Functional & Integrative Genomics

, Volume 13, Issue 3, pp 351–365 | Cite as

A suite of new genes defining salinity stress tolerance in seedlings of contrasting rice genotypes

  • Neelam Soda
  • Hemant R. Kushwaha
  • Praveen Soni
  • Sneh L. Singla-Pareek
  • Ashwani PareekEmail author
Original Paper


Salinity is one of the major constraints adversely influencing crop productivity. Saltol QTL is a major QTL associated with Na+-K+ ratio and seedling stage salinity tolerance in rice. With an aim to understand the contribution of individual genes localized within saltol towards salinity tolerance, we analysed the transcript abundance of a set of these genes in seedlings of contrasting genotypes of rice. We hypothesize that this approach may be helpful in identifying new ‘candidate genes’ for improving salinity tolerance in crops. For this purpose, seedlings of Oryza sativa cv. IR64 (sensitive) and the landrace Pokkali (tolerant) were subjected to short/long durations of salinity. qRT-PCR analysis clearly exhibited differential regulation of genes encoding signaling related protein (SRPs), where higher transcript abundance for most of them was observed in Pokkali than IR64 under non-stress conditions, thereby indicating towards well preparedness of the former to handle stress, in anticipation. Genes encoding proteins of unknown function (PUFs), though, constitute a considerable portion of plant genome, have so far been neglected in most studies. Time course analysis of these genes showed a continuous increase in their abundance in Pokkali, while in IR64, their abundance increased till 24 h followed by a clear decrease, thereby justifying their nomenclature as ‘salinity induced factors’ (SIFs). This is the first report showing possible involvement of SIFs localized within salinity related QTL towards salinity stress response. Based on the phenotypes of insertional mutants, it is proposed that these SIFs may have a putative function in vegetative growth (SIFVG), fertility (SIFF), viability (SIFV) or early flowering (SIFEF).


Salinity induced factors (SIFs) QTL qRT-PCR Saltol Salinity Signaling related proteins (SRP) 



Authors would like to thank financial and Infrastructure support received from JNU through PURSE & UGC-RNW and ICGEB. Department of Science and Technology (DST) and Department of Biotechnology (DBT), Govt. of India is also acknowledged for financial support. N. S. and P.S. would like to thank University Grants Commission and Council of Scientific and Industrial Research, New Delhi, India respectively, for the award of their Research Fellowships.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Neelam Soda
    • 1
  • Hemant R. Kushwaha
    • 1
    • 3
  • Praveen Soni
    • 1
  • Sneh L. Singla-Pareek
    • 2
  • 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.Synthetic Biology and BiofuelInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia

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