Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.)

Theoretical and Applied Genetics

Volumn 100, Issue 5, 2000, Pages 713-722

  Cho, Y G ^a,c   Ishii, T ^a,d   Temnykh, S ^a   Chen, X ^a   Lipovich, L ^a,e   McCouch, S R ^a   Park, W D ^b   Ayres, N ^b   Cartinhour, S ^a,b  

^a Department of Molecular Biology and Genetics   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c Chungbuk National University   (South Korea)

^d KOBE UNIVERSITY   (Japan)

^e UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Allelic diversity; Microsatellite marker; Rice (Oryza sativa L.); Simple sequence repeat (SSR)

Indexed keywords

EXPRESSED SEQUENCE TAG; GENE LOCATION; GENE LOCUS; GENETIC CONSERVATION; GENETIC CORRELATION; GENETIC CROSS; GENETIC DIVERSITY; GENETIC MARKER; GENETIC POLYMORPHISM; GENETIC SCREENING; GENETIC VARIANCE; GENOME LIBRARY; MICROSATELLITE DNA; REPETITIVE DNA;

EMBRYOPHYTA; ORYZA SATIVA;

EID: 0034090835     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s001220051343     Document Type: Article

References (35)

1. Akagi H, Yokozeki Y, Inagaki A, Fujimura T (1996) Microsatellite DNA markers for rice chromosomes. Theor Appl Genet 93: 1071-1077
2. Akagi H, Yokozeki Y, Inagaki A, Fujimura T (1997) Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theor Appl Genet 94: 61-67
3. Anderson JA, Churchill GA, Sutrique JE, Tanksley SD, Sorrels ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36: 181-186
4. Ayers NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD (1997) Microsatellites and a single nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germplasm. Theor Appl Genet 94: 773-781
5. Becker J, Heun M (1995) Barley microsatellites: allele variation and mapping. Plant Mol Biol 27: 835-845
6. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32: 314-331
7. Bowcock AM, Ruiz-Linares A, Tomfohrde J, Munch E, Kidd JR, Cavalli-Sforza LL (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455-457
8. Brinkmann B, Klintschar M, Neuhuber F, Huhne J, Rolf B (1998) Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. Am J Hum Genet 62: 1408-1415
9. Chakraborty R, Kimmel M, Strivers DN, Davison LJ, Deka R (1997) Relative mutation rates at di-tri-and tetranucleotide microsatellite loci. Proc Natl Acad Sci USA 94: 1041-1046
10. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95: 553-567
11. Chin ECL, Senior ML, Shu H, Smith JSC (1996) Maize simple repetitive DNA sequences: abundance and allele variation. Genome 39: 866-873
12. Dellaporta SL, Wood T, Hicks TB (1983) A plant DNA mini preparation: version II. Plant Mol Biol Rep 1: 19-21
13. Dib C, Fauré S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Seboun E, Lathrop M, Gyapay G. Mirissette J, Weissenbach J (1996) A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380: 152-154
14. Dietrich WF, Miller J, Steen R, Merchant MA, Damron-Boles D, Husain Z, Dredge R, Daly MJ, Ingalls KA, O'Connor TJ, Evans CA, DeAngelis MM, Levinson DM, Kruglyak L, Goodman N, Copelang NG, Jenkins NA, Hawkins TL, Stein L, Page DC, Lander ES (1996) A comprehensive genetic map of the mouse genome. Nature 380: 149-152
15. Di Rienzo A, Peterson AC, Gurza JC, Valdes AM, Slatkin M, Freimer NB (1994) Mutational process of simple-sequence repeat loci in human populations. Proc Natl Acad Sci USA 91: 3166-3170
16. Goldstein DB, Clark AG (1995) Microsatellite variation in North American populations of Drosophila melanogaster. Nucleic Acids Res 23: 3882-3886
17. Harr B, Zangerl B, Brem G, Schlötterer C (1998) Conservation of locus-specific microsatellite variability across species:a comparison of two Drosophila sibling species. D. melanogaster and D. simulans. Mol Biol Evol 15: 176-184
18. Innan H, Terauchi R, Miyashita T (1997) Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics 146: 1441-1452
19. Jarne P, Lagoda PJL (1996) Microsatellites from molecules to populations and back. Trends Ecol Evol 11: 424-429
20. Jurka J, Pethiyagoda C (1995) Simple repetitive DNA sequences from primates: compilation and analysis. J Mol Evol 40: 120-126
21. Levinson G, Gutman GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4: 203-221
22. McCouch SR, Chen X, Panaud O, Temnykh S, Xu Y, Cho YG, Huang N, Ishii T, Blair M (1997) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 35: 89-99
23. McMurray CT (1995) Mechanisms of DNA expansion. Chromosoma 104: 2-13
24. Meyer E, Wiegand P, Rand SP, Kuhlmann D, Brack M, Brinkmann B (1995) Microsatellite polymorphisms reveal phylogenetic relationships in primates. J Mol Evol 41: 10-14
25. Milbourne D, Meyer RC, Collins AJ, Ramsay LD, Gebhardt C, Waugh R (1998) Isolation, characterization and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259:233-245
26. Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSR) in rice (Oryza sativa L.). Mol Gen Genet 252: 597-607
27. Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1: 215-222
28. Schlötterer C, Vogl C, Tautz D (1997) Polymorphism and locus-specific effects on polymorphism at microsatellite loci in natural Drosophila melanogaster populations. Genetics 146: 309-320
29. Schug MD, Mackay TFC, Aquadro CF (1997) Low mutation rates of microsatellite loci in Drosophila melanogaster. Nat Genet 15: 99-102
30. Schug MD, Hutter CM, Wetterstrand KA, Gaudette MS, Mackay TFC, Aquadro CF (1998) The mutation rates of di-, tri-and tetranucleotide repeats in Drosophila melanogaster. Mol Biol Evol 5: 1751-1760
31. Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457-462
32. Temnykh S, Park W, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (1999) Mapping and genome organization of microsatellites in rice (Oryza sativa L). Theor Appl Genet 100:698-712
33. Weber JL (1990) Informativeness of human (dC-dA)n (dG-dT)n polymorphisms. Genomics 7: 524-530
34. Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241: 225-235
35. Yang GP, Saghai Maroof MA, Xu CG, Zhang Q, Biyashev RM (1994) Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet 245: 187-194