Similar articles

Abstract: drought, flood, salinity, or a combination of these limits rice production. Several rice varieties are well known for their tolerance to specific abiotic stresses. We determined genetic relationship among 12 rice varieties including 9 tolerant to drought, flood, or salinity using inter-simple sequence repeat (ISSR) markers. Based on all markers, the nine tolerant varieties formed one cluster distinct from the cluster of three control varieties. The salt-tolerant varieties were closest to two flood-tolerant varieties, and together they were distinct from the drought-tolerant varieties. (GA)₈YG was the most informative primer, showing the highest polymorphic information content (PIC) and resolving power (Rp). The drought-, flood-, and salt-tolerant varieties grouped in three distinct clusters within the group of tolerant varieties, when (GA)₈YG was used. Sabita was the only exception. The two aus varieties, Nagina22 and FR13A, were separated and grouped with the drought- and flood-tolerant varieties, respectively, but they were together in dendrograms based on other primers. The results show that ISSR markers associated with (GA)₈YG delineated the three groups of stress-tolerant varieties from each other and can be used to identify genes/new alleles associated with the three abiotic stresses in rice germplasm.

[1] Adkins, S.W., Kunanuvatchaidach, R., Godwin, I.D., 1995. Somaclonal variation in rice. 2. Drought tolerance and other agronomic characters. Aust. J. Bot., 43(2):201-209.

[2] Agarwal, P.K., Agarwal, P., Reddy, M.K., Sopory, S.K., 2006. Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep., 25(12):1263-1274.

[3] Chao, D.Y., Luo, Y.H., Shi, M., Luo, D., Lin, H.X., 2005. Salt-responsive genes in rice revealed by cDNA microarray analysis. Cell Res., 15(10):796-810.

[4] Davierwala, A.P., Chowdari, K.V., Kumar, S., Reddy, A.P.K., Ranjekar, P.K., Gupta, V.S., 2000. Use of three different marker systems to estimate genetic diversity of Indian elite rice varieties. Genetica, 108(3):269-284.

[5] Davierwala, A.P., Ramakrishna, W., Chowdari, V., Ranjekar, P.K., Gupta, V.S., 2001. Potential of (GATA)_n microsatellites from rice for inter- and intra-specific variability studies. BMC Evol. Biol., 1(1):7.

[6] de Datta, S., Malabuyoc, J., Aragon, E., 1988. A field screening technique for evaluating rice germplasm for drought tolerance during the vegetative stage. Field Crops Research, 19(2):123-134.

[7] Garland, S.H., Lewin, L., Abedinia, M., Henry, R., Blakeney, A., 1999. The use of microsatellite polymorphisms for the identification of Australian breeding lines of rice (Oryza sativa L.). Euphytica, 108(1):53-63.

[8] Garris, A.J., Tai, T.H., Coburn, J., Kresovich, S., McCouch, S.R., 2005. Genetic structure and diversity in Oryza sativa L. Genetics, 169(3):1631-1638.

[9] Glaszmann, J.C., 1987. Isozymes and classification of Asian rice varieties. Theor. Appl. Genet., 74(1):21-30.

[10] Gorantla, M., Babu, P.R., Lachagari, V.B., Reddy, A.M., Wusirika, R., Bennetzen, J.L., Reddy, A.R., 2007. Identification of stress-responsive genes in an indica rice (Oryza sativa L.) using ESTs generated from drought-stressed seedlings. J. Exp. Bot., 58(2):253-265.

[11] IRRI (International Rice Research Institute), 1995. Fragile Lives in Fragile Ecosystems. Manila, Philippines, p.976.

[12] Jagadish, S.V.K., Craufurd, P.Q., Wheeler, T.R., 2008. Phenotyping parents of mapping population of rice for heat tolerance during anthesis. Crop. Sci., 48(3):1140-1146.

[13] Joshi, S.P., Gupta, V.S., Aggarwal, R.K., Ranjekar, P.K., Brar, D.S., 2000. Genetic diversity and phylogenetic relationship as revealed by inter-simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor. Appl. Genet., 100(8):1311-1320.

[14] Kaushik, A., Sani, N., Jan, S., Singh, R.K., Jan, R., 2002. Genetic structure of a segregating CSR10×Taraori Basmati F₃ population for salinity tolerance. Rice Genetics Newsletter, 19:85-87.

[15] Lafitte, H.R., Yongsheng, G., Yan, S., Li, Z.K., 2007. Whole plant responses, key processes, and adaptation to drought stress: the case of rice. J. Exp. Bot., 58(2):169-175.

[16] Mackill, D.J., Coffman, W.R., Garrity, D.P., 1996. Rainfed Lowland Rice Improvement IRRI. Manila, Philippines, p.242.

[17] McCouch, S.R., Sweeney, M., Li, J., Jiang, H., Thomson, M., Septiningsih, E., Edwards, J., Moncada, P., Xiao, J., Garris, A., 2007. Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica, 154(3):317.

[18] McNally, K.L., Bruskiewich, R., Mackill, D., Buell, C.R., Leach, J.E., Leung, H., 2006. Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. Plant Physiol., 141(1):26-31.

[19] Mohammadi-Nejad, G., Arzani, A., Rezail, A.M., Singh, R.K., Gregorio, G.B., 2008. Assessment of rice genotypes for salt tolerance using microsatellite markers associated with the saltol QTL. African Journal of Biotechnology, 7(6):730-736.

[20] Olufowote, J.O., Xu, Y., Chen, X., Park, W.D., Beachell, H.M., Dilday, R.H., Goto, M., McCouch, S.R., 1997. Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome, 40(3):370-378.

[21] Prasad, G.S.V., Muralidharan, K., Rao, C.S., Prasad, A.S.R., 2001. Stability and yield performance of genotypes: a proposal for regrouping world rice area into mega environments. Curr. Sci., 81:1337-1346.

[22] Prevost, A., Wilkinson, M.J., 1999. A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor. Appl. Genet., 98(1):107-112.

[23] Qi, Y., Kawano, N., Yamauchi, Y., Ling, J., Li, D., Tanaka, K., 2005. Identification and cloning of a submergence-induced gene OsGGT (glycogenin glucosyltransferase) from rice (Oryza sativa L.) by suppression subtractive hybridization. Planta, 221(3):437-445.

[24] Rao, R., Corrado, G., Bianchi, M., DiMauro, A., 2006. (GATA)₄ DNA fingerprinting identifies morphologically characterized “San Marzano” tomato plants. Plant Breed., 125(2):173-176.

[25] Reddy, P.M., Sarla, N., Siddiq, E.A., 2002. Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica, 128(1):9-17.

[26] Rohlf, F.J., 1993. NTSYS-PC Version 2.0. State University of New York, Exeter Software, Setauket, New York.

[27] Sahi, C., Singh, A., Kumar, K., Blumwald, E., Grover, A., 2006. Salt stress response in rice: genetics, molecular biology, and comparative genomics. Funct. Integr. Genomics, 6(4):263-284.

[28] Sangwan, I., Brian, M.R.O., 2002. Identification of a soybean protein that interacts with GAGA element dinucleotide repeat DNA. Plant Physiol., 129(4):1788-1794.

[29] Santi, L., Wang, Y., Stile, M.R., Berendzen, K., Wanke, D., Roig, C., Pozzi, C., Muller, K., Muller, J., Rohde, W., Salamini, F., 2003. The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3. Plant J., 34(6): 813-826.

[30] Sarla, N., Bobba, S., Siddiq, E.A., 2003. ISSR and SSR markers based on AG and GA repeats delineate geographically diverse Oryza nivara accessions and reveal rare alleles. Curr. Sci., 84:683-690.

[31] Sarla, N., Neeraja, C.N., Siddiq, E.A., 2005. Use of anchored (AG)_n and (GA)_n primers to assess genetic diversity of Indian landraces and varieties of rice. Curr. Sci., 89:1371-1381.

[32] Shylaraj, K.S., Sasidharan, N.K., Sreekumaran, V., 2006. VTL 6: a semi-tall, non-lodging, and high yielding rice (Oryza sativa L.) variety for the coastal saline zones of Kerala. Journal of Tropical Agriculture, 44(1-2):48-51.

[33] Singh, D.N., 2006. Participatory plant breeding as a method of rice breeding. International Rice Research Notes, 31(2): 48-50.

[34] Singh, U.P., 2004. Farmers participatory diagnosis of flood prone deepwater rice-cropping system in eastern India. International Rice Research Notes, 29(2):85-87.

[35] Swamy, B.P.M., Sarla, N., 2008. Yield enhancing quantitative trait loci (QTLs) from wild species. Biotechnology Advances, 26(1):106-120.

[36] Swindell, W.R., 2006. The association among gene expression responses to nine abiotic stress treatments in Arabidopsis thaliana. Genetics, 174(4):1811-1824.

[37] Tanksley, S.D., McCouch, S.R., 1997. Seed banks and molecular maps: unlocking genetic potential from the wild. Science, 277(5329):1063-1066.

[38] van Steensel, B., Delrow, J., Bussemaker, H.J., 2003. Genome wide analysis of Drosophila GAGA factor target genes reveals context dependent DNA binding. Proc. Nat. Acad. Sci., 100(5):2580-2585.

[39] Xu, K., Xu, X., Fukao, T., Canlas, P., Maghirang-Rodriguez, R., Heuer, S., Ismail, A.M., Bailey-Serres, J., Ronald, P.C., Mackill, D.J., 2006. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature, 442(7103):705-708.

[40] Zhang, L.D., Yuan, D.J., Yu, S.W., Li, Z.G., Cao, Y.F., Miao, Z.Q., Qian, H.M., Tang, K.X., 2004. Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana. Bioinformatics, 20(7):1081-1086.

[41] Zhang, L., Zuo, K., Zhang, F., Cao, Y., Wang, J., Zhang, Y., Sun, X., Tang, K., 2006. Conservation of noncoding microsatellites in plants: implication for gene regulation. BMC Genomics, 7(1):323.

[42] Ziska, L.H., Manalo, P.A., Ordonez, R.A., 1996. Intraspecific variation in the response of rice (Oryza sativa L.) to increased CO₂ and temperature: growth and yield response of 17 cultivars. J. Exp. Bot., 47(9):1353-1359.