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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

Abstract

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.

Keywords

Genome Oryza sativa L. Salinity Transcriptome 

Notes

Acknowledgements

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).

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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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