Theoretical and Applied Genetics

, Volume 89, Issue 1, pp 54–59 | Cite as

The semidwarf gene, sd-1, of rice (Oryza sativa L.). II. Molecular mapping and marker-assisted selection

  • Y. G. Cho
  • M. Y. Eun
  • S. R. McCouch
  • Y. A. Chae


To establish the location of the semidwarf gene, sd-1, the anthocyanin activator (A), purple node (Pn), purple auricle (Pau), and the isozyme locus, EstI-2, in relation to DNA markers on the molecular linkage map of rice, 20 RFLP markers, previously mapped to the central region of chromosome 1 (McCouch et al. 1988), were mapped onto an F2 population derived from the cross Taichung 65 (A,Pn,Pau)/Taichung 65 (sd-1). sd-1 and EstI-2 were determined to be linked most tightly to RFLP markers RG 109 and RG 220, which cosegregated with each other. The distance between these RFLP markers and sd-1 was estimated to be 0.8 cM, based on an observed recombination value of 0.8%. The order of genes and markers in this region of chromosome 1 was determined to be sd-1 — (EstI-2 — RG220 — RG109) — RG381 — APnPau. To test the efficacy of selection for sd-1 based on these linked markers, 50-day-old F2 seedlings derived from another cross, Milyang 23/Gihobyeo, were analyzed for marker genotype. At this age, the semidwarf character could not be clearly detected based on phenotype. In addition, plant height was normally distributed in this population, making it difficult to unambiguously identify plants carrying sd-1. Thirteen seedlings homozygous for the sd-1-associated allele at EstI-2, RG220 and RG109, and 13 seedlings homozygous for the Sd-1-associated allele at all three marker loci were selected for further genetic analysis. At 20 days after heading, the culm lengths of these 26 plants were measured and the expected phenotype was confirmed in every case. These 26 plants were then selfed for four generations and F6 lines were again evaluated to determine whether any recombination among the three molecular markers, or between these markers and the sd-1 gene, could be detected. No recombinants were identified, confirming the tight linkage of these loci and the usefulness of genotypic selection for this recessive semidwarf character prior to the time when it can be evaluated based on phenotype.

Key words

Rice Semidwarf gene (sd-1) RFLP Molecular marker Marker-assisted selection 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Aquino RC, Jennings PR (1966) Inheritance and significance of dwarfism in an indica rice variety. Crop Sci 6:551–554Google Scholar
  2. 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
  3. Cho YG (1992) Genetics of esterase isozymes and RFLP markers, and their linkage with a semidwarf gene (sd-1) in rice (Oryza sativa L.). PhD thesis, Seoul National University, Republic of KoreaGoogle Scholar
  4. Cho YG, Eun MY, Kim YK, Chung TY, Chae YA (1994) The semidwarf gene, sd-1, of rice (Oryza sativa L.). I. Linkage with the esterase locus, EstI-2. Theor Appl Genet 89:49–53Google Scholar
  5. Choi HO, Bae SH, Chung GS, Cho CY, Heu MH, Beachell HM (1974) A new short-statured rice variety “Tongil”. The Research Reports of the Office of Rural Development Administration, vol. 16 (crop):1–12Google Scholar
  6. Eun MY, Cho YG, Chung TY (1991) Molecular markers linked tightly with semidwarf (sd-1) character and shattering habits in rice. Korean Soc Mol Biol SE-4:182–185Google Scholar
  7. Kinoshita T (1990) Report of the commitee on gene symbolization, nomenclature and linkage groups. Rice Genet Newslet 7:16–50Google Scholar
  8. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175Google Scholar
  9. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181Google Scholar
  10. Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science 262:1432–1436Google Scholar
  11. McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR, Tanksley SD (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815–829Google Scholar
  12. Oba S, Kikuch F, Maruyama K (1990) Genetic analysis of semidwarfness and grain shattering of Chinese rice variety “Ai-Jio-Nan-Te”. Japan J Breed 40:13–20Google Scholar
  13. Ogi Y, Kato H, Maruyama K, Saito A, and Kikuchi F (1993) Identification of RFLP markers closely linked to the semidwarfing gene at the sd-1 locus in rice. Japan J Breed 43:141–146Google Scholar
  14. Rommens JM, Iannuzzi MC, Kerem B, Drumm ML, Melmer G, Dean M, Rozmahel R, Cole JL, Kennedy D, Hidaka N, Zsiga M, Buchward M, Riordan JR, Tsui LC, Collins FS (1989) Identification of the cystic fibrosis gene: chromosome walking and jumping. Science 245:1059–1065Google Scholar
  15. Suh HS, Heu MH (1978) The segregation mode of plant height in the cross of rice varieties. II. Linkage analysis of the semidwarfness of rice variety “Tongil”. Korean J Breed 10(1):1–6Google Scholar
  16. Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Biotechnology 7:257–264Google Scholar
  17. Tsai KH (1991) Chromosomal location of gene sd-1 examined with isogenic translocation lines of Taichung 65. Rice Genet Newslet 8:109–110Google Scholar
  18. Wang ZY, Tanksley SD (1989) Restriction fragment length polymorphism in Oryza sativa L. Genome 32:1113–1118Google Scholar
  19. Wang ZY, Second G, Tanksley SD (1992) Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor Appl Genet 83:565–581Google Scholar
  20. Wang G, Mackill DJ, Bonman JM, McCouch SR, Champoux M, Nelson R (1993) RFLP mapping of genes conferring complete partial resistance to blast in a durably-resistant rice cultivar. Genetics 136:1421–1434Google Scholar
  21. Yokoo M, Saito S (1986) Association between grain shattering and semidwarfness in rice. Rice Genet Newslet 3:63–65Google Scholar
  22. Young ND, Zamir D, Ganal MW, Tanksley SD (1988) Use of isogenic lines and simultaneous probing to identify DNA markers tightly linked to the Tm-2a gene in tomato. Genetics 120:579–585Google Scholar
  23. Yu ZH (1991) Molecular mapping of rice (Oryza sativa L.) genes via linkage to restriction fragment length polymorphism (RFLP) markers. PhD thesis, Cornell University, Ithaca, N.Y.Google Scholar
  24. Yu ZH, Mackill DJ, Bonman JM, Tanksley SD (1991) Tagging genes for blast resistance in rice via linkage to RFLP markers. Theor Appl Genet 81:471–476Google Scholar

Copyright information

© Springer-Verlag 1994

Authors and Affiliations

  • Y. G. Cho
    • 1
  • M. Y. Eun
    • 1
  • S. R. McCouch
    • 2
  • Y. A. Chae
    • 3
  1. 1.Genetics DivisionAgricultural Biotechnology Institute, RDASuweonRepublic of Korea
  2. 2.Department of Plant Breeding and BiometryCornell UniversityIthacaUSA
  3. 3.Department of AgronomySeoul National UniversitySuweonRepublic of Korea

Personalised recommendations