Theoretical and Applied Genetics

, Volume 76, Issue 6, pp 815–829 | Cite as

Molecular mapping of rice chromosomes

  • S. R. McCouch
  • G. Kochert
  • Z. H. Yu
  • Z. Y. Wang
  • G. S. Khush
  • W. R. Coffman
  • S. D. Tanksley


We report the construction of an RFLP genetic map of rice (Oryza sativa) chromosomes. The map is comprised of 135 loci corresponding to clones selected from a PstI genomic library. This molecular map covers 1,389 cM of the rice genome and exceeds the current classical maps by more than 20%. The map was generated from F2 segregation data (50 individuals) from a cross between an indica and javanica rice cultivar. Primary trisomics were used to assign linkage groups to each of the 12 rice chromosomes. Seventy-eight percent of the clones assayed revealed RFLPs between the two parental cultivars, indicating that rice contains a significant amount of RFLP variation. Strong correlations between size of hybridizing restriction fragments and level of polymorphism indicate that a significant proportion of the RFLPs in rice are generated by insertions/delections. This conclusion is supported by the occurrence of null alleles for some clones (presumably created by insertion or deletion events). One clone, RG229, hybridized to sequences in both the indica and javanica genomes, which have apparently transposed since the divergence of the two cultivars from their last common ancestor, providing evidence for sequence movement in rice. As a by product of this mapping project, we have discovered that rice DNA is less C-methylated than tomato or maize DNA. Our results also suggest the notion that a large fraction of the rice genome (approximately 50%) is single copy.

Key words

Oryza sativa Molecular markers RFLP Genetic map Trisomies DNA methylalion 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Allard RW (1956) Formulas and tables to facilitate the calculation of recombination values in heredity. Hilgardia 24:235–278Google Scholar
  2. Barker D, Schafer M, White R (1984) Restriction sites containing CpG show a higher frequency of polymorphism in human DNA. Cell 36:131–138Google Scholar
  3. Beltz G, Jacobs K, Eickbush T, Cheerbas P, Kafatos F (1983) Isolation of multigene families and determination of homologies by filter hybridization methods. Methods Enzymol 100:266–285Google Scholar
  4. Bennett MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Philos Trans R Soc London, Ser B 274:227–274Google Scholar
  5. Bernatzky R, Tanksley SD (1986a) Toward a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics 112:887–898Google Scholar
  6. Bernatzky R, Tanksley SD (1986b) Majority of random cDNA clones correspond to single loci in the tomato genome. Mol Gen Genet 203:8–14Google Scholar
  7. Bonierbale M, Plaisted R, Tanksley SD (1988) Construction of comparative genetic maps of potato and tomato based on a common set of cloned sequences. Genetics (in press)Google Scholar
  8. Burr B, Evola SV, Burr RA, Beckman JS (1983) The application of restriction fragment lenth polymorphism to plant breeding. In: Setlow SK, Hollaender A (eds). Genetic engineering: principles and methods, vol 5. Plenum Press, New York, pp 45–59Google Scholar
  9. Burr B, Burr RA, Thompson KH, Albertsen MC, Stuber CW (1988) Gene mapping with recombinant inbreds in maize. Genetics 118:519–526Google Scholar
  10. Coffman WR, Bienvenido OJ (1987) Rice. Nutritional quality of cereal grains: genetic and agronomic improvement. Agronomy Monograph No. 28, ASA-CSSA-SSSA, Madison, WI, USA, pp 101–131Google Scholar
  11. Deshpande VG, Ranjekar PK (1980) Repetitive DNA in three Gramineae species with lwo DNA content. Hoppe Seyler's Z Physiol Chem 361:1223–1233Google Scholar
  12. Doerfler W (1983) DNA methylation and gene activity. Annu Rev Biochem 52:93–124Google Scholar
  13. Feinberg AP, Vogelstein B (1984) A technique for radiolabelling DNA restriction fragments to a high specific activity. Anal Biochem 132:6–13Google Scholar
  14. Flavell RB (1980) The molecular characterization and organization of plant chromosomal DNA sequences. Annu Rev Plant Physiol 31:569–596Google Scholar
  15. Galbraith DW, Harkins KR, Maddox JM, Ayres NM, Sharma D, Firoozabady E (1983) Rapid flow cytometry analysis of the cell cycle in intact plant tissue. Science 220:1049–1051Google Scholar
  16. Gerlach WL, Bedbrook JR (1979) Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res 7:1869–1885Google Scholar
  17. Gerlach WL, Dyer TA (1980) Sequence organization of the repeating units in the nucleus of wheat which contain 5s rRNA genes. Nucleic Acids Res 8:1851–1865Google Scholar
  18. Helentjaris T (1987) A genetic linkage map for maize based on RFLP's. Trends Genet 3:217–221Google Scholar
  19. Helentjaris T, King G, Slocum M, Siedenstrang C, Wegman S (1985) Restriction fragment polymorphisms as probes for plant diversity and their development as tools for applied plant breeding. Plant Mol Biol 5:109–118Google Scholar
  20. Herman RK, Shaw JE (1987) The transposable genetic element in the nematode Caenorhabdibs elegans. Trends Genet 3:222–225Google Scholar
  21. Iyengar GAS, Sen SK (1978) Nuclear DNA content of several wild and cultivated Oryza species. Environ Exp Bot 18:219–224Google Scholar
  22. Khush GS, Singh RJ (1986) Relationship between linkage groups and cytologically identifiable chromosome of rice. In: Rice genetics, Proc Int Rice Genet Symp, May 1985. Los Banos, Philippines, pp 239–248Google Scholar
  23. Khus GS, Singh RJ, Sur SC, Librojo AL (1984) Primary trisomics of rice: Origin, morphology, cytology, and use in linkage mapping. Genetics 107:141–163Google Scholar
  24. Kinoshita T (1986) Standardization of gene symbols and linkage maps in rice. In Rice Genetics, Proc Int Rice Gen Symp, May 1985, IRRI, Los Banos, Philippines, pp 215–228Google Scholar
  25. Kosambi DD (1944) Ann Eugen 12:172–175Google Scholar
  26. 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
  27. Landry BS, Kessell R, Leung H, Michelmore RW (1987) Comparison of restriction enconucleases and sources of probes for their efficiency in detecting restriction fragment length polymorphisms in lettuce (Lactuca sativa L.). Theor Appl Genet 74:646–653Google Scholar
  28. Lorz H, Gobel E (1986) In vitro culture of rice and direct gene transfer to cereal cells. In: Rice genetics, Proc Int Rice Genetics Symp (May 1985). IRRI, Los Banos, Philippines, pp 849–857Google Scholar
  29. Maniatis T, Fritsch E, Sambrook J (1982) Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory Press Cold Spring Harbor, NYGoogle Scholar
  30. Nelson M, McClelland M (1987) The effect of site-specific methylation on restriction-modification enzymes. Nucleic Acids Res 15 Suppl: 219–230Google Scholar
  31. Orkin SH (1986) Reverse genetics and human disease. Cell 47:845–850Google Scholar
  32. Paterson AH, Lander ES, Hewitt ID, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete RFLP linkage map. Nature (in press)Google Scholar
  33. Poehlman JM (1979) Breeding field crops, 2nd edn AVI Publishing Co, New YorkGoogle Scholar
  34. Ranjhan S, Glaszmann JL, Ramirez DA, Khush GS (1988) Chromosomal location of four isozyme loci by trisomic analysis in rice (Oryza sativa L.). Theor Appl Genet 75:541–545Google Scholar
  35. Rigby P, Dieckmann M, Rhodes C, Berg P (1977) Labeling deoxyribonucleic acid to high specific activity in vitro by nick-translation with DNA polymerase I. J Mol Biol 113:237–251Google Scholar
  36. Schwarz-Sommer Zsuzsanna, Gierl A, Cuypers H, Peterson PA, Saedler H (1985) Plant transposable elements generate the DNA sequence diversity needed in evolution. EMBO J 4:591–597Google Scholar
  37. Second G (1982) Origin of the genic diversity of cultivated rice (Oryza spp.): study of the polymorphism scored at 40 isozyme loci. Jpn J Genet 57:25–57Google Scholar
  38. Shastry SVS, Ranga Rao DR, Misra RN (1960) Pachytene analysis in Oryza — 1. Chromosome morphology in Oryza sativa. Indian J Genet 20:15–21Google Scholar
  39. Shaw CR, Prasad R (1970) Starch gel electrophoresis of enzymes — a complication of recipes. Biochem Genet 4:297–320Google Scholar
  40. Shure M, Wessler S, Federoff N (1983) Molecular identification of the Waxy locus in maize. Cell 35:225–233Google Scholar
  41. Tanksley SD (1982) Molecular markers in plant breeding. Plant Mol Biol Rep 1:3–8Google Scholar
  42. Tanksley SD, Miller J, Paterson A, Bernatzky R (1987) Molecular mapping of plant chromosomes. In: Gustafson JP, Appels RA (eds) Chromosome structure and function. Plenum Press, New York, pp 157–173Google Scholar
  43. Uchimiya H, Fushimi T, Hashimoto H, Harada H, Syono K, Sugawara Y (1986) Expression of a foreign gene in callus derived from DNA-treated protoplasts of rice (Oryza sativa L.) Mol Gen Genet 204:204–207Google Scholar
  44. Vallejos E (1983) Enzyme activity staining. In: Tanksley SD, Orton TJ (eds) Isozymes in plant genetics and breeding, part A. Elsevier, Amsterdam, pp 469–516Google Scholar
  45. Wilimzig (1985) LiCl-boiling method for plasmid minio-preps. Trends Genet 1:158Google Scholar
  46. Wu KS, Glaszmann JC, Khush GS (1988) Chromosomal location of ten isozymc loci in rice (Oryza sativa L.) through trisomic analysis. Biochem Genet 26:311–328Google Scholar
  47. Yamada Y, Yang ZQ, Tang DT (1985) Regeneration of rice plants from protoplasts. Rice Genet Newsl 2:94–95Google Scholar
  48. Young ND, Miller JC, Tanksley SD (1987) Rapid chromosomal assignment of multiple genomic clones in tomato using primary trisomics. Nucleic Acids Res 15:9339–9348Google Scholar
  49. Zamir D, Tanksley SD (1988) Tomato genome is comparised mainly of fast evolving single copy sequences. Mol Gen Genet 213:254–261Google Scholar

Copyright information

© Springer-Verlag 1988

Authors and Affiliations

  • S. R. McCouch
    • 1
  • G. Kochert
    • 1
  • Z. H. Yu
    • 1
  • Z. Y. Wang
    • 1
  • G. S. Khush
    • 1
  • W. R. Coffman
    • 1
  • S. D. Tanksley
    • 1
  1. 1.Department of Plant Breeding and BiometryCornell UniversityIthacaUSA

Personalised recommendations