Skip to main content
SpringerLink
Log in

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

  • Original Paper
  • Published:
Plant Molecular Biology Reporter Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Ahmadi J, Fotokian MH (2011) Identification and mapping of quantitative trait loci associated with salinity tolerance in rice (Oryza sativa) using SSR markers. Iran J Biotechnol 9:21–30

    CAS  Google Scholar 

  • Akbar M, Khush GS, Hillerislambers D (1986) Genetics of salt tolerance in rice. In: Rice genetics I. International Rice Research Institute, Philippines. pp 399–409

  • Alam R, Rahman MS, Seraj ZI, Thomson MJ, Ismail AM, Tumimbang-Raiz E, Gregorio G (2011) Investigation of seedling-stage salinity tolerance QTLs using backcross lines derived from Oryza sativa L. Pokkali. Plant Breed 130:430–437

    Article  CAS  Google Scholar 

  • Ammar MHW, Pandit A, Singh RK, Sameena S, Chauhan MS, Singh AK, Sharma PC, Gaikwad K, Sharma TR, Mohapatra T, Singh NK (2009) Mapping of QTLs controlling Na+, K+, Cl− ion concentrations in salt tolerant indica rice variety CSR27. J Plant Biochem Biotechnol 18:139–150

    Article  CAS  Google Scholar 

  • Ashraf M (2004) Some important physiological selection criteria for salt tolerance in plants. Flora 199:361–376

    Article  Google Scholar 

  • Bonilla P, Dvorak J, Mackill DJ, Deal K, Gregorio G (2002) RLFP and SSLP mapping of salinity tolerance genes in chromosome 1 of rice (Oryza sativa L.) using recombinant inbred lines. Philipp Agric Sci 85:68–76

    Google Scholar 

  • Chen DH, Ronald PC (1999) A rapid DNA minipreparation method suitable for AFLP and other applications. Plant Mol Biol Rep 17:53–57

    Article  CAS  Google Scholar 

  • Cheng L, Wang Y, Meng L, Hu X, Cui Y, Sun Y, Zhu L, Ali J, Xu J, Li Z (2012) Identification of salt-tolerant QTLs with strong genetic background effect using two sets of reciprocal introgression lines in rice. Genome 55:45–55

    Article  CAS  Google Scholar 

  • Chinnusamy V, Jagendorf A, Zhu JK (2005) Understanding and improving salt tolerance in plants. Crop Sci 45:437–448

    Article  CAS  Google Scholar 

  • Claes B, Dekejser R, Villarrod R, Van der Bulcke M, Bannu G, Van Montagu M, Caplan A (1990) Characterization of a rice gene showing organ-specific expression in response to salt stress and drought. Plant Cell 2:19–27

    Article  CAS  Google Scholar 

  • De Leon TB, Linscombe S, Gregorio G, Subudhi PK (2015) Genetic variation in southern rice genotypes for seedling salinity tolerance. Front Plant Sci 6:374

    PubMed  PubMed Central  Google Scholar 

  • De Leon TB, Linscombe S, Subudhi PK (2016) Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace Pokkali. PLoS One 12:e0175361

    Article  Google Scholar 

  • De Leon TB, Linscombe S, Subudhi PK (2017) Molecular dissection of seedling salinity tolerance in rice (Oryza sativa L.) using a high-density GBS-based SNP linkage map. Rice 9:52

    Article  Google Scholar 

  • Flowers T, Flowers S (2005) Why does salinity pose such a difficult problem for plant breeders? Agric Water Manag 78:15–24

    Article  Google Scholar 

  • Gimhani DR, Gregorio GB, Kottearachchi NS (2016) SNP-based discovery of salinity-tolerant QTLs in a bi-parental population of rice (Oryza sativa). Mol Gen Genomics 291:2081–2099

    Article  CAS  Google Scholar 

  • Gregorio GB, Senadhira D (1993) Genetic analysis of salinity tolerance in rice (Oryza sativa L). Theor Appl Genet 86:333–338

    Article  CAS  Google Scholar 

  • Gregorio GB, Senadhira D, Mendoza RD, Manigbas NL, Roxas JP, Cuerta CQ (2002) Progress in breeding for salinity tolerance and associated abiotic stresses in rice. Field Crop Res 76:91–101

    Article  Google Scholar 

  • Hossain MR, Bassel GC, Pritchard J, Sharma GP, Ford-Lloyd BV (2016) Trait specific expression profiling of salt stress responsive genes in diverse rice genotypes as determined by modified significance analysis of microarrays. Front Plant Sci 7:00567

    Google Scholar 

  • Islam MR, Salam MA, Hassan L, Collard BCY, Singh RK, Gregorio GB (2011) QTL mapping for salinity tolerance at seedling stage in rice. Emir J Food Agric 23:137–146

    Article  Google Scholar 

  • Iwata N, Fuzino K (2010) Genetic effects of major QTLs controlling low-temperature germinability in different genetic backgrounds in rice (Oryza sativa L.). Genome 10:763–768

    Article  Google Scholar 

  • Jones JB, Case VW (1990) Sampling, handling, and analyzing plant tissue samples. In: Westerman RL (ed) Soil testing and plant analysis. 3rd edn, Soil Science Society of America, book series no. 3, Madison, Wisconsin, pp 389–427

  • Khan SK, Saeed M, Iqbal J (2015) Identification of quantitative trait loci for Na+, K+, and Ca++ accumulation traits in rice grown under saline conditions using F2 mapping population. Braz J Bot 38:555–565

    Article  Google Scholar 

  • Koyama ML, Levesley A, Koebner RMD, Flowers TJ, Yeo AR (2001) Quantitative trait loci for component physiological traits determining salt tolerance in rice. Plant Physiol 125:406–422

    Article  CAS  Google Scholar 

  • Lang NT, Yanagihara S, Buu BC (2001a) A microsatellite marker for a gene conferring salt tolerance on rice at the vegetative and reproductive stages. SABRAO J Breed Genet 33:1–10

    Google Scholar 

  • Lang NT, Yanagihara S, Buu BC (2001b) QTL analysis of salt tolerance in rice (Oryza sativa L.). SABRAO J Breed Genet 33:11–20

    Google Scholar 

  • Lee SY, Ahn JH, Cha YS, Yun DW, Lee MC, Ko JC (2006) Mapping of quantitative trait loci for salt tolerance at the seedling stage in rice. Mol Cell 21:192–196

    CAS  Google Scholar 

  • 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 108:253–260

    Article  CAS  Google Scholar 

  • Linscombe SD, Sha X, Bearb K, Grith DE, White LM, Dunand RT (2006) Registration of ‘Cheniere’ rice. Crop Sci 46:1814

    Article  Google Scholar 

  • Lorieux M (2005) CSSL finder: a free program for managing introgression lines. http://mapdisto.free.fr/CSSLFinder/. Accessed13 April 2016

  • Negrão S, Courtois B, Ahmadi N, Abreu I, Saibo N, Oliveira M (2011) Recent updates on salinity stress in rice: from physiological to molecular responses. Crit Rev Plant Sci 30:329–377

    Article  Google Scholar 

  • Netondo GW, Onyango JC, Beck E (2004) Sorghum and salinity: II. Gas exchange and chlorophyll fluorescence of sorghum under salt stress. Crop Sci 44:806–811

    Article  Google Scholar 

  • Niones JM (2004) Fine mapping of the salinity tolerance gene on chromosome 1 of rice (Oryza sativa L.) using near- isogenic lines. MS Dissertation. University of the Philippines, Los Baños, Philippines

  • Puram VRR, Ontoy J, Linscombe S, Subudhi PK (2017) Genetic dissection of seedling stage salinity tolerance in rice using introgression lines of a salt tolerant land race Nona Bokra. J Hered 108:658–670

    Article  Google Scholar 

  • Qiu X, Yuan Z, Liu H, Xiang X, Yang L, He W, Du B, Ye G, Xu J, Xing D (2015) Identification of salt tolerance-improving quantitative trait loci alleles from a salt-susceptible rice breeding lines by introgression breeding. Plant Breed 134:653–660

    Article  CAS  Google Scholar 

  • Rajendran K, Tester M, Roy SJ (2009) Quantifying the three main components of salinity tolerance in cereals. Plant Cell Environ 32:237–249

    Article  CAS  Google Scholar 

  • Ren ZH, Gao JP, Li LG, Cai XL, Huang DY, Chao MZ, Zhu ZY, Wang S, Luan H, Lin X (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141–1146

    Article  CAS  Google Scholar 

  • Sabouri H, Sabouri A (2008) New evidence of QTLs attributed to salinity tolerance in rice. Afr J Biotechnol 7:4376–4383

    CAS  Google Scholar 

  • SAS Institute Inc (2012) SAS® 9.4 system options: reference, 2nd edn. SAS Institute Inc., Cary

    Google Scholar 

  • Thomson MJ, de Ocampo M, Egdane J, Rahman MA, Sajise AG, Adorada DL, Tumimbang-Raiz E, Blumwald E, Seraj ZI, Singh RK, Gregorio GB, Ismail AM (2010) Characterizing the Saltol quantitative trait locus for salinity tolerance in rice. Rice 3:148–160

    Article  Google Scholar 

  • Wang J, Li H, Zhang L, Meng L (2016a) Users’ manual of QTL IciMapping. China: The Quantitative Genetics Group, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Mexico: Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT)

  • Wang M, Lu X, Xu G, Yin X, Cui Y, Huang L, Rocha PSCF, Xia X (2016b) OsSGL, a novel pleiotropic stress related gene enhances grain length and yield in rice. Sci Rep 6:38157

    Article  CAS  Google Scholar 

  • Yue B, Xue W, Xiong L, Yu X, Luo L, Cui K, Jin D, Xing Y, Zhang Q (2006) Genetic basis of drought resistance at reproductive stage in rice: separation of drought tolerance from drought avoidance. Genetics 105:045602

    Google Scholar 

  • Zhang GY, Guo Y, Chen SL, Chen SY (1995) RFLP tagging of salt tolerance gene in rice. Plant Sci 110:227–234

    Article  CAS  Google Scholar 

  • Zhang J, Ou XX, Hu H, Du B, Lv WK, Yang LW, Xing DY, Xu JL, Qiu XJ, Zheng TQ, Xu JY, Li ZX, Zhang YB, Wang XY (2018) Identification of QTLs for yield-related traits using two sets of introgression lines with a common donor parent in rice. Int J Agric Biol 20:15–24

    Google Scholar 

  • Zheng H, Zhao H, Liu H, Wang J, Zou D (2015) QTL analysis of Na+ and K+ concentrations in shoots and roots under NaCl stress based on linkage and association analysis in japonica rice. Euphytica 201:109–121

    Article  CAS  Google Scholar 

Download references

Acknowledgments

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

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.

Author information

Author notes

  1. Venkata Ramana Rao Puram

    Present address: Andhra Pradesh Rice Research Institute and Regional Agricultural Research Station, Acharya N.G. Ranga Agricultural University, Maruteru, West Godavari District, Eluru, AP, 534122, India

Authors and Affiliations

  1. School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA

    Venkata Ramana Rao Puram, John Ontoy & Prasanta Kumar Subudhi

Authors
  1. Venkata Ramana Rao Puram
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. John Ontoy
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Prasanta Kumar Subudhi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Prasanta Kumar Subudhi.

Ethics declarations

Conflict of Interest

The authors declare that they have no conflict of interest.

Electronic Supplementary Material

ESM 1

(PDF 1990 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Puram, V.R.R., Ontoy, J. & Subudhi, P.K. Identification of QTLs for Salt Tolerance Traits and Prebreeding Lines with Enhanced Salt Tolerance in an Introgression Line Population of Rice. Plant Mol Biol Rep 36, 695–709 (2018). https://doi.org/10.1007/s11105-018-1110-2

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11105-018-1110-2

Keywords

Search

Navigation