Molecular and General Genetics MGG

, Volume 241, Issue 1–2, pp 225–235

Abundance, polymorphism and genetic mapping of microsatellites in rice

  • Kun-Sheng Wu
  • Steven D. Tanksley
Original Articles


Dinucleotide microsatellites have been characterized and used as genetic markers in rice. Screening of a rice genomic library with poly(dG-dA)·(dC-dT) and poly(dG-dT)·(dC-dA) probes indicated that (GA)n repeats occurred, on average, once every 225 kb and (GT)n repeats once every 480 kb. DNA sequencing of ten randomly selected microsatellites indicated that the numbers of repeats ranged from 12 to 34 and that the patterns of microsatellites in rice were similar to those of humans and other mammals. Primers to these microsatellite loci as well as to four published microsatellite-containing sequences have been designed and degrees of polymorphism has been examined with 20 rice accessions. Multiple alleles, ranging from 5 to 11, have been observed at all the microsatellite loci in 20 rice accessions. Alleles specific to two cultivated subspecies, indica and japonica, were found in some microsatellite loci. Heterozygosity values of all the microsatellite markers were significantly higher than those of RFLP markers, based upon a parallel comparison. Ten microsatellite loci have been genetically mapped to four rice chromosomes. The genomic distribution of microsatellites appears to be random in rice.

Key words

Microsatellites Simple sequence repeats Genetic mapping rice 


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  1. Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132:1131–1139Google Scholar
  2. Armour JAL, Wong A, Wilson V, Royle NJ, Jeffreys AJ (1989) Sequences flanking the repeat arrays of human minisatellites: Association with tandem and dispersed repeat elements. Nucleic Acids Res 17:4925–4935Google Scholar
  3. Arumuganathan K, Early ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218Google Scholar
  4. Beckmann JS, Weber JL (1992) Survey of human and rat microsatellites. Genomics 12:627–531Google Scholar
  5. 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 32:314–331Google Scholar
  6. Chunwongse J, Martin GB, Tanksley SD (1993) Pre-germination genotypic screening using PCR amplification of half-seeds. Theor Appl Genet, in pressGoogle Scholar
  7. Condit R, Hubbell SP (1991) Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. Genome 34:66–71Google Scholar
  8. Cornall RJ, Aitman TJ, Hearne CM, Todd JA (1991) The generation of a library of PCR-analyzed microsatellite variants for genetic mapping of the mouse genome. Genomics 10:874–881Google Scholar
  9. Decker RA, Moore J, Pondeer B, Weber JL (1992) Linkage mapping of human chromosome 10 microsatellite polymorphisms. Genomics 12:604–606Google Scholar
  10. Hamada H, Perrino MG, Kakunaga T (1982) A novel repeat element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci USA 79:6465–6469Google Scholar
  11. Hazan J, Dubay C, Pankowiak MP, Becuwe N, Weissenbach J (1992) A genetic linkage map of human chromosome 20 composed entirely of microsatellite markers. Genomics 12:183–189Google Scholar
  12. Jeffreys AJ, Royle NY, Wilson V, Wong Z (1988) Spontaneous mutation rates to new length alleles at tandem-repetitive hypervariable loci in human DNA. Nature 332:278–280Google Scholar
  13. Jeffreys AJ, Wilson V, Thein SL (1985) Hypervariable ‘minisatellite’ regions in human DNA. Nature 314:67–73Google Scholar
  14. Kay SA, Keith B, Shinozaki K, Chye ML, Chua NH (1989) The sequence of the rice phytochrome gene. Nucleic Acids Res 17:2865–2866Google Scholar
  15. Kondo H, Emori Y, Abe K, Suzuki K, Arai S (1989) Cloning and sequence analysis of the genomic fragment encoding oryzacystatin. Gene 81:259–265Google Scholar
  16. Kosambi D (1944) The estimation of map distances from recombination values. Ann. Eugen 12:172–175Google Scholar
  17. Kwiatkowski DJ, Henske EP, Weimer K, Ozelius L, Gusella JF, Haines J (1992) Construction of a GT polymorphism map of human 9q. Genomics 12:229–240Google Scholar
  18. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181Google Scholar
  19. Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 4:397–401Google Scholar
  20. Love JM, Knight AM, McAleer MA, Todd JA (1990) Towards construction of a high resolution map of the mouse genome using PCR-analyzed microsatellites. Nucleic Acids Res 18:4123–4130Google Scholar
  21. Matsuoka M (1990) Classification and characterization of cDNA that encodes the light-harvesting chlorophyll a/b binding protein of photosystem II from rice. Plant Cell Physiol 31:519–526Google Scholar
  22. Mills KA, Buetow KH, Xu Y, Weber JL, Altherr MR, Wasmuth JJ, Murray JC (1992) Genetic and physical maps of human chromosome 4 based on dinucleotide repeats. Genomics 14:209–219Google Scholar
  23. Nakamura Y, Leppert M, O'Connell P, Wolef R, Holm T, Culver M, Martin C, Fujimoto E, Hoff M, Kumlin E, White R (1987) Variable number of tandem repeat (VNTR) markers for human genome mapping. Science 235:1616–1622Google Scholar
  24. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590Google Scholar
  25. Royle NJ, Clarkson RE, Wong Z, Jeffreys AJ (1988) Clustering of hypervariable minisatellites in the proterminal regions of human autosomes. Genomics 3:352–360Google Scholar
  26. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 77:5463–5467Google Scholar
  27. Sano H, Youssefian S (1991) A novel Ras-related RGP1 gene encoding a GTP-binding protein has reduced expression in 5-azacytidine-induced dwarf rice. Mol Gen Genet 228:227–232Google Scholar
  28. Starllings RL, Ford AF, Nelson D, Torney DC, Hildebrand CD, Moyzis RK (1991) Evolution and distribution of (GT)n repetitive sequences in mammalian genomes. Genomics 10:807–815Google Scholar
  29. Tautz D (1989) Hypervariability of simple sequences as a general source of polymorphic DNA markers. Nucleic Acids Res 17:6463–6471Google Scholar
  30. Thomfohrde J, Wood S, Schertzer M, Wagner MJ, Wells DE, Parrish J, Sadler LA, Blanton SH, Daiger SP, Wang Z, Wilkie PJ, Weber JL (1992) Human chromosome 8 linkage map based on short tandem repeat polymorphisms: effect of genotyping errors. Genomics 14:144–152Google Scholar
  31. Thompson AD, Shen Y, Holman K, Sutherland GR, Callen DF, Richards RI (1992) Isolation and characterization of (AC)n microsatellilte genetic markers from human chromosome 16. Genomics 13:402–408Google Scholar
  32. Wang Y, Zhang W, Cao J, McElroy D, Wu R (1992) Characterization of cis-acting elements regulating transcription from the promotor of a constitutively active rice actin gene. Mol Cell Biol 12:3399–3406Google Scholar
  33. Wang ZY, Tanksley ST (1989) Restriction fragment length polymorphism in Oryza sativa L. Genome 32:1113–1118Google Scholar
  34. Wang ZY, Weber JL (1992) Continuous linkage map of human chromosome 14 short tandem repeat polymorphisms. Genomics 13:532–536Google Scholar
  35. Weber JL (1990) Human DNA polymorphisms based on length variations in simple-sequence tandem repeats. In: Tilghman S, Davies K (eds) Genome analysis Vol. 1: Genetic and physical mapping. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 159–181Google Scholar
  36. Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396Google Scholar
  37. Weber JL, Polymeropoulos MH, May PE, Kwitek AE, Xiao H, McPherson JD, Wasmuth JJ (1991) Mapping of human chromosome 5 microsatellite DNA polymorphisms. Genomics 11:695–700Google Scholar
  38. Weissenbach J, Gyapay G, Dib C, Virgnal A, Morissette J, Millasseau P, Vaysseix G, Lathrop M (1992) A second-generation linkage map of the human genome. Nature 359:794–801Google Scholar
  39. Wilkie PJ, Krizman DB, Weber JL (1992) Linkage map of human chromosome 9 microsatellite polymorphisms. Genomics 12:607–609Google Scholar
  40. Winterø AK, Fredholm M, Thomsen PD (1992) Variable (dGdT)n·(dC-dA)n sequences in the porcine genome. Genomics 12:281–288Google Scholar
  41. Xie Y, Wu R (1988) Nucleotide sequence of a ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit gene (irbcS) in rice. Nucleic Acids Res 16:7749Google Scholar
  42. Xie Y, Wu R (1989) Rice alcohol dehydrogenase genes: anaerobic induction, organ specific expression and characterization of cDNA clones. Plant Mol Biol 13:53–68Google Scholar
  43. Xie Y, Wu R (1990) Molecular analysis of an alcohol dehydrogenase-encoding genomic clone (adh-2) from rice. Gene 87:185–191Google Scholar
  44. Zhao X, Kochert G (1992) Characterization and genetic mapping of a short, highly repeated, interspersed DNA sequence from rice (Oryza sativa L.). Mol Gen Genet 231:353–359Google Scholar
  45. Zhao Y, Kung S, Dube S (1990) Nucleotide sequence of rice 4-coumarate-CoA ligase gene, 4CL1. Nucleic Acids Res 18:6144–6144Google Scholar

Copyright information

© Springer-Verlag 1993

Authors and Affiliations

  • Kun-Sheng Wu
    • 1
  • Steven D. Tanksley
    • 1
  1. 1.Department of Plant Breeding and BiometryCornell UniversityIthacaUSA

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