Investigation and comparison of aerobic and Iranian rice based on markers linked to traits related to drought and salinity tolerance and their relationship with germination traits under osmotic stress

Document Type : Research Paper


1 Former M.Sc. Student of Plant Breeding, Department of Agronomy & Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran

2 Assistant Professor of Plant Breeding, Department of Agronomy & Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran


Aerobic rice is as useful potential in reducing of water problem. Comparison and investigation of genetic differences between Iranian rice varieties and aerobic rice can be useful in identification of genomic regions influencing in drought tolerance. In the present study in addition to an examination of germination genotypes under osmotic stress, allelic diversity were evaluated in 53  genotypes including 31 aerobic rice and 22 lowland Iranian rice varieties based on 26 SSR markers linked to QTL associated with drought and salinity tolerance. A total of 118 polymorphic alleles of microsatellite loci were produced with an average of 4.54 per marker. The highest calculated PIC level of 0.77 and 0.76 and the maximum range genetic diversity of 0.80 and 0.79 were related to RM10793 and RM493 respectively. Overview of genetic diversity statistics showed that two markers RM10793 and RM493 had higher values the other markers and more obvious role played in genotype differentiation. Grouping of genotypes according to Jaccard similarity coefficient using algorithms neighbor joining assigned them into two groups. This classification had significant compliance with the results of cluster analysis using the WARD algorithm based on germination traits. This may indicate the effectiveness and confirmation of used microsatellite markers in the separation of genotypes for osmotic tolerance.


Main Subjects

  1. Abdul-Baki, A. A. & Anderson, J. D. (1973). Vigour deterioration in soybean seeds by multiple criteria. Journal of Crop Science, 13, 630-633.
  2. Abdolshahi, R., Omidi, M., Talei, A. R. & Yazdi Samadi, B. (2010). Evaluation of bread wheat genotypes form drougth tolerance. Esci Journal of Crop Prduction. 3 (1), 159-171. (in Farsi)
  3. Allahgholipor, M., Mohamadsaleh, M. S. & Eebadi, G. H. A. (2004). Genetic variation in the classification of varieties of rice. Iranian Journal of Agricultural Sciences, 35(4), 973-981. (in Farsi)
  4. Baalbaki, R. Z., Zurayk, R. A., Blelk, M. M. & Tahouk, S. N. (1999). Germination and seedling development of drought tolerant and susceptible wheat under moisture stress. Seed Science and Technology, 27, 291-302.
  5. Belhassen, E. (Ed) (1996). Drought in higher plants: genetical, physiological and molecular biological analysis. ENSA-INRA SGAP, Montpellier, France. 152 pp.
  6. Bernier, J., Kumar, A., Ramaiah, V., Spaner, D. & Atlin, G. (2007). A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice. Journal of Crop Science, 47(2), 507-518.
  7. Bouman, B. A., Xiaoguang, M., Huaqi, Y., Zhiming, W., Junfang, W., Changgui, Z. & Bin, C. (2002). Aerobic Rice (Han Dao): A New Way of Growing Rice in Water-Short Areas, Proceedings of the 12th ISCO Conference, May 26-31, Beijing, China.
  8. Bounphanousay, C., Jaisil, P., McNally, K. L., Sanitchon, J. & Sackville Hamilton, N. R. (2008). Variation of microsatellite markers in collection of Lao, black glutinous rice (Oryza sativa L.). Asian Journal of Plant science, 7 (2), 140-148.
  9. Camberato, J. & Mccarty, B. (1999). Irrigation water quality: part I. Salinity. South CarolinaTurfgrass Foundation New, 6 (2), 6-8.
  10. Collard, B. C. Y. & Mackill, D. J. (2008). Marker assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences, 363, 557-572.
  11. Diwan, J. M., Channbyregowda, V., Shenoy, Salimath, P. & Bhat, R. (2013). Molecular mapping of early vigour related QTLs in rice. Research Journal of Biology, 1, 24-30.
  12. Ehdaie, B. & Waines, J. G. (1993). Variation in water use efficiency and its components in wheat. Crop Science, 31, 1282-1288.
  13. Emam E (2007). Careal production. Shiraz University Press. pp190. (in Farsi)
  14. Hunter. E. A., Glasbey, C. A. & Naylor R. E. L. (1984). The analyses of data from germination test. Journal of Agricultural Sciences, Cambridge, 102, 207-213.
  15. Ghoulam, C. & Fares, K. (2001). Effect of salinity on seed germination and early seedling growth of sugar beet (Beta vulgaris L.). Seed Science and Technology, 29, 357-364.
  16. Kanagara, P., Silvas, K. & Babu, C. (2010). Microsatellite markers linked to drought resistance in rice (Oryza sativa L.). Journal of Current Science, 98, 836-839.
  17. Karimi, H. (1996). Crops. Tehran University Press. pp714. (in Farsi)
  18. Khavazeh, M. (1998). Effect of salinity on germination, growth, and Cl, Na content of four arid and esertspecies. MSc Thesis, Isfahan University of Technology, Isfahan.
  19. Lapitan, V. C., Brar, D. S., Abe, T. & Redona, E.D. (2007). Assessment of genetic diversity of Pilippine rice carrying good quality traits using SSR markers. Journal of Breeding Science, 57, 263-270.
  20. Luan, Li., Wang, X., Long, W. B.,  Liu, Y. H.,  Tu, S. B., Zhao, Z. P., Kong, F. L. & Yu, M. Q. (2008). Microsatellite analysis of genetic variation and population genetic differentiation in autotetraploid and diploid rice. Biochemical Genetic, 46, 248-266.
  21. Mohammadi, S.A. (2006). Analysis of molecular data from perspective of genetic diversity, 9th Iranian crop science congress, Aburaihan Campus-University of Tehran, Aug, 27-29, Tehran, Iran. (in Farsi)
  22. Nei, M. (1972). Genetic distance between populations. American Naturalist. 106 (949), 283-292.
  23. Nori, Z. (2006). Molecular genetic diversity of rice varieties using microsatellite markers in comparison with the results of quantitative methods. MSc. Thesis. University of Gilan. pp 120. (in Farsi)
  24. Ribeiro-Carvalho, C., Guedes-Pinto, H. & Igregas, G. (2004). High levels of genetic diversity throughout the range of Portuguese wheat landrace Barbela. Annals of Botany, 94, 699-705.
  25. Roumani, A. & Ehteshami, S. M. R. (2013). Effect of Different Levels of Salinity Strees on Germination Indices and Seedling Growth of Fenugreek (Trigonella foenum L.). 2nd National Congress on Medicinal Plants.15, 16 May, Tehran, Iran.
  26. Sabouri, H., Nahvi, M., Biabani, A., Torabi, A., Dadras, A. R. & Sabouri, A. (2009). Classification of Iranian rice genotypes based on Fischer linear discrimination functions under different levels of osmotic potential caused by Sorbitol. EJANG. Electronic Journal of Agriculture and Natural Resources of Golestan, 2(2), 49-65.
  27. Saghai Mroof, M. A., Biyashev, R. M., Yang, G. P., Zhang, Q. & Allard, R.W. (1994). Extraordinarily polymorphic DNA in barely species diversity, chromosomal location, and population dynamics. In: Proceeding of the Natioal Academy of Sceinces, USA. 91, 5466-5570.
  28. Shannon, C. E. & Weaver, W. (1963). The mathematical theory of communication. University of Illinois Press, Urbana, Ill.
  29. Singh, V. K., Upadhyay, p., Sinha, p., Mall, A. K., Jaiswal,S. K., Singh, A., Ellur, R. K., Biradar, S., Sundaram R. M., Singh, S., Ahmed, I., Mishra, B., Singh, A. K. &  Kole, C. (2011). Determination of genetic relationships among elite thermosensitive genic male sterile (TGMS) of rice (Oryza sativa L.) employing morphological and simple sequence rapeat (SSR) marker. Journal of Genetics, 90, 11-19.
  30. Soltani, A. & Maddah, V. (2010). Simple, Applied Programs for Education and Research in Agronomy. Niak Press. Page 80.
  31. Thomson, M. J., De Ocampo, M., Egdane, J., Rahman, M. A., Sajise, A. G., Adorada, D. L., Tumimbang, Raiz, E., Blumwald, 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(2-3), 148-160.
  32. Venuprasad, R., Bool, M. E., Quiatchon, L. & Atlin, G. N. (2011). A QTL for rice grain yield in aerobic environments with large effects in three genetic backgrounds. Theoretical and Applied Genetics, 124 (2), 323-32.
  33. Vial, L. K. (2007). Aerobic and Alternate-wet-and-dry (AWD) Rice Systems. Nuffield Australia publishing. Griffith NSW 2680. Australia.
  34. Vikram, P., M. Swamy, B. P. & Dixit, S. (2011). qDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genetics. 12, 89.
  35. Wang, Xu-S., Zhu, J. & Mansueto, L. (2005). Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map. Journal of Zhejiang University. Science. B 6, 382-388.
  36. Willenborg, C. J., Wildeman, J. C., Miller, A. K., Rossnagel, B. G. &  Shirtliffe, S. J. (2005). Oat germination characteristics differ among genotypes, seed size and osmotic potentials. Crop Science. 45, 2023-2029.
  37. Yang, X., Yan, J., Shah, T., Warburton, M. L., Li, Q., Li, L., Gao, Y., Chai, Y., Fu, Z., Zhou, Y., Xu, S., Bai, G., Meng, Y., Zheng, Y. & Li, J. (2010). Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection. Theoretical and Applied Genetics, 121, 417-431.
  38. Yeh, F. C., Yang, R. C., Boyle, T. J. B., Ye, Z. H. & Mao, J. X. (1997). Popgene, the user-friendly shareware for population genetic analysis. Edmonton, Molecular Biology and Biotechnology Center, University of Alberta, Canada.
Volume 47, Issue 3 - Serial Number 3
January 2017
Pages 503-514
  • Receive Date: 29 June 2015
  • Revise Date: 30 January 2016
  • Accept Date: 01 February 2016
  • Publish Date: 21 November 2016