Skip to main content

Genetic analysis seedling vigour under osmotic stress in rice by QTL mapping


Seed vigour is one of the most important parameters for establishing rice seed that affects high yielding production, especially under stress condition in rice (Oryza sativa L.). Improvement of rice yields under abiotic stress through breeding requires a good understanding of genetic factors controlling important traits such as seedling vigour and related traits. To understand the genetic background of the relationships among these traits in indicia rice, we genetically analyzed F2:3 population derived from a cross between Tarommahalli × Khazar, under osmotic stress caused by sorbitol. In this investigation, a simple sequence repeat (SSR) linkage map of 1231.50 cM of rice was constructed by using 74 markers and quantitative trait loci (QTL) analysis was accomplished for eight traits including germination percent, seed germination rate, radicle length, plumule length, coleoptile length, radicle dry matter, plumule dry matter, and coleoptile dry matter. A total of 32 QTLs were identified for the eight traits. Among them, one QTL for percent of germination (qGP-8) was located in RM6208-8264 on chromosome 8 showed large effect (28.99%) on the trait. These results suggest the potential for increase productivity by transferring osmotic stress tolerance gene from Tarommahalli to other rice lines and identification of QTLs with large effects could be considered for use in marker assisted selection (MAS).

This is a preview of subscription content, access via your institution.


  1. 1.

    Association of Official Seed Analysts, Rule of Testing Seeds, Proceeding of the Association of Official Seed Analysts, 2000, vol. 60, p. 39.

  2. 2.

    Basten, C.J., Weir, B.S., and Zeng, Z.B., QTL Cartographer: A Reference Manual and Tutorial for QTL Mapping, USA, NC: North Carolina State University, Raleigh, 2001, p. 163.

    Google Scholar 

  3. 3.

    Causse, M.A., Fultion, T.M., Cho, Y.G., Ahn, S.N., Chunwongse, J., Wu, K., Xiao, J., Yu, Z., Ronal, P.C., Harrington, S.E., Second, G., McCouch, S.R., and Tanksly, S.D., Saturated Molecular Map of the Rice Genome Based on an Inter-Specific Backcross Population, Genetics, 1994, vol. 138, pp. 1251–1274.

    PubMed  CAS  Google Scholar 

  4. 4.

    Choi, W.Y., Kang, S.Y., and Park, H.K., Effects of Water Stress by PEG on Growth and Physiological Traits in Rice Seedlings, Korean J. Crop Sci., 2000, vol. 45, pp. 112–117.

    Google Scholar 

  5. 5.

    Cui, K.H., Peng, S.B., Xing, Y.Z., Xu, C.G., Yu, S.B., and Zhang, Q., Molecular Dissection of Seedling-Vigour and Associated Physiological Traits in Rice, Theor. Appl. Genet., 2002, vol. 105, pp. 745–753.

    PubMed  Article  CAS  Google Scholar 

  6. 6.

    Dowling, N.G., Greenfield, S.M., and Fisher, K.S., Sustainability of Rice in the Global Food System, Philippines, Los Banos: International Rice Research Institute, 1998, p. 404.

    Google Scholar 

  7. 7.

    Ellis, R.H., Hong, T.D., and Roberts, E.H., The Low-Moisture-Content Limit to the Negative Logarithmic Relation between Seed Longevity and Moisture Content in Three Subspecies of Rice, Annals Bot., 1992, vol. 69, pp. 53–58.

    Google Scholar 

  8. 8.

    Foolad, M.R. and Lin, G.Y., Genetic Potential for Salt Tolerance during Germination in Lycopersicon Species, Hort Science, 1997, vol. 32, pp. 296–300.

    Google Scholar 

  9. 9.

    Fukai, S., Phenology in Rainfed Lowland Rice, Field Crops Res., 1999, vol. 64, pp. 51–60.

    Article  Google Scholar 

  10. 10.

    Fujino, K., Sekiguchi, H., Sato, T., Kiuchi, H., Nonoue, Y., Takeuchi, Y., Ando T., Lin, S.Y., and Yano, M., Mapping of Quantitative Trait Loci Controlling Low-Temperature Germinability in Rice (Oryza sativa L.), Theor. Appl. Genet., 2004, vol. 108, pp. 794–799.

    PubMed  Article  CAS  Google Scholar 

  11. 11.

    Hou, M.Y., Wang, C.M., Jiang, L., Wan, J.M., Hidshi, Y., and Atdushi, Y., Inheritance and QTL Mapping of Low Temperature Germinability in Rice (Oryza sativa L.), Acta Genetica Sinica, 2004, vol. 31, pp. 701–706.

    PubMed  CAS  Google Scholar 

  12. 12.

    Jha, B.N. and Singh, R.A., Physiological Responses of Rice Varieties to Different Levels of Moisture Stress, Ind. J. Plant. Physiol., 1997, vol. 2, pp. 81–84.

    Google Scholar 

  13. 13.

    Kanbar, A., Janamatti, M., Sudheer, E., Vinod, M.S., and Shashidhar, H.E., Mapping QTLs Underlying Seedling Vigour Traits in Rice (Oryza sativa L.), Curr. Sci., 2006, vol. 90, pp. 24–26.

    Google Scholar 

  14. 14.

    Li, C.C. and Rutger, J.N., Inheritance of Cool-Temperature Seedling Vigour in Rice and Its Relationship with Other Agronomic Characters, Crop. Sci., 1980, vol. 20, pp. 295–298.

    Article  Google Scholar 

  15. 15.

    Manly, K.F. and Olson, J.M., Overview of QTL Mapping Software and Introduction to Map Manager, QTMammalian Genome, 1999, vol. 10, pp. 327–334.

    Article  CAS  Google Scholar 

  16. 16.

    McCouch, S.R., Teytelman, L., Xu, Y., Lobos, K.B., Clare, K., Walton, M., Fu, B., Maghirang, R., Li, Z., Xing, Y., Zhang, Q., Kono, I., Yano, M., Fjellstrom, R., Declerk, G., Schneider, D., Cartinhour, S., Ware, D., and Stein, L., Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.), DNA Res., 2002, vol. 9, pp. 199–207.

    PubMed  Article  CAS  Google Scholar 

  17. 17.

    Mckenzie, K.S., Johnson, C.W., Tseng, S.T., Oster, J., and Brandon, D.M., Breeding Improved Rice Cultivars for Temperate Regions: a Case Study, Austral. J. Exp. Agric., 1994, vol. 34, pp. 897–905.

    Article  Google Scholar 

  18. 18.

    Reddy, P.C. and Vajaranabhiah, S.N., Drought Induced Lipid Peroxidation, Defensive Mechanism in Upland Rice (Oryza saliva L.) Seeds during Germination, Adv. Plant Sci., 1993, vol. 6, pp. 229–236.

    Google Scholar 

  19. 19.

    Redona, E.D. and Mackill, D.J., Mapping Quantitative Trait Loci for Seedling-Vigor in Rice Using RFLPs, Theor. Appl. Genet., 1996a, vol. 92, pp. 395–402.

    Article  CAS  Google Scholar 

  20. 20.

    Redona, E.D. and Mackill, D.J., Genetic Variation for Seedling Vigor Traits in Rice, Crop. Sci., 1996b, vol. 36, pp. 285–290.

    Article  Google Scholar 

  21. 21.

    Redona, E.D. and Mackill, D.J., Quantitative Trait Locus Analysis for Rice Panicle and Grain Characteristics, Theor. Appl. Genet., 1998, vol. 96, pp. 957–963.

    Article  CAS  Google Scholar 

  22. 22.

    Sabouri, H., Rezai, A., and Moumeni, A., Evaluation of Salt Tolerance in Iranian Landrace and Improved Rice Cultivars, J. Sci. Tech. Agric. Nat. Res., 2008, vol. 45, pp. 47–63.

    Google Scholar 

  23. 23.

    Saghai Maroof, M.A., Biyashev, R.M., Yang, G.P., Zhang, Q., and Allard, R.W., Extraordinarily Polymorphic Microsatellite DNA in Barely: Species Diversity, Chromosomal Locations, and Population Dynamics, Proc. Nat. Acad. Sci. USA, 1994, vol. 91, pp. 5466–5570.

    PubMed  Article  CAS  Google Scholar 

  24. 24.

    SAS User’s Guide: Statistics Cary, NC: SAS Institute, SAS Institute, Inc., 1996.

  25. 25.

    Tan, Y.F., Xing, Y.Z., Li, J.X., Yu, S.B., Xu, C.G., and Zhang, Q., Genetic Bases of Appearance Quality of Rice Grains in Shanyou 63, an Elite Rice Hybrid, Theor. Appl. Genet., 2000, vol. 101, pp. 823–829.

    Article  CAS  Google Scholar 

  26. 26.

    Yamauchi, M. and Winn, T., Rice Seed Vigor and Seedling Establishment in Anaerobic Soil, Crop. Sci., 1996, vol. 36, pp. 680–686.

    Article  Google Scholar 

  27. 27.

    Zhang, Z.H., Qu, X.S., Wan, S., Chen, L.H., and Zhu, Y.G., Comparison of QTL Controlling Seedling Vigour under Different Temperature Conditions Using Recombinant Inbred Lines in Rice (Oryza sativa L.), Annals Botany, 2005, vol. 95, pp. 423–429.

    Article  CAS  Google Scholar 

Download references

Author information



Corresponding author

Correspondence to Atefeh Sabouri.

About this article

Cite this article

Sabouri, A., Sabouri, H. & De Ocampo, M. Genetic analysis seedling vigour under osmotic stress in rice by QTL mapping. Russ. Agricult. Sci. 38, 423–429 (2012).

Download citation


  • Germination
  • Oryza sativa
  • simple sequence repeat
  • sorbitol
  • quantitative trait loci