Biologia Plantarum

, Volume 53, Issue 4, pp 657–662 | Cite as

QTLs mapping of physiological traits related to salt tolerance in young rice seedlings

  • H. Sabouri
  • A. M. Rezai
  • A. Moumeni
  • A. Kavousi
  • M. Katouzi
  • A. Sabouri
Original Papers


Oryza sativa L. F2 population and F2:3 derived from a cross between salt tolerance cv. Tarommahali and salt sensitive cv. Khazar were used in this study. A linkage map based on F2 population was constructed (74 SSR markers on 192 individuals), which covered a total of 1231.50 cM with an average two locus interval of 19.83 cM. Two QTLs related to Na+/K+ ratio were found on chromosome 3 and 6. qDM-3 and qDM-8 (for dry mass of shoot) are major QTLs with very large effects explained 20.90 and 17.72 % of the total phenotypic variance, respectively. Major locus for DM (qDM-3) was bracketed by RM1022 — RM6283 spread over 13.6 cM on chromosome 3. Major part of the variability for standard tolerance ranking (STR) was explained by the qSTR-6 flanked by RM3727 — RM340 on chromosome 6, which exhibited phenotypic variance of 17.25 % and peak likelihood ratio (LR) of 17.51. The length of this QTL is 8.8 cM and identification of any tightly linked markers in this region will serve as a candidate gene for fine-mapping. qSTR-3 overlapped with qNA-3 and qNAK-3. The qSTR-3 may contain a new major gene for salt stress tolerance at seedling stage in rice. Major QTLs identified in this paper, after fine-mapping, could be used for marker assisted selection.

Additional key words

marker-assisted selection Oryza sativa SSR 



composite interval mapping


logarithmic odds


likelihood ratio


marker assisted selection


quantitative trait locus


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Abler, B.S.B., Edwards, M.D., Stuber, C.W.: Isoenzymatic identification of quantitative trait loci in crosses of elite maize inbreds. — Crop Sci 31: 267–274, 1991.CrossRefGoogle Scholar
  2. Balint, A.F., Roder, M.S., Hell, R., Galiba, G., Borner, A.: Mapping of QTLs affecting copper tolerance and the Cu, Fe, Mn and Zn contents in the shoots of wheat seedlings. — Biol. Plant. 51: 129–134, 2007.CrossRefGoogle Scholar
  3. Bassam, B.J., Caetano-Anolles, G., Gresshoff, P.M.: Fast and sensitive silver staining of DNA in polyacrylamide gels. — Anal. Biochem. 196: 80–83, 1991.CrossRefPubMedGoogle Scholar
  4. Basten, C.J., Weir, B.S., Zeng, Z.B.: QTL Cartographer: A Reference Manual and Tutorial for QTL Mapping — Academic Press, New York 2001.Google Scholar
  5. Chen, X., Temnykh, S., Xu, Y., Cho Y.G., McCouch. S.R.: Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). — Theor. appl. Genet. 95: 553–567, 1997.CrossRefGoogle Scholar
  6. Creste, S., Tulmann Neto, A., Figueira, A.: Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining. — Plant. mol. Biol. Rep. 19: 299–306, 2001.CrossRefGoogle Scholar
  7. Dubcovsky, J., Santa, M.G., Epstein, E., Luo, M.O., Dvorak, J.: Mapping of K+/Na+ discrimination locus Kna1 in wheat. — Theor. appl. Genet. 92: 448–454, 1996.CrossRefGoogle Scholar
  8. Flowers, T.J., Troke, P.F., Yeo, A.R.: The mechanisms of salt tolerance in halophytes. — Annu. Rev. Plant. Physiol. 28: 89–121, 1977.CrossRefGoogle Scholar
  9. Garcia, A.B., Almeida, E., Iyer, S., Gerats, T., Van Montagu, M., Caplan, A.: Effects of osmoprotectants upon NaCl stress in rice. — Plant Physiol. 115: 159–169, 1997.PubMedGoogle Scholar
  10. Gregorio, G.B., Senadhira, D.: Genetic analysis of salinity tolerance in rice (Oryza sativa L.). — Theor. appl. Genet. 86: 333–338, 1993.CrossRefGoogle Scholar
  11. Gregorio, G. B., Senadhira, D., Mendoza, R.: Screening rice for salinity tolerance. — IRRI. Dis. Paper No. 22, Los Baños 1997.Google Scholar
  12. Gu, X.Y., Zhen, S.L., Yan, X.L., Lu, Y.G.: [Analysis of generation means for the inheritance of salt tolerance in rice seedling.] — Acta. agron. Sin. 6: 686–690, 1999. [In Chin.]Google Scholar
  13. Kosambi, D.D.: The estimation of map distances from recombination values. — Ann. Eugen. 12: 172–175, 1944.Google Scholar
  14. Koyama, M.L., Levesley, A., Koebner, R.M.D., Flowers, T.J., Yeo, A.R.: Quantitative trait loci for component physiological trait determining salt tolerance in rice. — Plant. Physiol. 125: 406–422, 2001.CrossRefPubMedGoogle Scholar
  15. Lee, S.Y., Ahn, Y.S., Cha, D.W., Yun, M.C., Lee, J.C., Ko, K.S., Lee, K.S., Eun, M.Y.: Mapping QTLs related to salinity tolerance of rice at the young seedling stage. — Plant. Breed. 126: 43–46, 2007.CrossRefGoogle Scholar
  16. Lin, H.X., Yanagihara, S., Zhuang, J.Y., Senboku, T., Zheng, K.L., Yashima, S.: Identification of QTL for salt tolerance in rice via molecular markers. — Chin. J. Rice Sci. 12: 72–78, 1998.Google Scholar
  17. Lin, H.X., Zhu, M.Z., Yano, M., Gao, J.P., Liang, Z.W., Su, W.A., Hu, X.H., Ren, Z.H., Chao, D.Y.: QTLs for Na and K uptake of the shoots and roots controlling rice salt tolerance. — Theor. appl. Genet. 108: 253–260, 2004.CrossRefPubMedGoogle Scholar
  18. Manly, K.F., Olson, J.M.: Overview of QTL mapping software and introduction to map manager QTX. — Mammalian Genome 10: 327–334, 1999.CrossRefPubMedGoogle Scholar
  19. 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., De Clerck, G., Schneider, D., Cartinhour, S., Ware, D., Stein, L.: Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). — DNA Res. 9: 199–207, 2002.CrossRefPubMedGoogle Scholar
  20. Ming, Z.Y., Jian F.W., Hong Y.C., Hu Q.Z., Hong S.Z.: Inheritance and QTL mapping of salt tolerance in rice. — Rice Sci. 12: 25–32, 2005.Google Scholar
  21. Moeljopawiro, S., Ikehashi, H.: Inheritance of salt tolerance in rice. — Euphytica, 30: 291–300, 1981.CrossRefGoogle Scholar
  22. Paterson, A.H.: Making genetic maps. — In: Paterson, A.H. (ed.): Genome Mapping in Plants. Pp. 23–39. Academic Press, Austin 1996.Google Scholar
  23. Prasad, S.R., Bagali, P.G., Hittalmani, S., Shashidhar, H.E.: Molecular mapping of quantitative trait loci associated with seedling tolerance to salt stress in rice (Oryza sativa L.). — Curr. Sci. 78: 162–164, 2000.Google Scholar
  24. Sabouri, H., Rezai, A., Moumeni, A., Kavousi, M.: Investigation of genetic diversity of Iranian rice genotypes under salinity condition: compare means, sensitive and tolerance index. — In: Bocchi, S., Ferrero, A., Porro, A. (ed.): Proceedings of the 4th International Temperate Rice Conference. Pp. 50–51. Tipografia Fiordo, Novara 2007a.Google Scholar
  25. Sabouri, H., Rezai, A., Moumeni, A., Kavousi, M.: Investigation of genetic diversity of Iranian rice genotypes under salinity condition: multivariate analysis. In: In: Bocchi, S., Ferrero, A., Porro, A. (ed.): Proceedings of the 4th International Temperate Rice Conference. Pp. 52–53. Tipografia Fiordo, Novara 2007b.Google Scholar
  26. Sabouri, H., Rezai, A., Moumeni, A., Kavousi, M.: Study the variation of physiological and agronomical characters Iranian rice (Oryza sativa L.) cultivars in seedling and vegetative stages under salinity condition. — In: Bocchi, S., Ferrero, A., Porro, A. (ed.): Proceedings of the 4th International Temperate Rice Conference. Pp. 284–285. Tipografia Fiordo, Novara 2007c.Google Scholar
  27. Saghi Maroof, M.A., Biyashev, R.M., Yang, G.P., Zhang, Q., Allard, R.W.: Extraordinarily polymorphic microsatillate DNA in barely species diversity, choromosomal location, and population dynamics. — Proc. nat. Acad. Sci. USA. 91: 5466–5570, 1994.CrossRefGoogle Scholar
  28. Silva, C., Martinez, V., Carvajal, M.: Osmotic versus toxic effects of NaCl on pepper plants. — Biol. Plant. 52: 72–79, 2008.CrossRefGoogle Scholar
  29. Takehisa, H., Shimodate, T., Fukuta, Y., Ueda, T., Yano, M., Yamaya, T., Kameya T., Sato, T.: Identification of quantitative trait loci for plant growth of rice in paddy field flooded with salt water. — Field Crops Res. 89. 85–95, 2004.CrossRefGoogle Scholar
  30. Temnykh, S., Park, W.D., Ayres, N., Cartinhour, S., Hauck, N., Lipovich, L., Cho, Y.G., Ishii, T., McCouch, S.R.: Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). — Theor. appl. Genet. 100: 697–712, 2000.CrossRefGoogle Scholar
  31. Veldboom, L.R., Lee, M., Woodman, W.L.: Molecular-markers facilitated studies in an elite maize population. I. Linkage analysis and determination of QTLs for morphological traits. — Theor. appl. Genet. 88: 7–16, 1994.CrossRefGoogle Scholar
  32. Waling, I., Van, W., Houba, V.J.G., Van der Lee, I.J.: Soil and Plant Analysis. — Wageningen Agr. Univ., Wageningen 1989.Google Scholar
  33. Xu, Y.: Quantitative trait loci: separating, pyramiding, and cloning. — Plant. Breed. Rev. 15: 85–139, 1997.Google Scholar
  34. Yadav, R., Courtois, B., Huang, N., McLaren, G.: Mapping genes controlling root morphology and root distribution in a double haploid population of rice. — Theor. appl. Genet. 94: 619–632, 1997.CrossRefGoogle Scholar
  35. Yeo, A.R., Flowers, T.J.: Mechanisms of salinity resistance in rice and their role as physiological criteria in plant breeding. — In: Staples, R.C., Toenniessen, G.H. (ed.): Salinity Tolerance in Plant: Strategies for Crop Improvement. — John Wiley and Sons, New York 1984.Google Scholar
  36. Yeo, A.R., Flowers, T.J.: Selection for physiological characters — examples from breeding for salt tolerance. — In: Flowers, T.J., Jones, M.B. (ed.): Plant under Stress. Biochemistry, Physiology and Ecology and their Application to Plant Improvement. Pp. 217–234. Cambridge University Press, Cambridge 1989.Google Scholar
  37. Yoshida, S., Forno, D.A., Cock, J.H., Gomez, K.A.: Laboratory Manual for Physiological Studies of Rice. — IRRI, Los Baños 1976.Google Scholar
  38. Zeng, Z.B.: Precision mapping of quantitative traits loci. — Genetics 136: 1457–1468, 1994.PubMedGoogle Scholar
  39. Zhang, G.Y., Guo, Y., Chen, S.L., Chen, S.Y.: RFLP tagging of a salt tolerance gene in rice. — Plant. Sci. 110: 227–234, 1995.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • H. Sabouri
    • 1
  • A. M. Rezai
    • 2
  • A. Moumeni
    • 3
  • A. Kavousi
    • 3
  • M. Katouzi
    • 3
  • A. Sabouri
    • 4
  1. 1.Department of Plant Production, Gonbad High Education CenterGorgan University of Agriculture Science and Natural ResourceGonbadIran
  2. 2.Faculty of Agriculture SciencesIsfahan University of TechnologyIsfahanIran
  3. 3.Researchers in Plant BreedingRice Research Institute of IranRashtIran
  4. 4.Faculty of Agriculture SciencesUniversity of GuilanRashtIran

Personalised recommendations