AJPS  Vol.6 No.12 , August 2015
Physio-Biochemical and Genetic Exploration for Submergence Tolerance in Rice (Oryza sativa L.) Landraces with Special References to Sub1 Loci
Abstract: In the present study a group of four indigenous and less popular rice genotypes (Meghi, Panibhasha, Jabra and Sholey) reported by growers as submergence tolerant lines from flood prone areas of south Bengal were explored through study of nodal anatomy, physio-biochemical screening under submergence and genotyping with submergence tolerance linked rice microsatellite loci (RM loci). To identify the different allelic forms of different Sub1 compnents (Sub1A, Sub1B and Sub1C) among the studied lines, the genomic DNA of individual genotypes was amplified with three ethylene response factor like genes from Sub1 loci, located on rice chromosome 9. From the different physio-biochemical experiments performed in this investigation, it has been shown that Meghi and Jabra are the two probable potent genotypes which share common properties of both submergence tolerant and deep water nature whereas rest two genotypes (Sholey and Panibhasha) behave like typical deep water rice. The submergence tolerance property of Meghi was also confirmed from submergence tolerance linked SSR based genotyping by sharing with FR13A for some common alleles as reflected in fingerprint derived dendrogram. The rest of the genotypes shared a number of alleles and were included in a separate cluster. The common behaviour of Meghi and FR13A under submergence was also confirmed from genetic study of Sub1 loci through sharing of some common alleles for three Sub1 components (Sub1A, Sub1B and Sub1C loci). One SSR loci (RM 285) was identified as a potent molecular marker for submergence tolerance breeding programme involving these two selected rice lines (Meghi and Jabra) as donor plant through marker assisted selection.
Cite this paper: Goswami, S. , Labar, R. , Paul, A. , Kumar Adak, M. and Dey, N. (2015) Physio-Biochemical and Genetic Exploration for Submergence Tolerance in Rice (Oryza sativa L.) Landraces with Special References to Sub1 Loci. American Journal of Plant Sciences, 6, 1893-1904. doi: 10.4236/ajps.2015.612190.

[1]   Sarkar, R.K., Reddy, J.N., Sharma, S.G. and Ismail, A.M. (2006) Physiological Basis of Submergence Tolerance in Rice and Implications for Crop Improvement. Current Science, 91, 899-896.

[2]   Adkins, S.W., Shiraishi, T. and McComb, J.A. (1990) Submergence Tolerance of Rice—A New Glasshouse Method for the Experimental Submergence of Plants. Physiologia Plantarum, 80, 642-646.

[3]   Jackson, M.B. and Ram, P.C. (2003) Physiological and Molecular Basis of Susceptibility and Tolerance of Rice Plants to Complete Submergence. Annals of Botany, 91, 227-241.

[4]   Yamada, N. (1959) Physiological Basis of Resistance of Rice Plant against Overhead Flooding. Bulletin of the National Institute of Agricultural Sciences, 8, 111-112.

[5]   Ito, O., Ella, E. and Kawano, N. (1999) Physiological Basis of Submergence Tolerance in Rainfed Lowland Rice Ecosystem. Field Crops Research, 64, 75-90.

[6]   Sarkar, R.K., Das, S. and Ravi, I. (2001) Changes in Certain Antioxidative Enzymes and Parameters as a Result of Complete Submergence and Subsequent Re-Aeration of Rice Cultivars Differing in Submergence Tolerance. Journal of Agronomy and Crop Science, 187, 69-74.

[7]   Ella, E.S., Kawano, N., Yamauchi, Y., Tanaka, K. and Ismail, A.M. (2003) Blocking Ethylene Perception Enhances Flooding Tolerance in Rice Seedlings. Functional Plant Biology, 30, 813-819.

[8]   Das, K.K., Sarkar, R.K. and Ismail, A.M. (2005) Elongation Ability and Non-Structural Carbohydrate Levels in Relation to Submergence Tolerance in Rice. Plant Science, 168, 131-136.

[9]   Hattori, Y., Nagai, K. and Ashikari, M. (2011) Rice Growth Adapting to Deep Water. Current Opinion in Plant Biology, 14, 100-105.

[10]   Banerjee, S., Dey, N. and Adak, M.K. (2015) Assessment of Some Biomarkers under Submergence Stress in Some Rice Cultivars Varying in Responses. American Journal of Plant Sciences, 6, 84-94.

[11]   Xu, K. and Mackill, D.J. (1996) A Major Locus for Submergence Tolerance Mapped on Rice Chromosome 9. Molecular Breeding, 2, 219-224.

[12]   Xu, K., Xia, X., Fukao, T., Canlas, P., Maghirang-Rodriguez, R., Heuer, S., Ismail, A.M., Bailey-Serres, J., Ronald, P.C. and Mackill, D.J. (2006) Sub1A Is an Ethylene Response Factor-Like Gene That Confers Submergence Tolerance to Rice. Nature, 442, 705-708.

[13]   Xiong, H., Yang, J. and Li, Y. (2012) Identification of Submergence-Responsive Genes in Two Indica Rice Genotypes Carrying SUB1A-1 but Exhibiting Differential Tolerance. Journal of Plant Biology, 55, 233-241.

[14]   Bailey-Serres, J., Fukao, T., Ronald, P., Ismail, A., Heuer, S. and Mackill, D. (2010) Submergence Tolerant Rice: SUB1’s Journey from Landrace to Modern Cultivar. Rice, 3, 138-147.

[15]   Sarkar, R.K. and Bhattacharjee, B. (2011) Rice Genotypes with SUB1 QTL Differ in Submergence Tolerance, Elongation Ability during Submergence and Resubmergence and Regeneration Growth at Reemergence. Rice, 5, 7.

[16]   Biswas, T., Das, A. and Bhattacharyya, S. (2012) Microsatellite Marker Based Diversity Analysis for Submergence Tolerance in Some Bengal Landraces of Rice (Oryza sativa L.). Journal of Tropical Agriculture, 50, 67-71.

[17]   Khanh, T.D., Linh, L.H., Linh, T.H., Ham, L.H. and Xuan, T.D. (2013) Rapid and High-Precision Marker Assisted Backcrossing to Introgress the SUB1 QTL into the Vietnamese Elite Rice Variety. Journal of Plant Breeding and Crop Science, 5, 26-33.

[18]   Sarkar, R.K., Reddy, J.N., Das, K.K., Ram, P.C., Singh, P.N., Mazid, M.A., Sommut, W., Pane, H., Sharma, S.G. and Ismail, A.M. (2009) Biophysical Constraints in Flood-Prone Ecosystems: Impacts and Prospects for Enhancing and Sustaining Productivity. In: Haefele, S.M. and Ismail, A.M., Eds., Natural Resource Management for Poverty Reduction and Environmental Sustainability in Fragile Rice-Based Systems, Limited Proceedings, No. 15, International Rice Research Institute, Philippines, 67-81.

[19]   Neeraja, C.N., Maghirang-Rodriguez, R., Pamplona, A., Heuer, S., Collard, B.C.Y., Septiningsih, E.M., Vergara, G., Sanchez, D., Xu, K., Ismail, A.M. and Mackill, D.J. (2007) A Marker-Assisted Backcross Approach for Developing Submergence-Tolerant Rice Cultivars. Theoretical and Applied Genetics, 115, 767-776.

[20]   Singh, S., Mackill, D.J. and Ismail, A.M. (2009) Responses of SUB1 Rice Introgression Lines to Submergence in the Field: Yield and Grain Quality. Field Crops Research, 113, 12-23.

[21]   Iftekharuddaula, K.M., Newaz, M.A., Salam, M.A., Ahmed, H.U., Mahbub, M.A.A., Septiningsih, E.M., Collard, B.C.Y., Sanchez, D.L., Pamplona, A.M. and Mackill, D.J. (2011) Rapid and High-Precision Marker Assisted Backcrossing to Introgress the SUB1 QTL into BR11, the Rainfed Lowland Rice Mega Variety of Bangladesh. Euphytica, 178, 83-97.

[22]   Das, T. and Das, A.K. (2014) Inventory of the Traditional Rice Varieties in Farming System of Southern Assam: A Case Study. Indian Journal of Traditional Knowledge, 13, 157-163.

[23]   Lang, N.T., Tao, N.V. and Buu, B.C. (2011) Marker-Assisted Backcrossing (MAB) for Rice Submegence Tolerance in Mekong Delta. Omonrice, 18, 11-21.

[24]   Manangkil, O.E., Vu, H., Yoshida, S., Mori, N. and Nakamura, C. (2008) A Simple, Rapid and Reliable Bioassay for Evaluating Seedling Vigor under Submergence in Indica and Japonica Rice (Oryza sativa L.) Euphytica, 163, 267-274.

[25]   Yamauchi, M. and Winn, T. (1996) Rice Seed Vigor and Seedling Establishment in Anaerobic Soil. Crop Science, 36, 680-681.

[26]   Sadasivam, S. and Manikam, A. (2010) Biochemical Methods. Third Print, New Age International, New Delhi.

[27]   Arnon, D.I. (1949) Copper Enzymes in Isolated Chloroplasts, Polyphenoxidase in Beta vulgaris. Plant Physiology, 24, 1-15.

[28]   Lodha, T., Karmakar, J., Roychoudhuri, R. and Dey, N. (2011) 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, 5, 35-39.

[29]   Karmakar, J., Roychowdhury, R., Kar, R.K., Deb, D. and Dey, N. (2012) Profiling of Selected Indigenous Rice (Oryza sativa L.) Landraces of Rarh Bengal in Relation to Osmotic Stress Tolerance. Physiology and Molecular Biology of Plants, 18, 125-132.

[30]   Ganie, S.A. and Mondal, T.K. (2015) Genome-Wide Development of Novel miRNA-Based Microsatellite Markers of Rice (Oryza sativa) for Genotyping Applications. Molecular Breeding, 35, 51.

[31]   Peng, B., Wang, L., Fan, C., Jiang, G., Luo, L., Li, Y. and He, Y. (2014) Comparative Mapping of Chalkiness Components in Rice Using Five Populations across Two Environments. BMC Genetics, 15, 49.

[32]   Sambrook, J. and Russell, D.W. (2001) Molecular Cloning: A Laboratory Manual. 3rd Edition, Cold Spring Harbor, New York, 5.42-5.46.

[33]   Hwang, T.Y., Sayama, T., Takahashi, M., Takada, Y., Nakamoto, Y., Funatsuki, H., et al. (2009) High-Density Integrated Linkage Map Based on SSR Markers in Soybean. DNA Research, 16, 213-225.