Skip to main content
PMC home page
Genetics logoLink to Genetics
. 1994 Dec;138(4):1251–1274. doi: 10.1093/genetics/138.4.1251

Saturated Molecular Map of the Rice Genome Based on an Interspecific Backcross Population

M A Causse 1, T M Fulton 1, Y G Cho 1, S N Ahn 1, J Chunwongse 1, K Wu 1, J Xiao 1, Z Yu 1, P C Ronald 1, S E Harrington 1, G Second 1, S R McCouch 1, S D Tanksley 1
PMCID: PMC1206261  PMID: 7896104

Abstract

A molecular map has been constructed for the rice genome comprised of 726 markers (mainly restriction fragment length polymorphisms; RFLPs). The mapping population was derived from a backcross between cultivated rice, Oryza sativa, and its wild African relative, Oryza longistaminata. The very high level of polymorphism between these species, combined with the use of polymerase chain reaction-amplified cDNA libraries, contributed to mapping efficiency. A subset of the probes used in this study was previously used to construct an RFLP map derived from an inter subspecific cross, providing a basis for comparison of the two maps and of the relative mapping efficiencies in the two crosses. In addition to the previously described PstI genomic rice library, three cDNA libraries from rice (Oryza), oat (Avena) and barley (Hordeum) were used in this mapping project. Levels of polymorphism detected by each and the frequency of identifying heterologous sequences for use in rice mapping are discussed. Though strong reproductive barriers isolate O. sativa from O. longistaminata, the percentage of markers showing distorted segregation in this backcross population was not significantly different than that observed in an intraspecific F(2) population previously used for mapping. The map contains 1491 cM with an average interval size of 4.0 cM on the framework map, and 2.0 cM overall. A total of 238 markers from the previously described PstI genomic rice library, 250 markers from a cDNA library of rice (Oryza), 112 cDNA markers from oat (Avena), and 20 cDNA markers from a barley (Hordeum) library, two genomic clones from maize (Zea), 11 microsatellite markers, three telomere markers, eleven isozymes, 26 cloned genes, six RAPD, and 47 mutant phenotypes were used in this mapping project. Applications of a molecular map for plant improvement are discussed.

Full Text

The Full Text of this article is available as a PDF (8.9 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ahn S., Anderson J. A., Sorrells M. E., Tanksley S. D. Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet. 1993 Dec;241(5-6):483–490. doi: 10.1007/BF00279889. [DOI] [PubMed] [Google Scholar]
  2. Ahn S., Tanksley S. D. Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):7980–7984. doi: 10.1073/pnas.90.17.7980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Alexander M. P. Differential staining of aborted and nonaborted pollen. Stain Technol. 1969 May;44(3):117–122. doi: 10.3109/10520296909063335. [DOI] [PubMed] [Google Scholar]
  4. Bernatzky R., Tanksley S. D. Toward a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics. 1986 Apr;112(4):887–898. doi: 10.1093/genetics/112.4.887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bonierbale M. W., Plaisted R. L., Tanksley S. D. RFLP Maps Based on a Common Set of Clones Reveal Modes of Chromosomal Evolution in Potato and Tomato. Genetics. 1988 Dec;120(4):1095–1103. doi: 10.1093/genetics/120.4.1095. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Borts R. H., Haber J. E. Meiotic recombination in yeast: alteration by multiple heterozygosities. Science. 1987 Sep 18;237(4821):1459–1465. doi: 10.1126/science.2820060. [DOI] [PubMed] [Google Scholar]
  7. Burr B., Burr F. A., Thompson K. H., Albertson M. C., Stuber C. W. Gene mapping with recombinant inbreds in maize. Genetics. 1988 Mar;118(3):519–526. doi: 10.1093/genetics/118.3.519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chao L F. Linkage Studies in Rice. Genetics. 1928 Mar;13(2):133–169. doi: 10.1093/genetics/13.2.133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  10. Giovannoni J. J., Wing R. A., Ganal M. W., Tanksley S. D. Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations. Nucleic Acids Res. 1991 Dec 11;19(23):6553–6558. doi: 10.1093/nar/19.23.6553. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Helentjaris T., Weber D., Wright S. Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics. 1988 Feb;118(2):353–363. doi: 10.1093/genetics/118.2.353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Huang N., Sutliff T. D., Litts J. C., Rodriguez R. L. Classification and characterization of the rice alpha-amylase multigene family. Plant Mol Biol. 1990 May;14(5):655–668. doi: 10.1007/BF00016499. [DOI] [PubMed] [Google Scholar]
  13. Hulbert S. H., Richter T. E., Axtell J. D., Bennetzen J. L. Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. Proc Natl Acad Sci U S A. 1990 Jun;87(11):4251–4255. doi: 10.1073/pnas.87.11.4251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kay S. A., Keith B., Shinozaki K., Chye M. L., Chua N. H. The rice phytochrome gene: structure, autoregulated expression, and binding of GT-1 to a conserved site in the 5' upstream region. Plant Cell. 1989 Mar;1(3):351–360. doi: 10.1105/tpc.1.3.351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Khush G. S., Singh R. J., Sur S. C., Librojo A. L. Primary trisomics of rice: origin, morphology, cytology and use in linkage mapping. Genetics. 1984 May;107(1):141–163. doi: 10.1093/genetics/107.1.141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lander E. S., Green P., Abrahamson J., Barlow A., Daly M. J., Lincoln S. E., Newberg L. A., Newburg L. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics. 1987 Oct;1(2):174–181. doi: 10.1016/0888-7543(87)90010-3. [DOI] [PubMed] [Google Scholar]
  17. Manly K. F. A Macintosh program for storage and analysis of experimental genetic mapping data. Mamm Genome. 1993;4(6):303–313. doi: 10.1007/BF00357089. [DOI] [PubMed] [Google Scholar]
  18. Michelmore R. W., Paran I., Kesseli R. V. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9828–9832. doi: 10.1073/pnas.88.21.9828. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Paterson A. H., DeVerna J. W., Lanini B., Tanksley S. D. Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics. 1990 Mar;124(3):735–742. doi: 10.1093/genetics/124.3.735. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Paterson A. H., Lander E. S., Hewitt J. D., Peterson S., Lincoln S. E., Tanksley S. D. Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature. 1988 Oct 20;335(6192):721–726. doi: 10.1038/335721a0. [DOI] [PubMed] [Google Scholar]
  21. Rick C. M. Controlled Introgression of Chromosomes of SOLANUM PENNELLII into LYCOPERSICON ESCULENTUM: Segregation and Recombination. Genetics. 1969 Aug;62(4):753–768. doi: 10.1093/genetics/62.4.753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Ronald P. C., Albano B., Tabien R., Abenes L., Wu K. S., McCouch S., Tanksley S. D. Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21. Mol Gen Genet. 1992 Dec;236(1):113–120. doi: 10.1007/BF00279649. [DOI] [PubMed] [Google Scholar]
  23. Shure M., Wessler S., Fedoroff N. Molecular identification and isolation of the Waxy locus in maize. Cell. 1983 Nov;35(1):225–233. doi: 10.1016/0092-8674(83)90225-8. [DOI] [PubMed] [Google Scholar]
  24. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  25. Tanksley S. D., Ganal M. W., Prince J. P., de Vicente M. C., Bonierbale M. W., Broun P., Fulton T. M., Giovannoni J. J., Grandillo S., Martin G. B. High density molecular linkage maps of the tomato and potato genomes. Genetics. 1992 Dec;132(4):1141–1160. doi: 10.1093/genetics/132.4.1141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Wang G. L., Mackill D. J., Bonman J. M., McCouch S. R., Champoux M. C., Nelson R. J. RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics. 1994 Apr;136(4):1421–1434. doi: 10.1093/genetics/136.4.1421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Whitkus R., Doebley J., Lee M. Comparative genome mapping of Sorghum and maize. Genetics. 1992 Dec;132(4):1119–1130. doi: 10.1093/genetics/132.4.1119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Wu K. S., Tanksley S. D. Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet. 1993 Oct;241(1-2):225–235. doi: 10.1007/BF00280220. [DOI] [PubMed] [Google Scholar]
  29. Wu K. S., Tanksley S. D. Genetic and physical mapping of telomeres and macrosatellites of rice. Plant Mol Biol. 1993 Aug;22(5):861–872. doi: 10.1007/BF00027371. [DOI] [PubMed] [Google Scholar]
  30. Young N. D., Zamir D., Ganal M. W., Tanksley S. D. Use of isogenic lines and simultaneous probing to identify DNA markers tightly linked to the tm-2a gene in tomato. Genetics. 1988 Oct;120(2):579–585. doi: 10.1093/genetics/120.2.579. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Zhu Q., Lamb C. J. Isolation and characterization of a rice gene encoding a basic chitinase. Mol Gen Genet. 1991 Apr;226(1-2):289–296. doi: 10.1007/BF00273615. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES