Functional & Integrative Genomics

, Volume 17, Issue 1, pp 69–83 | Cite as

Transcription dynamics of Saltol QTL localized genes encoding transcription factors, reveals their differential regulation in contrasting genotypes of rice

  • Kamlesh K. Nutan
  • Hemant R. Kushwaha
  • Sneh L. Singla-Pareek
  • Ashwani PareekEmail author
Original Article


Salinity is one of the major environmental factors affecting the growth and yield of rice crop. Salinity stress response is a multigenic trait and numerous approaches have been used to dissect out the key determinants of complex salt tolerance trait and their regulation in plant. In the current study, we have investigated expression dynamics of the genes encoding transcription factors (SalTFs) localized within a major salinity tolerance related QTL—‘Saltol’ in the contrasting cultivars of rice. SalTFs were found to be differentially regulated between the contrasting genotypes of rice, with higher constitutive expression in the salt tolerant landrace, Pokkali than the cultivar IR64. Moreover, SalTFs were found to exhibit inducibility in the salt sensitive cultivar at late duration (after 24 h) of salinity stress. Further, the transcript abundance analysis of these SalTFs at various developmental stages of rice revealed that low expressing genes may be involved in developmental responses, while high expressing genes can be linked with the salt stress response. Grouping of these genes was well supported by in silico protein–protein interaction studies and distribution of single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in the promoter and genic regions of these genes. Taken together, we propose that out of 14 SalTFs, eight members are strongly correlated with the salinity stress tolerance in rice and six are involved in plant growth and development.


Contrasting genotypes Gene expression QTL Rice Salinity stress Saltol SalTFs 



This work was financially supported by the Department of Science and Technology (Indo-Sri Lanka collaborative project). KKN thanks the Department of Biotechnology, India, for providing DBT-JRF fellowship during his PhD programme. HRK acknowledges the financial assistance received as DST-INSPIRE Faculty award.

Supplementary material

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Table S2 (DOCX 23 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Kamlesh K. Nutan
    • 1
  • Hemant R. Kushwaha
    • 2
  • Sneh L. Singla-Pareek
    • 3
  • Ashwani Pareek
    • 1
    Email author
  1. 1.Stress Physiology and Molecular Biology Laboratory, School of Life SciencesJawaharlal Nehru UniversityNew DelhiIndia
  2. 2.Synthetic Biology and BiofuelInternational Center for Genetic Engineering and BiotechnologyNew DelhiIndia
  3. 3.Plant Stress BiologyInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia

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