Transcriptome map for seedling stage specific salinity stress response indicates a specific set of genes as candidate for saline tolerance in Oryza sativa L.

  • Sumita Kumari
  • Vaishali Panjabi nee Sabharwal
  • Hemant R. Kushwaha
  • Sudhir K. Sopory
  • Sneh L. Singla-PareekEmail author
  • Ashwani PareekEmail author
Original Paper


Oryza sativa L. cv IR64 is a widely cultivated, salt-sensitive indica rice, while Pokkali is a well-known, naturally salt-tolerant relative. To understand the molecular basis of differences in their salinity tolerance, three subtractive cDNA libraries were constructed. A total of 1,194 salinity-regulated cDNAs are reported here that may serve as repositories for future individual gene-based functional genomics studies. Gene expression data using macroarrays and Northern blots gives support to our hypothesis that salinity tolerance of Pokkali may be due to constitutive overexpression of many genes that function in salinity tolerance and are stress inducible in IR64. Analysis of genome architecture revealed the presence of these genes on all the chromosomes with several distinct clusters. Notably, a few mapped on one of the major quantitative trait loci – Saltol – on chromosome 1 and were found to be differentially regulated in the two contrasting genotypes. The present study also defines a set of known abiotic stress inducible genes, including CaMBP, GST, LEA, V-ATPase, OSAP1 zinc finger protein, and transcription factor HBP1B, that were expressed at high levels in Pokkali even in the absence of stress. These proposed genes may prove useful as “candidates” in improving salinity tolerance in crop plants using transgenic approach.


Genome Oryza sativa L. Salinity Transcriptome 



This work was supported by research grants received from the International Atomic Energy Agency (Vienna), International Foundation for Science (Sweden), Department of Science and Technology, Department of Biotechnology, Government of India, and fellowship (S. K.) from the Council of Scientific and Industrial Research, Government of India.

Supplementary material

10142_2008_88_MOESM1_ESM.pdf (289 kb)
Table S1 Details of the total 1194 unique ESTs from the three subtractive libraries (PDF 288 KB).
10142_2008_88_MOESM2_ESM.pdf (73 kb)
Table S2 Details of the ESTs from two subtractive libraries selected for reverse northern analysis (PDF 73.3 KB).
10142_2008_88_MOESM3_ESM.pdf (26 kb)
Table S3 Details of set of selected ESTs used for Northern analysis (PDF 28.0 KB).
10142_2008_88_MOESM4_ESM.pdf (127 kb)
Supplementary Figure 1 (PDF 126 KB).
10142_2008_88_MOESM5_ESM.pdf (190 kb)
Figure S2 Graphical representation (with Laserdensitometry values) generated from northernhybridization of selected genes in early and late phaseof salinity stress in the sensitive cultivar IR64 (in blue color) and the tolerant cultivar Pokkali (in red color). LecRK:Lectinreceptor like kinase protein; STK:Serinethreonine protein kinase receptor precursor; MAPK:Mitogen-activated protein kinase homolog 6; CIPK:CIPK like protein 1; VDAC1:Voltage dependent anion-selective channel ; ATP synthase:VacuolarATP synthase 16 kdaproteolipid subunit; VDAC2 :Voltage dependent anion-selective channel; HBP1B:Transcription factor HBP1B; Zinc finger:Multiplestress responsive zinc finger protein OSAP1; Myb:Myb related protein HV33; NPP:Nicotinate-nucleotide pyrophosphorylase; CaM:SF16 protein with calmodulin binding motif; Clp protease:ATP-dependent Clp protease proteolytic subunit; Ubiquitin:Ubiquitin-like protein 5; cyclophilin:Peptidyl-prolylcis-trans isomeraseprotein; LEA:Lateembryogenesis abundant protein; GSTF2:Glutathione-s-transferaseII; RuBP:Ribulosebisphosphatecarboxylasesmall chain; RHN1:Ras related protein RHN1; His D:Histidinedecarboxylase; DD:Dihydrolipoyldehydrogenase; RP isomerase:Ribose-5-phosphate isomerase; UCE:Ubiquitin-conjugating enzyme family protein; Hypo1:Hypothetical protein 1; Reteroposon protein:Retrotransposonprotein; CBS:CBS domain protein; HCS:Hypotheticalprotein expressed under carbonate stress; SDCP:Swirmdomain containing expressed protein (PDF 190 KB).


  1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedCrossRefGoogle Scholar
  2. Babu RC, Zhang J, Blumc A, Hod TDH, Wu R, Nguyen HT (2004) HVA1, a LEA gene from barley confers dehydration tolerance in transgenic rice (Oryza sativa L.) via cell membrane protection. Plant Sci 166:855–862CrossRefGoogle Scholar
  3. Bajji M, Kinet JM, Lutts S (2004) The use of the electrolyte leakage method for assessing cell membrane stability as a water stress tolerance test in durum wheat. J Plant Growth Regul 36:61–70Google Scholar
  4. Bates LS, Waldren RP, Teare D (1973) Rapid determination of free proline for water stress studies. Plant Soil 39:205–297CrossRefGoogle Scholar
  5. Bohnert HJ, Gong Q, Li P, Ma S (2006) Unravelling abiotic stress tolerance mechanisms—getting genomic going. Curr Opin Plant Biol 9:180–188PubMedCrossRefGoogle Scholar
  6. Bonilla P, Dvorak J, Mackill D, Deal K, Gregorio G (2002) RFLP and SSLP mapping of salinity tolerance genes in chromosome 1 of rice (Oryza sativa L.) using recombinant inbred lines. Philipp J Agric Sci 85:68–76Google Scholar
  7. Chao DY, Lou YH, Shi M, Lou D, Lin HX (2005) Salt-responsive genes in rice revealed by cDNA microarray analysis. Cell Res 15:796–810PubMedCrossRefGoogle Scholar
  8. Chen F, Li Q, Sun L, He Z (2006) The rice 14–3–3 gene family and its involvement in responses to biotic and abiotic stress. DNA Res 13:53–63PubMedCrossRefGoogle Scholar
  9. Chen A-P, Wang G-L, Qu Z-L, Lu C-X, Liu N, Wang F, Xia G-X (2007) Ectopic expression of ThCYP1, a stress-responsive cyclophilin gene from Thellungiella halophila, confers salt tolerance in fission yeast and tobacco cells. Plant Cell Rep 26:237–245PubMedCrossRefGoogle Scholar
  10. Chinnusamy V, Jagendorf A, Zhu JK (2005) Understanding and improving salt tolerance in plants. Crop Sci 45:437–448Google Scholar
  11. Czernic P, Visser B, Sun W, Savoure A, Deslandes L (1999) Characterization of an Arabidopsis thaliana receptor-like protein kinase gene activated by oxidative stress and pathogen attack. Plant J 18:321–327PubMedCrossRefGoogle Scholar
  12. Das-Chatterjee A, Goswami L, Maitra S, Dastidar KG, Ray S, Majumder AL (2006) Introgression of a novel salt-tolerant L-myo-inositol 1-phosphate synthase from Porteresia coarctata (Roxb.) Tateoka (PcINO1) confers salt tolerance to evolutionary diverse organisms. FEBS Lett 580:3980–3988PubMedCrossRefGoogle Scholar
  13. Desai MK, Mishra RN, Verma D, Nair S, Sopory SK, Reddy MK (2006) Structural and functional analysis of a salt stress inducible gene encoding voltage dependent anion channel (VDAC) from pearl millet (Pennisetum glaucum). Plant Physiol Biochem 44:483–493PubMedCrossRefGoogle Scholar
  14. Devos KM, Gale MD (2000) Genome relationships: the grass model in current research. Plant Cell 12:637–646PubMedCrossRefGoogle Scholar
  15. Du L, Chen Z (2000) Identification of genes encoding receptor-like kinases as possible targets of pathogen-and salicylic acid-induced WRKY DNA-binding proteins in Arabidopsis. Plant J 24:837–847PubMedCrossRefGoogle Scholar
  16. Fox TC, Guerinot ML (1998) Molecular biology of cation transport in plants. Annu Rev Plant Physiol Plant Mol Biol 49:669–696PubMedCrossRefGoogle Scholar
  17. Hayashi F, Ichino T, Osanai M, Wada K (2000) Oscillation and regulation of proline content by P5CS and ProDH gene expressions in the light/dark cycles in Arabidopsis thaliana L. Plant Cell Physiol 41:1096–1101PubMedCrossRefGoogle Scholar
  18. Huner NPA, Öquist G, Sarhan F (1998) Energy balance and acclimation to light and cold. Trends Plant Sci 3:224–230CrossRefGoogle Scholar
  19. Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert HJ (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13:889–905PubMedCrossRefGoogle Scholar
  20. Khush GS, Virk PS (2005) Selection criteria. In: Hardy B (ed) IR varieties and their impact. vol. 15. International Rice Research Institute, Los BonasGoogle Scholar
  21. Lin HX, Zhu MZ, Yano M, Gao JP, Liang ZW, Su WA, Hu XH, Ren ZH, Chao DY (2004) QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet 108:253–260PubMedCrossRefGoogle Scholar
  22. Lutts S, Kinet J-M, Bouhar, mont J (1995) Changes in plant responses to NaCl during development of rice (Oryza sativa L.) varieties differing in salinity resistance. J Exp Bot 46:1843–1852CrossRefGoogle Scholar
  23. Ma S, Bohnert HJ (2007) Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biol 8:R49PubMedCrossRefGoogle Scholar
  24. Mahalakshmi S, Christopher GS, Reddy TP, Rao KV, Reddy VD (2006) Isolation of a cDNA clone (PcSrp) encoding serine-rich-protein from Porteresia coarctata T. and its expression in yeast and finger millet (Eleusine coracana L.) affording salt tolerance. Planta 224:347–359PubMedCrossRefGoogle Scholar
  25. Mehta PA, Sivaprakash K, Parani M, Venkataraman G, Parida AK (2005) Generation and analysis of expressed sequence tags from the salt-tolerant mangrove species Avicennia marina (Forsk) Vierh. Theor Appl Genet 110:416–424PubMedCrossRefGoogle Scholar
  26. Mukhopadhyay A, Vij S, Tyagi AK (2004) Overexpression of a zinc-finger protein gene from rice confers tolerance to cold, dehydration, and salt stress in transgenic tobacco. Proc Natl Acad Sci U S A 101:6309–6314PubMedCrossRefGoogle Scholar
  27. Munns R (2005) Genes and salt tolerance: bringing them together. New Phytol 167:645–663PubMedCrossRefGoogle Scholar
  28. Nagaki K, Cheng Z, Ouyang S, Talbert PB, Kim M, Jones KM, Henikoff S, Buell CR, Jiang J (2004) Sequencing of a rice centromere uncovers active genes. Nat Genet 36:138–145PubMedCrossRefGoogle Scholar
  29. Ohtake Y, Takahashi T, Komeda Y (2000) Salicylic acid induces the expression of a number of receptor-like kinase genes in Arabidopsis thaliana. Plant Cell Physiol 41:1038–1044PubMedCrossRefGoogle Scholar
  30. Ozturk ZN, Talame V, Deyholos M, Michalowski CB, Galbraith DW, Gozukirmizi N, Tuberosa R, Bohnert HJ (2002) Monitoring large-scale changes in transcript abundance in drought and salt-stressed barley. Plant Mol Biol 48:551–573CrossRefGoogle Scholar
  31. Pareek A, Singla-Pareek SL, Sopory SK, Grover A (2007) Analysis of salt stress-related transcriptome fingerprints from diverse plant species. In: Varshney RK, Tuberosa R (eds) Genomics-assisted crop improvement. Springer, Dordrecht, pp 267–287CrossRefGoogle Scholar
  32. Ren Z-H, Gao J-P, Li L-G, Cai X-L, Huang W, Chao D-Y, Zhu M-Z, Wang Z-Y, Luan S, Lin H-X (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141–1146PubMedCrossRefGoogle Scholar
  33. Ruepp A, Zollner A, Dieter M, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munssterkotter M et al (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res 32:5539–5545PubMedCrossRefGoogle Scholar
  34. Sahi C, Agarwal M, Reddy M, Sopory S, Grover A (2003) Isolation and expression analysis of salt stress-associated ESTs from contrasting rice cultivars using a PCR-based subtraction method. Theor Appl Genet 106:620–628PubMedGoogle Scholar
  35. 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 6:263–284PubMedCrossRefGoogle Scholar
  36. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, ed 2. Cold Spring Harbour Laboratory Press, Cold Spring HarborGoogle Scholar
  37. Shiozaki N, Yamada M, Yoshiba Y (2005) Analysis of salt-stress-inducible ESTs isolated by PCR-subtraction in salt-tolerant rice. Theor Appl Genet 110:1177–1186PubMedCrossRefGoogle Scholar
  38. Sottosanto JB, Gelli A, Blumwald E (2004) DNA array analyses of Arabidopsis thaliana lacking a vacuolar Na+/H+ antiporter: impact of AtNHX1 on gene expression. Plant J 40:752–771PubMedCrossRefGoogle Scholar
  39. Sreenivasulu N, Sopory SK, Kavi Kishor PB (2007) Deciphering the regulatory mechanisms of abiotic stress tolerance in plants by genomic approaches. Gene 388:1–13PubMedCrossRefGoogle Scholar
  40. Taji T, Seki M, Satou M, Sakurai T, Kobayashi M, Ishiyama K, Narusaka Y, Narusaka M, Zhu JK, Shinozaki K (2004) Comparative genomics in salt tolerance between Arabidopsis and Arabidopsis-related halophyte salt cress using Arabidopsis microarray. Plant Physiol 135:1697–1709PubMedCrossRefGoogle Scholar
  41. Ueda A, Shi W, Nakamura T, Takabe T (2002) Analysis of salt-inducible genes in barley roots by differential display. J Plant Res 115:119–130PubMedCrossRefGoogle Scholar
  42. Ueda A, Kathiresan A, Bennet J, Takabe T (2006) Comparative transcriptome analyses of barley and rice under salt stress. Theor Appl Genet 112:1286–1294PubMedCrossRefGoogle Scholar
  43. Vij S, Tyagi AK (2007) Emerging trends in functional genomics of abiotic response in crop plants. Plant Biotech J 5:361–380CrossRefGoogle Scholar
  44. Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, Close TJ (2005) Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol 139:822–835PubMedCrossRefGoogle Scholar
  45. Walia H, Wilson C, Zeng L, Ismail AM, Condamine P, Close TJ (2007) Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage. Plant Mol Biol 63:609–623PubMedCrossRefGoogle Scholar
  46. Wong CE, Li Y, Labbe A, Guevara D, Nuin P, Whitty B, Diaz C, Golding GB, Gray GR, Weretilnyk EA et al (2006) Transcriptional profiling implicates novel interactions between abiotic stress and hormonal responses in Thellungiella, a close relative of Arabidopsis. Plant Physiol 140:1437–1450PubMedCrossRefGoogle Scholar
  47. Xie JH, Zapata-Arias FJ, Shen M, Afza R (2000) Salinity tolerant performance and genetic diversity of four rice varieties. Euphytica 116:105–110CrossRefGoogle Scholar
  48. Yamaguchi-Shinozaki K, Shinozaki K (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Ann Rev Plant Biol 57:781–803CrossRefGoogle Scholar
  49. Yoshiba Y, Kiyosue T, Katagiri T, Ueda H, Mizoguchi T, Yamaguchi-Shinozaki K, Wada K, Harada Y, Shinozaki K (1995) Correlation between the induction of a gene for D1-Pyroline-5′-carboxylate synthase and the accumulation of proline in Arabidopsis thaliana under osmotic stress. Plant J 7:751–760PubMedCrossRefGoogle Scholar
  50. Zhou J, Wang X, Jiao Y, Qin Y, Liu X, He K, Chen C, Ma L, Wang J, Xiong L et al (2007) Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Mol Biol 63:591–608PubMedCrossRefGoogle Scholar
  51. Zhu J-K (2003) Regulation of ion homeostasis under salt stress. Curr Opin Plant Biol 6:441–445PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Sumita Kumari
    • 1
  • Vaishali Panjabi nee Sabharwal
    • 1
  • Hemant R. Kushwaha
    • 3
  • Sudhir K. Sopory
    • 2
  • Sneh L. Singla-Pareek
    • 2
    Email author
  • Ashwani Pareek
    • 1
    Email author
  1. 1.Stress Physiology and Molecular Biology Laboratory, School of Life SciencesJawaharlal Nehru UniversityNew DelhiIndia
  2. 2.Plant Molecular BiologyInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
  3. 3.Centre for Computational Biology and BioinformaticsJawaharlal Nehru UniversityNew DelhiIndia

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