Microsatellite based linkage disequilibrium analyses reveal Saltol haplotype fragmentation and identify novel QTLs for seedling stage salinity tolerance in rice (Oryza sativa L.)

  • N. Naresh Babu
  • K. K. Vinod
  • S. L. Krishnamurthy
  • S. Gopala Krishnan
  • Ashutosh Yadav
  • P. K. Bhowmick
  • M. Nagarajan
  • N. K. Singh
  • K. V. Prabhu
  • A. K. Singh
Original Article


A set of 84 diverse rice genotypes were assessed for seedling stage salt tolerance and their genetic diversity using 41 polymorphic SSR markers comprising of 19 Saltol QTL linked and 22 random markers. Phenotypic screening under hydroponics identified three indica landraces (Badami, Shah Pasand and Pechi Badam), two Oryza rufipogon accessions (NKSWR2 and NKSWR17) and one each of Basmati rice (Seond Basmati) and japonica cultivars (Tompha Khau) as salt tolerant, having similar tolerance as of Pokkali and FL478. Among the salt tolerant genotypes, biomass showed positive correlation with shoot fresh weight and negative association with root and shoot Na+ content. The results indicated repression of Na+ loading within the tolerant plants. Linkage disequilibrium (LD) of the Saltol linked markers was weak, suggestive of high fragmentation of Pokkali haplotype, a result of evolutionary active recombination events. Poor haplotype structure of the Saltol region, may reduce its usefulness in marker assisted breeding programmes, if the target foreground markers chosen are wide apart. LD mapping identified eight robust marker-trait associations (QTLs), of which RM10927 was found linked to root and shoot Na+ content and RM10871 with shoot Na+/K+ ratio. RM271 on chromosome 10, an extra Saltol marker, was found associated to root Na+/K+ ratio. This marker showed a distinct allele among O. rufipogon accessions. There were also other novel loci detected on chromosomes 2, 5 and 10 influencing salt tolerance in the tested germplasm. Although Saltol remained as the key locus, the role of other genomic regions cannot be neglected in tailoring seedling stage salt tolerance in rice.


Rice Salt tolerance Saltol haplotype Association mapping QTLs 





Linkage disequilibrium


Quantitative trait locus


Mean salt tolerance score


Polymorphism information content


Principal component analysis


Mixed linear model

Supplementary material

13562_2016_393_MOESM1_ESM.pdf (709 kb)
Supplementary material 1 (PDF 709 kb)
13562_2016_393_MOESM2_ESM.pdf (747 kb)
Supplementary material 2 (PDF 747 kb)


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Copyright information

© Society for Plant Biochemistry and Biotechnology 2016

Authors and Affiliations

  • N. Naresh Babu
    • 1
  • K. K. Vinod
    • 2
  • S. L. Krishnamurthy
    • 3
  • S. Gopala Krishnan
    • 1
  • Ashutosh Yadav
    • 1
  • P. K. Bhowmick
    • 1
  • M. Nagarajan
    • 2
  • N. K. Singh
    • 4
  • K. V. Prabhu
    • 1
  • A. K. Singh
    • 1
  1. 1.Division of GeneticsICAR-Indian Agricultural Research InstituteNew DelhiIndia
  2. 2.Rice Breeding and Genetics Research CentreICAR-Indian Agricultural Research InstituteAduthuraiIndia
  3. 3.ICAR-Central Soil Salinity Research InstituteKarnalIndia
  4. 4.ICAR-National Research Centre on Plant BiotechnologyNew DelhiIndia

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