Cereal Research Communications

, Volume 43, Issue 2, pp 236–248 | Cite as

Morpho-physiological and Molecular Variability in Salt Tolerant and Susceptible Popular Cultivars and their Derivatives at Seedling Stage and Potential Parental Combinations in Breeding for Salt Tolerance in Rice

  • K. ChattopadhyayEmail author
  • D. Nath
  • R. L. Mohanta
  • B. C. Marndi
  • D. P. Singh
  • O. N. Singh


Saltol, a major QTL for salt exclusion, was derived from ‘Pokkali’, a salt-tolerant rice cultivar. Apart from Pokkali, many genotypes with wide variation for salinity tolerance offer ample scope for identifying new genes or QTLs underlying various tolerance mechanisms. Such genes could be aggregated into high-yielding backgrounds to reinforce a breeding programme. To identify potential donors for salt tolerance and prospective parental combinations for developing high-yielding salt-tolerant cultivars, ten genotypes were subjected to salt stress and evaluated for morpho-physiological traits and marker-allele polymorphism in the Saltol-QTL region. Although the salt-susceptible high-yielding varieties clustered together in a 3-D plot, principal component analysis showed marked spatial isolation among the tolerant genotypes. Unlike Pokkali and its derivative FL496, Rahspunjar maintained a higher level of K+ despite high Na+ influx in shoots. The wider genetic distances observed at both phenotypic and genotypic levels suggest the possibility of getting transgressive segregants among the offspring of crosses between Rahspunjar and Gayatri or Swarna Sub1. Similarly, SR 26B, which coped with the stress by diluting the Na+ load by maintaining a higher growth rate, differed from Pokkali or Nona Bokra: these two coped with the stress by regulating the transmission of Na+ from roots to photosynthetically active sites. The F2:3 population derived from Savitri × SR 26B showed wide morpho-physiological diversity for salt tolerance. SR 26B was the most distant genotype from Pokkali in the Saltol QTL region and was salt tolerant despite the absence of Pokkali alleles in this region.


salt tolerance principal component analysis ion exclusion Saltol QTL genetic diversity 



shoot length (cm)


root length (cm)


dry weight of shoots per plant (mg)


dry weight of roots per plant (mg)


shoot Na+ concentration (µg/mg)


shoot Na+ content (mg)


shoot K+ concentration (µg/mg)


shoot K+ content per plant (mg)


shoot Na+/K+ ratio


root Na+ concentration (µg/mg)


root Na+ content per plant (mg)


root K+ concentration (µg/mg)


root K+ content per plant (mg)


root Na+/K+ ratio


total Na+ content per plant (mg)


total K+ content per plant (mg)


plant Na+/K+ ratio


growth rate (%)


standard evaluation system score (on a scale from 1 to 9)


coefficient of variance


critical difference


standard error of mean


mean sum of squares


standard deviation


quantitative trait locia


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  1. Akita, S., Cabuslay, G.S. 1990. Physiological basis of differential response to salinity in rice cultivars. Plant Soil 123:227–294.CrossRefGoogle Scholar
  2. Anderson, J.A., Churchill, G.A., Autrique, J.E., Tanksley, S.D., Sorrells, M.E. 1993. Optimizing parental selection for genetic linkage maps. Genome 36:181–186.CrossRefGoogle Scholar
  3. Ben-Rais, L., Alpha, M.J., Bhal, J. 1993. Lipid and protein contents of jojoba leaves in relation to salt adaptation. Plant Physiol. 31:547–557.Google Scholar
  4. Berthomieu, P., Conejero, G., Nublat, A., Brackenbury, W.J., Lambert, C., Savio, C., Uozumi, N., Oiki, S., Yamada, K., Cellier, F., Gosti, F., Simonnean, T., Essah, P.A., Tester, M., Very, A. A., Sentenac, H., Casoe, F. 2003. Functional analysis of AtHKT1 in Arabidopsis shows that Na(+) recirculation by the phloem is crucial for salt tolerance. EMBO J. 22:2004–2014.CrossRefGoogle Scholar
  5. Chattopadhyay, K., Nath, D., Mohanta, R.L., Bhattacharyya, S., Marndi, B.C., Nayak, A.K., Singh, D.P., Sarkar, R.K., Singh, O.N. 2014. Diversity and validation of microsatellite markers in Saltol-QTL region in contrasting rice genotypes for salt tolerance at the early vegetative stage. Aus. J. Crop Sci. 8:356–362.Google Scholar
  6. Garcia, A., Rizzo, C.A., Uddin, J., Bartos, S.L., Senadhira, D., Flowers, T.J., Yeo, A.R. 1997. Sodium and potassium transport to the xylem are inherited independently in rice, and the mechanism of sodium: Potassium selectivity differs between rice and wheat. Plant Cell Environ. 20:1167–1174.CrossRefGoogle Scholar
  7. Garciadebleas, B., Senn, M.E., Bañuelos, M.A., Rodriquez-Navarro, A. 2003. Sodium transport and HKT transporters: the rice model. Plant J. 34:788–801.CrossRefGoogle Scholar
  8. Gregorio, G.B., Islam, M.R., Vergara, G.V., Thirumeni, S. 2013. Recent advances in rice science to design salinity and other abiotic stress tolerant rice varieties. SABRAO J. Breed. Genet. 45:31–41.Google Scholar
  9. Gregorio, G.B., Senadhira, D., Mendoza, R.I. 1997. Screening rice for salinity tolerance. IRRI Discussion paper series no. 22. BRRI, Philippines, pp. 1–30.Google Scholar
  10. Islam, M.R., Gregorio, G.B., Salam, M.A., Collard, B.C.Y., Singh, R.K., Hassan, L. 2012. Validation of SalTol linked markers and haplotype diversity on chromosome 1 of rice. Mol. Plant Breed. 3:103–114.Google Scholar
  11. Jolliffe, I.T. 1986. Principal Component Analysis. Springer-Verlag, Berlin.CrossRefGoogle Scholar
  12. Koyama, L.M., Levesley, A., Koebner, R.M.D., Flowers, T.J., Yeo, A.R. 2001. Quantitative trait loci for component physiological traits determining salt tolerance in rice. Plant Physiol. 125:406–422.CrossRefGoogle Scholar
  13. Lee, K.S., Choi, W.Y., Ko, J.C., Kim, T.S., Gregorio, G.B. 2003. Salinity tolerance of japonica and indica rice (Oryza sativa L.) at the seedling stage. Planta 216:1043–1046.CrossRefGoogle Scholar
  14. 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. 2004. QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theor. Appl. Genet. 108:253–260CrossRefGoogle Scholar
  15. Munns, R., Tester, M. 2008. Mechanisms of salinity tolerance. Ann. Rev. Plant Bio. 59:651–681.CrossRefGoogle Scholar
  16. Negrao, S., Almadanim, M.C., Pires, I.S., Abreu, I.A., Maroco, J., Courtois, B., Gregorio, G.B., McKnally, K.L., Oliviera, M.M. 2013. New allelic variants found in key rice salt-tolerant genes: an association study. Plant Biotech. J. 11: 87–100.CrossRefGoogle Scholar
  17. Platten, J.D., Egdane, J.A., Ismail, A.M. 2013. Salinity tolerance, Na+ exclusion and allele mining of HKT 1;5 in Oryza sativa and O. glaberrima: many sources, many genes, one mechanism? BMC Plant Biol. 13:32.CrossRefGoogle Scholar
  18. Rauf, S., Teixeira de Silva, J.A., Khan, A.A., Naveed, A. 2010. Consequences of plant breeding on genetic diversity. Internal J. Plant Breed. 4:1–21.Google Scholar
  19. Rogers, S.O., Bendich, A.J. 1988. Extraction of DNA from plant tissues. In: Gelvin, S.B., Schilperoort, R.A. (eds), Plant Molecular Biology Manual. Kluwer Academic Publishers, Boston, MA, USA, pp. A6:1–10Google Scholar
  20. Rohlf, F.J. 2000. NTSYS-pc Numerical Taxonomy and Multivariate Analysis System version 2.1 Applied Biostatistics, New York, USA.Google Scholar
  21. Senadheera, P., Singh, R.K., Maathuis, F.J.M. 2009. Differentially expressed membrane transporters in rice roots may contribute to cultivar dependent salt tolerance. J. Exp. Bot. 60:2553–2563.CrossRefGoogle Scholar
  22. Shabala, S., Cuin, T.A. 2008. Potassium transport and plant salt tolerance. Physio. Plant 133:651–669.CrossRefGoogle Scholar
  23. Singh, R.K., Gregorio, G.B., Jain, R.K. 2007. QTL mapping for salinity tolerance in rice. Physio. Mol. Bio. Plants 13:87–99.Google Scholar
  24. Singh, R.K., Flowers, T.J. 2010. The physiology and molecular biology of the effects of salinity on rice. In: Pessarakli, M. (ed.), Handbook of Plant and Crop Stress, 3rd edn. Taylor and Francis, Florida, USA, pp. 901–942.Google Scholar
  25. Thomson, M.J., De Ocampo, M., Egdane, J., Rahman, M.A., Sajise, A.G., Adorada, D.L., Tumimbang-Raiz, E., Blumward, E., Seraj, Z.I., Singh, R.K., Gregorio, G.B., Ismail, A.M. 2010. Characterizing the Saltol quantitative trait locus for salinity tolerance in rice. Rice 3:148–160.CrossRefGoogle Scholar
  26. Yeo, A. 2007. Salinity. In: Yeo, A.R., Flowers, T.J. (eds), Plant Solute Transport. Blackwell Publishing. London, UK. pp. 340–356.CrossRefGoogle Scholar
  27. Yeo, A.R., Yeo, M.E., Flowers, S.A., Flowers, T.J. 1990. Screening of rice (Oryza sativa L.) genotypes for physiological characters contributing to salinity resistance and their overall performance. Theor. App. Genet. 79:377–384.CrossRefGoogle Scholar
  28. Yoshida, S., Forno, D.A., Cock, J.H., Gomez, K.A. 1976. Laboratory Manual for Physiological Studies of Rice. 3rd edn. IRRI. Los Banos, Philippines. pp. 61–66.Google Scholar
  29. Zhang, J.L., Flowers, T.J., Wang, S.M. 2010. Mechanisms of sodium uptake by roots of higher plants. Plant Soil 326:45–60.CrossRefGoogle Scholar

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© Akadémiai Kiadó, Budapest 2015

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Authors and Affiliations

  • K. Chattopadhyay
    • 1
    Email author
  • D. Nath
    • 1
  • R. L. Mohanta
    • 1
  • B. C. Marndi
    • 1
  • D. P. Singh
    • 1
  • O. N. Singh
    • 1
  1. 1.Central Rice Research InstituteCuttackIndia

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