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Journal of Zhejiang University SCIENCE B 2009 Vol.10 No.2 P.133-141


ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought, flood, or salinity

Author(s):  Ch Surendhar REDDY, A. Prasad BABU, B.P. Mallikarjuna SWAMY, K. KALADHAR, N. SARLA

Affiliation(s):  Biotechnology Laboratory, Crop Improvement Section, Directorate of Rice Research, Rajendranagar, Hyderabad 500030, India

Corresponding email(s):   sarla_neelamraju@yahoo.com, nsarla@drricar.org

Key Words:  Drought, Submergence, Salinity, Inter-simple sequence repeat-polymerase chain reaction (ISSR-PCR), (GA)8YG, Nagina22 (N22), FR13A, Pokkali

Ch Surendhar REDDY, A. Prasad BABU, B.P. Mallikarjuna SWAMY, K. KALADHAR, N. SARLA. ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought, flood, or salinity[J]. Journal of Zhejiang University Science B, 2009, 10(2): 133-141.

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author="Ch Surendhar REDDY, A. Prasad BABU, B.P. Mallikarjuna SWAMY, K. KALADHAR, N. SARLA",
journal="Journal of Zhejiang University Science B",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought, flood, or salinity
%A Ch Surendhar REDDY
%A A. Prasad BABU
%A B.P. Mallikarjuna SWAMY
%J Journal of Zhejiang University SCIENCE B
%V 10
%N 2
%P 133-141
%@ 1673-1581
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%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B0820183

T1 - ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought, flood, or salinity
A1 - Ch Surendhar REDDY
A1 - A. Prasad BABU
A1 - B.P. Mallikarjuna SWAMY
J0 - Journal of Zhejiang University Science B
VL - 10
IS - 2
SP - 133
EP - 141
%@ 1673-1581
Y1 - 2009
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B0820183

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.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


[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.

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