Markers for Saltol, a major salt-tolerance QTL in rice

Product Description/Background

Salt stress is a major constraint across many rice-producing areas because of the high sensitivity of modern rice varieties to salinity. This forces farmers to grow their traditional landraces with low yield and poor grain quality. In Bangladesh, salt stress affects more than 1 million hectares across the southern parts of the country, and poses a serious problem for resource-poor farmers who depend on rice production for their livelihoods, where other crops can barely grow during the monsoon season. Previously, a major salinity-tolerance QTL on rice chromosome 1, named Saltol, was mapped at IRRI using a recombinant inbred line (RIL) population between tolerant Pokkali and sensitive IR29, explaining 43% of the variation for seedling shoot Na+ uptake (Bonilla et al 2002). Numerous physiological traits are known to be associated with salinity tolerance in rice and Saltol seems to confer tolerance through restricting sodium uptake.  The SSR markers indicated in Table 1 below were derived from a study  (Thomson et al [2010]) that characterized Pokkali-derived quantitative trait loci (QTLs) for seedling stage salinity tolerance in preparation for use in marker-assisted breeding.  An analysis of 100 SSR markers on 140 IR29/Pokkali recombinant inbred lines (RILs) confirmed the location of the Saltol QTL on chromosome 1 and identified additional QTLs associated with tolerance.  However, the occurrence of Pokkali alleles associated with the Saltol region and and their undetermined relationship with it necessitates a cautious breeding approach to negate these influences as much as possible.  After testing markers for robustness and polymorphism across the Saltol region in several donors and potential parents, the best markers within and flanking the Saltol region were determined and, as well, markers that can be used for negative selective above and below the region.  These are shown and so designated in Table 1.

In addition to the original SSR markers described above, GCP  in-silico mapping studies have revealed closely associated or co-localized SNP markers and these are shown in Table 2.  These markers have not been validated but are assumed to be diagnostic for the QTL given the proximity of these to the originals particularly those that are co-locatized.  SNPs have been converted to the KASPar platform of LGC Genomics (KBiosciences).

Access to Markers

Markers cited above are freely available for use.  This information can be taken to any qualified laboratory for generation of markers and subsequent genotyping of germplasm materials.  In addition, the Integrated Breeding Platform Genotyping Service provides a set of options for users to access different marker service laboratories in the public and private sector with clear contractual conditions. The service identifies laboratories able to provide services for genetic diversity analysis and plant breeding  applications and negotiates favourable terms for IBP clients. Laboratories are selected on the basis of competitive cost, fit with quality control requirements and expeditious delivery. Click here for a list and description of laboratories and services. Click on  Service request for details of how to access genotyping services through the platform. For additional information and help on using the IBP Marker Service, contact Chunlin He.

If you need assistance in the use of these markers refer to  IBP Breeding Services or for more information contact Mark Sawkins or Chunlin He.

Supporting Germplasm Resources

If it is determined that the local collection contains little or insufficient tolerance to elevated salinity conditions, introgression of the Saltol allele(s) from outsourced germplasm may be necessary.  Salt tolerant germplasm lines in good agronomic backgrounds continue to be developed but the following highly tolerant accessions containing the Saltol QTL may be  recommended at this time:


IRGC 108921

IRGC 26896

Among these, FL478 has been promoted as a recommeded breeding line by IRRI.  All are available and accessible  from IRRI Germplasm Resources.  To request germplasm from IRRI send a request either by:

1)  letter addressed to Dr. Nigel Ruaraidh Sackville Hamilton, Head, Genetic Resources Center, IRRI, DAPO Box 7777 Metro Manila, Philippines; or

2) electronic mail to Dr. N. Ruaraidh Sackville Hamilton ( or

3) access germplasm information directly thru the System-wide Information Network for Genetic Resources (SINGER) website (

To obtain recommendations for additional germplasm contact Dr. Abdelbagi Ismail, IRRI at

Supporting Resources

Thomson MJ, de Ocampo M, Egdane J, Akhlasur Rahman M, Godwin Sajise A, Adorada DL, Tumimbang-Raiz E, Blumwald E, Seraj ZI, Singh RK, Gregorio GB and Ismail AM (2010). Characterizing the Saltol Quantitative Trait Locus for Salinity Tolerance in Rice. Rice 3:148–160 (DOI 10.1007/s12284-010-9053-8)

Alam R, Sazzadur Rahman M, Seraj ZI, Thomson MJ, Ismail AM, Tumimbang-Raiz E and Gregorio GB (2011). Investigation of seedling-stage salinity tolerance QTLs using backcross lines derived from Oryza sativa L. Pokkali. Plant Breeding 130(4):430–437 (DOI: 10.1111/j.1439-0523.2010.01837.x). (G4008.16 – SP3)

Ismail AM, Heuer S, Thomson MJ, Wissuwa M. 2007. Genetic and genomic approaches to develop rice germplasm for problem soils. Plant Mol. Biol. 65:547-570.

Bonilla P, Dvorak J, Mackill D, 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.

Final Technical Report for GCP Project G4010.04  Enhancing capacity for use of advance genotyping for fine-mapping and pyramiding of major salt tolerant QTLs through MABC for the development of durable saline tolerant rice varieties. - See attachment below.

Final Technical Report for  G4008.16  Speeding the Development of Salt-Tolerant Rice Varieties through Marker-Assisted Selection and Their Dissemination in Salt-Affected Areas of Bangladesh available under Other Resources below which preceded G4010.04 and provides valuable marker development information. – See attachment below.

Datasets for G4008.16:

Supplementary Resources

Alpuerto VEB, Norton GW , Alwang J and Ismail AM (2009). Economic Impact Analysis of Marker-Assisted Breeding for Tolerance to Salinity and Phosphorous Deficiency in Rice. Review of Agricultural Economics 31 (4):779–792 (DOI: 10.1111/j.1467-9353.2009.01466.x).  Abstract

Chapter 20  entitled “Marker Assisted Breeding” from: A. Pareek, S.K. Sopory, H.J. Bohnert and Govindjee (eds.), Abiotic Stress Adaptation in Plants: Physiological, Molecular and Genomic Foundation,pp.451–469. DOI 10.1007/978-90-481-3112-9_20, © Springer Science + Business Media B.V. 2010.



Markers were developed and validated in part through GCP Projects :

G4008.16  Speeding the Development of Salt-Tolerant Rice Varieties through Marker-Assisted Selection and Their Dissemination in Salt-Affected Areas of Bangladesh - See attachment below


G4010.04  Enhancing capacity for use of advance genotyping for fine-mapping and pyramiding of major salt tolerant QTLs through MABC for the development of durable saline tolerant rice varieties. See Attachment below.  

In both projects, the Principal Investigator was  Abdelbagi Ismail, IRRI, Los Baños, Philippines (

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