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Association of an allele-specific marker with dehydration stress tolerance in foxtail millet suggests SiDREB2 to be an important QTL


Dehydration-responsive element binding (DREB) genes assist in improving stress tolerance of plants by activating the expression of several stress-responsive genes. Therefore, development of functional markers for useful alleles utilizing DREB genes is crucial for crop improvement strategies. Earlier we reported a synonymous single nucleotide polymorphism (SNP) associated with dehydration tolerance at 558th bp (an A/G transition) in the SiDREB2 gene of foxtail millet (Setaria italica L.) and developed an allele-specific marker (ASM) for SiDREB2. In the present study, we validated this ASM using a set of 122 foxtail accessions, of which 45 were investigated in an earlier study. The QTL associated with SiDREB2 contributed to ~20 % of the total phenotypic variation (PV) for relative water content (RWC) and this signified the importance of this QTL for dehydration tolerance in foxtail millet.

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Fig. 1



Dehydration Responsive Element Binding


Single Nucleotide Polymorphism


Allele-Specific Marker


Single Marker Regression


Relative Water Content


Quantitative Trait Loci


Poly Ethylene Glycol


Lipid Peroxidation


  • Anderson JR, Asp T, Lu YC, Kloiber-Maitz M, Ouzonova M, Luebberstedt T (2009) Development and mapping of gene-tagged SNP markers in laccases of maize (Zea mays L.). Plant Breed 128:423–425

    Article  Google Scholar 

  • Barrs HD, Weatherley PE (1962) A re-examination of the relative turgidity technique for estimating water deficit in leaves. Aus J Biol Sci 15:413–428

    Google Scholar 

  • Garcés-Claver A, Fellman SM, Gil-Ortega R, Jahn M, Arnedo-Andrés MS (2007) Identification, validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in Capsicum spp. Theor Appl Genet 115:907–916

    PubMed  Article  Google Scholar 

  • Hussain SS, Kayani MA, Amjad M (2011) Transcription factors as tools to engineer enhanced drought tolerance in plants. Am Inst Chem Eng 27:297–306

    Google Scholar 

  • Kearsey MJ, Hyne V (1994) QTL analysis: a simple marker regression approach. Theor Appl Genet 89:698–702

    CAS  PubMed  Article  Google Scholar 

  • Lata C, Sahu PP, Prasad M (2010) Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress. Biochem Biophys Res Commun 393:720–727

    CAS  PubMed  Article  Google Scholar 

  • Lata C, Bhutty S, Bahadur RP, Majee M, Prasad M (2011) Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)]. J Exp Bot 62:3387–3401

    CAS  PubMed  Article  Google Scholar 

  • Lata C, Prasad M (2012) Validation of an allele-specific marker associated with dehydration stress tolerance in a core set of foxtail millet accessions. Plant Breed. doi:10.1111/j.1439-0523.2012.01983.x

  • Lata C, Prasad M (2011) Role of DREBs in regulation of abiotic stress responses in plants. J Exp Bot 62:4731–4748

    CAS  PubMed  Article  Google Scholar 

  • Li YM (1997) Drought-resistant mechanism and genetic expression of foxtail millet. In: Li YM (ed) Foxtail millet breeding. Agricultural Press, Beijing, pp 433–434

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  Google Scholar 

  • Price A, Steele K, Townend J, Gorham J, Audebert A, Jones M, Courtois B (1999) Mapping roots and shoot traits in rice: experience in UK, IRRI and WARDA. In: Ito O, O’Toole JC, Hardy B (eds) Genetic improvement of rice for water-limited environments. IRRI, Philippines, pp 257–273

    Google Scholar 

  • Rajalakshmi S, Parida A (2012) Halophytes as a source of genes for abiotic stress tolerance. J Plant Biochem Biotech 21:63–67

    CAS  Article  Google Scholar 

  • Smart RE, Bingham GE (1974) Rapid estimates of relative water content. Plant Physiol 53:258–260

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Witcombe JR, Hollington PA, Howarth CJ, Reader S, Steele KA (2008) Breeding for abiotic stresses for sustainable agriculture. Phil Trans R Soc B 363:703–716

    CAS  PubMed  Article  Google Scholar 

  • Zhu JK (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247–273

    CAS  PubMed Central  PubMed  Article  Google Scholar 

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This study was supported by the Department of Biotechnology (Grant No. BT/PR9851/AGR/02/521/2007), Govt. of India, New Delhi and core grant from the National Institute of Plant Genome Research, New Delhi, India. Dr. Charu Lata acknowledges Department of Science & Technology, Govt. of India for the INSPIRE Faculty award [IFA-11LSPA-01]. We thank Dr. Swarup K Parida and Mr. Mehanathan Muthamilarasan, NIPGR, New Delhi for critically reading the manuscript. We are thankful to NBPGR, Hyderabad and UAS, GKVK, Bangalore, India for providing the seed materials.

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Correspondence to Manoj Prasad.

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Supplementary Table S1

Description of 122 foxtail millet accessions along with the level of RWC at control and 24 h duration of dehydration stress, respectively; their allelic information and group position obtained by structure analysis. (DOC 334 kb)

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Lata, C., Prasad, M. Association of an allele-specific marker with dehydration stress tolerance in foxtail millet suggests SiDREB2 to be an important QTL. J. Plant Biochem. Biotechnol. 23, 119–122 (2014).

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  • Allele-specific marker
  • Dehydration stress
  • Foxtail millet
  • Marker-aided breeding
  • SiDREB2
  • Single marker regression
  • Single nucleotide polymorphism