science Society of America, Madison, WI (1991).
15. Lawler FC, Stoffel S, Saiki RK, Chang S-Y, Landre PA, Abramson RD, Gelfand DH: High-level expression, purification, and enzymatic characterization of full-length Thermus aquaticus DNA polymerase and a truncated form deficient in 5′ to 3′ exonuclease activity. PCR Meth Appl 2: 275-287 (1993).
16. Li Z, Furnier GR: Comparison of allozyme, RFLP, and RAPD markers for revealing genetic variation within and between trembling aspen and bigtooth aspen. Theor Appl Genet 87: 97-105 (1993).
17. Lin J-J, Kuo J: AFLP™ : A Novel PCR-Based Assay for Plant and Bacterial DNA Fingerprinting. Focus 17: 66-70 (1995).
18. Mantel N: The dedection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220 (1967).
19. Marshall DR, Allard RW: Isozyme polymorphisms in natural populations of Aven fatua and Avena barbata. Heredity 25: 373-382 (1970).
20. Morgante M, Olivieri AM: PCR-amplified microsatellites as markers in plant genetics. Plant J 3: 175-182 (1993).
21. Morgante M, Rafalski JA, Biddle P, Tingey S, Olivieri AM: Genetic mapping and variability of seven soybean simple sequence repeat loci. Genome 37: 763-769 (1994).
22. Nei M: Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70: 3321-3323 (1973).
23. Nei M, Li WH: Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76: 5269-5273 (1979).
24. Parks C, Chang L-S, Shenk T: A polymerase chain reaction mediated by a single primer: cloning of genomic sequences adjacent to a serotonin receptor protein coding region. Nucl Acids Res 19: 7155-7160 (1991).
25. Peakall R, Smouse PE, Huff DR: Evolutionary Implications of allozyme and RAPD variation in diploid populations of dioecious buffalograss Buchloe dactyloides. Mol Ecol 4: 135-147 (1995).
26. Rafalski A, Tingey S: RFLP map of soybean (Glycine max) 2n=40. In: O'Brien SJ (ed) Genetic Maps. Locus Maps of Complex Genomes. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1993).
27. Rafalski A, Tingey S, Williams JGK: Random amplified polymorphic DNA (RAPD) markers. In: Gelvin SB, Schilperoort RA, Eds. Plant Molecular Biology Manual, pp. 1-8. Kluwer Academic Publishers, Dordrecht (1994).
28. Rafalski JA, Morgante M, Powell W, Vogel JM, Tingey SV: Generating and using DNA markers in plants. In: Birren B, Lai E, (eds) Analysis of Non-mammalian Genomes: A practical Guide, press. Academic Press, Boca Raton, FL (1996).
29. Rafalski JA, Tingey SV: Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trends Genet 9: 275-280 (1993).
30. Rohlf FJ: NTSYS-pc Numerical Taxonomy and Multivariate Analysis System version 1.7. Owner manual (1992).
31. Rongwen J, Akkaya MS, Bhagwat AA, Lavi U, Cregan PB: The use of microsatellite DNA markers for soybean genotype identification. Theor Appl Genet 90: 43-48 (1995).
32. Rus-Kortekass W, Smulders MJM, Arens P, Vosman B: Direct comparison of levels of genetic variation in tomato detected by a GACA-containing microsatellite probe and by random amplified polymorphic DNA. Genome 37: 375-381 (1994).
33. Saghai Maroof MA, Biyashev RM, Yang GP, Zhang Q, Allard RW: Extraordinarily polymorphic microsatellite DNA in Barley: Species diversity, chromosomal locations, and population dynamics. Proc Natl Acad Sci USA 91: 5466-5470 (1994).
34. Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (1989).
35. Senior ML, Heun M: Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer. Genome 36: 884-889 (1993).
36. Serikawa T, Kuramoto T, Hilbert P, Mori M, Yamada J, Dubay CJ, Lindpainter K, Ganten D, Guenet J-L, Lathrop GM, Beckman JS: Rat gene mapping using PCR-analyzed microsatellites. Genetics 131: 701-721 (1992).
37. Smith OS, Smith JSC, Bowen SL, Tenborg RA, Wall SJ: Similarities among a group of elite maize inbreds as measured by pedigree, F1 grain-yield, heterosis and RFLPs. Theor Appl Genet 80: 833-840 (1990).
38. Sokal RR, Michener CD: A statistical method for evaluating systematic relationships. Univ Kansas Sci Bull 38: 1409-1438 (1958).
39. Tautz D: Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucl Acids Res 17: 6463-6471 (1989).
40. Tautz D, Renz M: Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucl Acids Res 12: 4127-4138 (1984).
41. Tautz D, Trick M, Dover GA: Cryptic simplicity in DNA is a major source of genetic variation. Nature 322: 652-656 (1986).
42. Thomas MR, Cain P, Scott NS: DNA typing of grapwvine: A universal methodology and database for describing cultivars and evaluating genetic relatedness. Plant Mol Biol 25: 939-949 (1994).
43. Thomas MR, Scott NS: Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theor Appl Genet 86: 985-990 (1993).
44. Thormann CE, Ferreira ME, Camargo LEA, Tivang JG, Osborn TC: Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species. Theor Appl Genet 88: 973-980 (1994).
45. Tibayrenc M, Neubauer K, Barnabe C, Guerrini F, Skarecky D, Ayala FJ: Genetic characterization of six parazitic protozoa: Parity between random-primer DNA typing and multilocus enzyme electrophoresis. Proc Natl Acad Sci USA 90: 1335-1339 (1993).
46. Tingey SV, del Tufo JP: Genetic Analysis with RAPD Marklers. Plant Physiol 101: 349-352 (1993).
47. Todd JA: La carte des microsatellites est arrivé! Human Mol Genet 1: 663-666 (1992).
48. Waugh R, Powell W: Using RAPD markers for crop improvement. Trends Bio/technol 10: 186-191 (1992).
49. Weber J, May PE: Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44: 388-396 (1989).
50. Weissenbach J Ed.: The Genethon microsatellite map catalogue. Genethon, Evry, France (1992).
51. Welsh J, McClelland M: Fingerprinting genomes using PCR with arbitrary primers. Nucl Acids Res 18: 7213-7218 (1990).
52. Whitkus R, Doebley J, Wendel JF: Nuclear DNA Markers in systematics and evolution. In: Phillips RL. Vasil IK, (eds) DNA Based Markers in Plants pp. 116-141. Kluwer Academic Publishers, Dordrecht (1994).
53. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV: DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acids Res 18: 6531-6535 (1990).
54. Williams JGK, Rafalski JA, Tingey SV: Genetic analysis using RAPD markers. Meth Enzymol 218: 704-780 (1993).
55. Wu K-S, Tanksley SD: Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241: 225-235 (1993).
56. Yang GP, Saghai Maroof MA, Xu CG, Zhang Q, Biyashev RM: Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet 245: 187-194 (1994).
57. Zabeau M, Voss P: Selective restriction fragment amplification: a general method for DNA fingerprinting. European Patent Application 92402629.7 (1993).