Plant Molecular Biology Reporter

, Volume 36, Issue 5–6, pp 695–709 | Cite as

Identification of QTLs for Salt Tolerance Traits and Prebreeding Lines with Enhanced Salt Tolerance in an Introgression Line Population of Rice

  • Venkata Ramana Rao Puram
  • John Ontoy
  • Prasanta Kumar SubudhiEmail author
Original Paper


Salinity is a major abiotic stress that limits rice productivity worldwide. Due to involvement of multiple genes and multiple mechanisms in salinity tolerance, development of tolerant varieties has been challenging. The present study used 112 introgression lines (ILs) of a salt-tolerant donor ‘Nona Bokra’ in the genetic background of a US cultivar ‘Cheniere’ to elucidate the genetic basis of seedling stage salinity tolerance and develop salt-tolerant prebreeding lines for use in breeding program. The ILs were evaluated under salt stress and control conditions and were genotyped using 116 microsatellite markers. A total of 32 QTLs were identified for eight morpho-physiological traits whereas 18 QTLs were detected for salt tolerance indices. Comparison of the QTL results with an earlier study involving the same donor indicated that detection of few common QTLs could be due to genetic background effects. Both studies suggested shoot Na+/K+ homeostasis, Na+ exclusion, and compartmentation as possible salt tolerance mechanisms in ‘Nona Bokra’. Candidate gene identification and gene ontology analysis revealed that the genes involved in ion transport, ion homeostasis, and signaling may have important role in improving salinity tolerance. In addition to their utility in isolation of salt-tolerant determinants, the prebreeding lines with enhanced salt tolerance will accelerate development of salt-tolerant varieties by accumulating favorable alleles through marker-assisted selection.


Candidate genes Oryza sativa Quantitative trait loci Salinity Seedling stage Simple sequence repeat marker 



We thank Dr. Brenda Tubana for allowing digestion of tissue samples in her laboratory for Na+ and K+ estimations. This manuscript is approved for publication by the Director of Louisiana Agricultural Experiment Station, USA as manuscript number 2018-306-32282. Raman postdoctoral fellowship awarded to Venkata Ramana Rao Puram by the University Grants Commission of the Government of India is gratefully acknowledged.

Funding information

This research was supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture (Grant No. 2013-67013-21238) and the Louisiana Rice Research Board.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

11105_2018_1110_MOESM1_ESM.pdf (1.9 mb)
ESM 1 (PDF 1990 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.School of Plant, Environmental, and Soil SciencesLouisiana State University Agricultural CenterBaton RougeUSA
  2. 2.Andhra Pradesh Rice Research Institute and Regional Agricultural Research StationAcharya N.G. Ranga Agricultural UniversityEluruIndia

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