AJPS  Vol.4 No.12 C , December 2013
Physio-Biochemical and Microsatellite Based Profiling of Lowland Rice (Oryza sativa L.) Landraces for Osmotic Stress Tolerance
Abstract: Global climate changes accelerate a wide range of abiotic stresses leading to a series of physiological, biochemical and molecular changes that adversely affect the growth and productivity of rice (Oryza sativa L.). In this background, there is limited knowledge and profiling reports of lowland, less popular rice landraces in relation to their osmotic stress tolerance. Laboratory mediated physiological and biochemical screening for a selected set of 20 lowland rice landraces was done in induced drought and salinity stress conditions. Varietal genetic diversity and inter-relatedness were assessed by using osmotic stress tolerance linked forty-five rice microsatellite markers. For representing the allelic diversity of the studied microsatellite loci across the selected genotypes, a microsatellite panel was constructed and PIC values of all used microsatellite markers were calculated. The obtained database can be used for varietal identification, characterization and genetic information in relation to osmotic stress tolerance.
Cite this paper: R. Roychowdhury, J. Karmakar, J. Karmakar, M. Kumar Adak and N. Dey, "Physio-Biochemical and Microsatellite Based Profiling of Lowland Rice (Oryza sativa L.) Landraces for Osmotic Stress Tolerance," American Journal of Plant Sciences, Vol. 4 No. 12, 2013, pp. 52-63. doi: 10.4236/ajps.2013.412A3007.

[1]   FAO (Food and Agricultural Organization), “Food Outlook Global Market,” 2008.

[2]   R. Wassmann, S. V. K. Jagadish, S. Heuer, A. Ismail, E. Redona, R. Serraj, R. K. Singh, G. Howell, H. Pathak and K. Sumfleth, “Climate Change Affecting Rice Production: The Physiological and Agronomic Basis for Possible Adaptation Strategies,” In: D. L. Sparks, Ed., Advances in Agronomy, Elsevier Inc., Academic Press, Burlington, 2009, pp. 59-122.

[3]   E. P. Guimaraes, “Rice Breeding,” In: M. J. Carena, Ed., Cereals, The Banks and The Italian Economy, Springer, New York, 2009, pp. 99-126.

[4]   B. K. Joshi, “Rice Gene Pool for Tarai and Inner Tarai Areas of Nepal,” Nepal Agric. Research Journal, Vol. 6, 2005, pp. 10-22.

[5]   N. G. Hanamaratti, S. K. Prashanthi, P. M. Salimath, R. R. Hanchinal, H. D. Mohankumar, K. G. Parameshwarappa and S. D. Raikar, “Traditional Land Races of Rice in Karnataka: Reservoirs of Valuable Traits,” Current Science, Vol. 94, No. 2, 2008, pp. 242-247.

[6]   X. Huang, X. Wei, T. Sang, Q. Zhao, Q. Feng, Y. Zhao, C. Li, C. Zhu, T. Lu, Z. Zhang, M. Li, D. Fan, Y. Guo, A. Wang, L. Wang, L. Deng, W. Li, Y. Lu, Q. Weng, K. Liu, T. Huang, T. Zhou, Y. Jing, W. Li, Z. Lin, E. S. Buckler, Q. Qian, Q-F. Zhang, J. Li and B. Han, “Genome-Wide Association Studies of 14 Agronomic Traits in Rice Landraces,” Nature Genetics, Vol. 42, No. 11, 2010, pp. 961-967.

[7]   Z. H. Pervaiz, S. Tehrim, M. A. Rabbani, M. S. Masood and S. A. Malik, “Diversity in Major Seed Storage Proteins of Rice Landraces of Pakistan,” Pakistan Journal of Botany, Vol. 43, 2011, pp. 1607-1612.

[8]   S. G. Ram, V. Thiruvengadam and K. K. Vinod, “Genetic Diversity among Cultivars, Landraces and Wild Relatives of Rice as Revealed by Microsatellite Markers,” Journal of Applied Genetics, Vol. 48, No. 4, 2007, pp. 337-345.

[9]   R. Mahajan, S. Tabia, G. Raina and N. Mangotra, “Assessment of Genetic Diversity of Non-Basmati Rice of Jammu and Kashmir Using Microsatellite Markers,” Journal of Cereals and Oil Seeds, Vol. 3, No. 2, 2012, pp. 21-27.

[10]   B. K. Chakravarthi and R. Naravaneni, “SSR Marker Based DNA Fingerprinting and Diversity Study in Rice (Oryza sativa L.),” African Journal of Biotechnology, Vol. 5, No. 9, 2006, pp. 684-688.

[11]   C.Vanniarajan, K. K. Vinod and A. Pereira, “Molecular Evaluation of Genetic Diversity and Association Studies in Rice (Oryza sativa L.),” Journal of Genetics, Vol. 91, No. 1, 2012, pp. 9-19.

[12]   A. M. Sajib, M. M. Hossain, A. T. M. J. Mosnaz, H. Hossain, M. M. Islam, M. S. Ali and S. H. Prodhan, “SSR Marker-Based Molecular Characterization and Genetic Diversity Analysis of Aromatic Landraces of Rice (Oryza sativa L.),” Journal of BioScience and Biotechnology, Vol. 1, No. 2, 2012, pp. 107-116.

[13]   B. I. G. Haussmann, H. K. Parzies, T. Presterl, Z. Susic and T. Miedaner, “Plant Genetic Resources in Crop Improvement,” Plant Genetic Resources, Vol. 2, No. 1, 2004, pp. 3-21.

[14]   C. Brondani, T. C. O. Borba, P. H. N. Rangel and R. P. V. Brondani, “Determination of Genetic Variability of Traditional Varieties of Brazilian Rice Using Microsatellite Markers,” Genetics and Molecular Biology, Vol. 29, No. 4, 2006, pp. 676-684.

[15]   N. Dey, S. Biswas, T. Ray Chaudhury, S. R. Dey, M. De and T. K. Ghose, “RAPD-Based Genetic Diversity Analysis of Aromatic Rice (Oryza sativa L.),” Plant Cell Biotechnology and Molecular Biology, Vol. 6, 2005, pp. 133-142.

[16]   T. Chattopadhyay, T. Biswas, M. Chatterjee, N. Mandal and S. Bhattacharyya, “Biochemical and SSR Marker Based Characterization of Some Bengal Landraces of Rice Suffixed with ‘Sail’ in Their Name,” Indian Journal of Genetics, Vol. 68, No. 1, 2008, pp. 15-20.

[17]   T. Lodha, J. Karmakar, R. Roychoudhuri and N. Dey, “Assessment of Genetic Diversity of Some Commonly Grown Rice Genotypes of South Bengal Using Microsatellite Markers Associated with the saltol QTL Mapped on 1st Chromosome,” NBU Journal of Plant Sciences, Vol. 5, No. 1, 2011, pp. 35-39.

[18]   J. Karmakar, R. Roychowdhury, R. K. Kar, D. Deb and N. Dey, “Profiling of Selected Indigenous Rice (Oryza sativa L.) Landraces of Rarh Bengal in Relation to Osmotic Stress Tolerance,” Physiology and Molecular Biology of Plants, Vol. 18, No. 2, 2012, pp. 125-132.

[19]   B. Das, S. Sengupta, S. K. Parida, B. Roy, M. Ghosh, M. Prasad and T. K. Ghose, “Genetic Diversity and Population Structure of Rice Landraces from Eastern and North Eastern States of India,” BMC Genetics, Vol. 14, No. 1, 2013, p. 71.

[20]   H. Akagi, Y. Yokozeki, A. Inagaki and T. Fujimura, “Microsatellite DNA Markers for Rice Chromosomes,” Theoretical and Applied Genetics, Vol. 93, No. 7, 1996, pp. 1071-1077.

[21]   S. R. McCouch, X. Chen, O. Panaud, S. Temnykh, Y. Xu, Y. G. Cho, N. Huang, T. Ishii and M. Blair, “Microsatellite Marker Development, Mapping and Applications in Rice Genetics and Breeding,” Plant Molecular Biology, Vol. 35, No. 1-2, 1997, pp. 89-99.

[22]   S. R. McCouch, S. Temnykh, A. Lukashova, J. Coburn, G. DeClerck, S. Cartinhour, S. Harrington, M. Thomson, E. Septiningsih, M. Semon, P. Moncada and L. Jiming, “Microsatellite Markers in Rice: Abundance, Diversity and Applications,” In: G. S. Khush, et al., Eds., Rice Genetics IV, IRRI, Los Baños, Philippines, 2001

[23]   S. R. Berilus, A. Pattanayak and G. Ram, “Analysis of Genetic Variability in Rice Cultivars of Arunachal Pradesh (India) Using Microsatellite Marker,” African Journal of Biotechnology, Vol. 12, No. 8, 2013, pp. 798-810.

[24]   B. Choudhury, M. L. Khan and S. Dayanandan, “Genetic Structure and Diversity of Indigenous Rice (Oryza sativa) Varieties in the Eastern Himalayan Region of Northeast India,” SpringerPlus, Vol. 2, 2013, p. 228.

[25]   S. M. Shah, S. A. Naveed and M. Arif, “Genetic Diversity in Basmati and Non-Basmati Rice Varieties Based on Microsatellite Markers,” Pakistan Journal of Botany, Vol. 45, No. S1, 2013, pp. 423-431.

[26]   M.-H. Lin, C.-W. Lin, J.-C. Chen, Y.-C. Lin, S.-Y. Cheng, T.-H. Liu, F.-J. Jan, S.-T. Wu, F.-S. Thseng and H.-M. Ku, “Tagging Rice Drought-Related QTL with SSR DNA Markers,” Crop, Environment & Bioinformatics, Vol. 4, No. 1, 2007, pp. 65-76.

[27]   R. Venuprasad, M. E. Bool, L. Quiatchon, M. T. Sta Cruz, M. Amante and G. N. Atlin, “A Large-Effect QTL for Rice Grain Yield Under Upland Drought Stress on Chromosome 1,” Molecular Breeding, Vol. 30, No. 1, 2012, pp. 535-547.

[28]   L. H. Linh, T. H. Linh, T. D. Xuan, T. H. Ham, A. M. Ismail and T. D. Khanh, “Molecular Breeding to Improve Salt Tolerance of Rice (Oryza sativa L.) in the Red River Delta of Vietnam,” International Journal of Plant Genome, 2012, Article ID: 949038.

[29]   M. A. Haque, M. A. Mahmud, M. M. Islam and S. N. Begum, “Identification of Introgressed Rice Lines of Binadhan-7×FL-378 under Salt Stress through SSR Markers,” Journal of Bangladesh Agriculture University, Vol. 10, No. 1. 2012, pp. 49-54.

[30]   T. Biswas, A. Das and S. Bhattacharyya, “Microsatellite Marker Based Diversity Analysis for Submergence Tolerance in Some Bengal Landraces of Rice (Oryza sativa L.),” Journal of Tropical Agriculture, Vol. 50, No. 1-2, 2012, pp. 67-71.

[31]   N. R. M. K. N. D. Rathnayake, A. P. Bentota, D. M. N. Dissanayake, K. L. N. S. Perera, S. D. S. S. Sooriyapathirana and G. A. U. Jayasekera, “DNA Markers RM 464A and RM 219 Haplotypes are Effective in Selecting sub-1 Locus for the Introgression of Submergence Tolerance Into New Rice Varieties,” Ceylon Journal of Science (Biological Science), Vol. 41, No. 2, 2012, pp. 125-136.

[32]   R. K. Agnihotri, L. M. S. Palni and D. K. Pandey, “Germination and Seedling Growth under Moisture Stress: Screening of Landraces of Rice (Oryza sativa L.) from Kumaun Region of India Central Himalaya,” Journal of Plant Biology, Vol. 34, No. 1, 2007, pp. 21-27.

[33]   P. Shanthi, S. Jebaraj and S. Geetha, “In vitro Screening for Salt Tolerance in Rice (Oryza sativa),” Electronic Journal of Plant Breeding, Vol. 1, No. 4, 2010, pp. 1208-1212.

[34]   ISTA, “International Rules for Seed Testing,” Seed Science and Technology, Vol. 24, 1996.

[35]   D. I. Arnon, “Copper Enzymes in Isolated Chloroplasts: Polyphenoloxidase in Beta vulgaris,” Plant Physiology, Vol. 24, No. 1, 1949, pp. 1-15.

[36]   S. Sadasivam and A. Manickam, “Biochemical Methods,” New Age International Publishers (P) Ltd., New Delhi, 2010.

[37]   H. W. Li, B. S. Zang, X. W. Deng and X. P. Wang, “Overexpression of the Trehalose-6-Phosphate Synthase Gene OsTPS1 Enhances Abiotic Stress Tolerance in Rice,” Planta, Vol. 234, No. 5, 2011, pp. 1007-1018.

[38]   V. G. Panse and P. V. Sukhatme, “Statistical Methods for Agricultural Workers,” 2nd Edition, ICAR publication, New Delhi, 1967.

[39]   R. Roychowdhury, J. Karmakar and N. Dey, “PCR-Compatible Genomic DNA Isolation From Different Tissues of Rice (Oryza sativa) for SSR Fingerprinting,” EurAsian Journal of BioSciences, Vol. 6, 2012, pp. 85-90.

[40]   G. Mohammadi-Nejad, A. Arzani, A. M. Rezai, R. K. Singh and G. B. Gregorio, “Assessment of Rice Genotypes for Salt Tolerance Using Microsatellite Markers Associated With the saltol QTL,” African Journal of Biotechnology, Vol. 7, No. 6, 2008, pp. 730-736.

[41]   M. S. Rahman, M. K. H. Sohag and L. Rahman, “Microsatellite Based DNA Fingerprinting of 28 Local Rice (Oryza sativa L.) Varieties of Bangladesh,” Journal of Bangladesh Agriculture University, Vol. 8, No. 1, 2010, pp. 7-17.

[42]   H. H. Lee, P. P. N. Neoh, W. S. T. Bong, J. Puvaneswaran, S. C. Wong, P. H. Yiu and A. Rajan, “Genotyping of Sarawak Rice Cultivars Using Microsatellite Markers,” Pertanika Journal of Tropical Agricultural Science, Vol. 34, No. 1, 2011, pp. 123-136.

[43]   T. Y. Hwang, T. Sayama, T. Takahashi, Y. Takada, Y. Nakamoto, H. Funatsuki, H. Hisano, S. Sasamoto, S. Sato, S. Tabata, I. Kono, M. Hoshi, M. Hanawa, C. Yano, Z. Xia, K. Harada, K. Kitamura and M. Ishimoto, “High-Density Integrated Linkage Map Based on SSR Markers in Soybean,” DNA Research, Vol. 16, No. 4, 2009, pp. 213-225.

[44]   S. Gulzar and A. Khan, “Seed Germination of a Halophytic Grass Aeluropus agopoides,” Annals of Botany, Vol. 87, No. 3, 2001, pp. 319-324.

[45]   M. Z. Alam, T. Stuchbury and R. E. L. Naylor, “Effect of NaCl and PEG Induced Osmotic Potentials on Germination and Early Seedling Growth of Rice Cultivars Differing in Salt Tolerance,” Pakistan Journal of Biological Science, Vol. 5, No. 11, 2002, pp. 1207-1210.

[46]   C. Guoxiong, T. Krugman, T. Fahima, A. B. Korol and E. Nevo, “Comparative Study on Morphological and Physiological Traits Related to Drought Resistance between Xeric and Mesic Hordeum spontaneum Lines in Isreal,” Barley Genetics Newsletter, Vol. 32, 2002, pp. 22-33.

[47]   S. K. Pradhan, K. R. Mahanta and G. Ramkrishnayya, “Response of Upland Rice Cultivars Under Varying Soil Moisture Regimes,” Indian Journal of Plant Physiology, Vol. 8, No. 3, 2003, pp. 292-296.

[48]   E. G. Castillo, P. T. Tuong, A. M. Ismail and K. Inubushi, “Response to Salinity in Rice: Comparative Effects of Osmotic and Ionic Stresses,” Plant Production Science, Vol. 10, No. 2, 2007, pp. 159-170.

[49]   S. Cha-um, P. Vejchasarn and C. Kirdmanee, “An Effective Defensive Response in Thai Aromatic Rice Varieties (Oryza sativa L. spp. indica) to Salinity,” Journal of Crop Science and Biotechnology, Vol. 10, No. 4, 2007, pp. 257-264.

[50]   E. S. Koksal, H. Ustun, H. Ozcan and A. Gunturk, “Estimating Water Stressed Dwarf Green Bean Pigment Concentration through Hyperspectral Indices,” Pakistan Journal of Botany, Vol. 42, No. 3, 2010, pp. 1895-1901.

[51]   R. Roy, P. B. Mazumder and G. D. Sharma, “Proline, Catalase and Root Traits as Indices of Drought Resistance in Bold Grained Rice (Oryza sativa) Genotypes,” African Journal of Biotechnology, Vol. 8, No. 23, 2009, pp. 6521-6528.

[52]   S. Temnykh, G. DeClerck, A. Lukashova, L. Lipovich, S. Cartinhour and S. McCouch, “Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations and Genetic Marker Potential,” Genome Research, Vol. 11, 2001, pp. 1441-1452.

[53]   S. Temnykh, W. D. Park, N. Ayres, S. Cartinhour, N. Hauck, L. Lipovich, Y. G. Cho, T. Ishii and S. R. McCouch, “Mapping and Genome Organization of Microsatellite Sequences in Rice (Oryza sativa L.),” Theoretical and Applied Genetics, Vol. 100, No. 5, 2000, pp. 697-712.

[54]   S. Pal, S. Jain, N. Saini, A. Arti and R. K. Jain, “Identification of Microsatellite Markers for Differentiating Some Basmati and Non-Basmati Rice Varieties,” Indian Journal of Biotechnology, Vol. 3, No. 4, 2004, pp. 519-526.