Molecular Genetics and Genomics

, Volume 272, Issue 1, pp 35–46 | Cite as

Saturation mapping of QTL regions and identification of putative candidate genes for drought tolerance in rice

  • T. T. T. Nguyen
  • N. Klueva
  • V. Chamareck
  • A. Aarti
  • G. Magpantay
  • A. C. M. Millena
  • M. S. Pathan
  • H. T. NguyenEmail author
Original Paper


We have developed 85 new markers (50 RFLPs, 5 SSRs, 12 DD cDNAs, 9 ESTs, 8 HSP-encoding cDNAs and one BSA-derived AFLP marker) for saturation mapping of QTL regions for drought tolerance in rice, in our efforts to identify putative candidate genes. Thirteen of the markers were localized in the close vicinity of the targeted QTL regions. Fifteen of the additional markers mapped, respectively, inside one QTL region controlling osmotic adjustment on chromosome 3 ( oa3.1) and 14 regions that affect root traits on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, 10 and 12. Differential display was used to identify more putative candidate genes and to saturate the QTL regions of the genetic map. Eleven of the isolated cDNA clones were found to be derived from drought-inducible genes. Two of them were unique and did not match any genes in the GenBank, while nine were highly similar to cDNAs encoding known proteins, including a DnaJ-related protein, a zinc-finger protein, a protease inhibitor, a glutathione-S-transferase, a DNA recombinase, and a protease. Twelve new cDNA fragments were mapped onto the genetic linkage map; seven of these mapped inside, or in close proximity to, the targeted QTL regions determining root thickness and osmotic adjustment capacity. The gene I12A1, which codes for a UDP-glucose 4-epimerase homolog, was identified as a putative target gene within the prt7.1/brt7.1 QTL region, as it is involved in the cell wall biogenesis pathway and hence may be implicated in modulating the ability of rice roots to penetrate further into the substratum when exposed to drought conditions. RNAs encoding elongation factor 1β, a DnaJ-related protein, and a homolog of wheat zinc-finger protein were more prominently induced in the leaves of IR62266 (the lowland rice parent of the mapping materials used) than in those of CT9993 (the upland rice parent) under drought conditions. Homologs of 18S ribosomal RNA, and mRNAs for a multiple-stress induced zinc-finger protein, a protease inhibitor, and a glutathione-S-transferase were expressed at significantly higher levels in CT9993 than in IR62266. Thus several genes involved in the regulation of DNA structure and mRNA translation were found to be drought-regulated, and may be implicated in drought resistance.


Rice Drought Quantitative trait loci (QTL) Osmotic adjustment (OA) Differential display (DD) 



We would like to thank Dr. S.D. Tanksley, Dr. S.R. McCouch and Dr. T. Sasaki for their kindly providing the RFLP clones. cDNA sequencing was provided by the Center for Biotechnology and Genomics at Texas Tech University. This work was funded by a grant from the Rockefeller Foundation’s International Program on Rice Biotechnology


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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • T. T. T. Nguyen
    • 1
    • 3
  • N. Klueva
    • 1
    • 4
  • V. Chamareck
    • 1
  • A. Aarti
    • 1
    • 5
  • G. Magpantay
    • 1
    • 6
  • A. C. M. Millena
    • 1
    • 7
  • M. S. Pathan
    • 1
    • 2
  • H. T. Nguyen
    • 1
    • 2
    Email author
  1. 1.Plant Molecular Genetics Laboratory, Department of Plant and Soil SciencesTexas Tech UniversityLubbockUSA
  2. 2.Department of Agronomy, Plant Sciences UnitUniversity of MissouriColumbiaUSA
  3. 3.Fungal Disease Laboratory, Department of Plant PathologyNational Agricultural Research CenterTsukubaJapan
  4. 4.Center for Biotechnology and GenomicsTexas Tech UniversityLubbockUSA
  5. 5.COAHaryana Agricultural UniversityKaul (Kaithal)India
  6. 6.Ceres Inc.MalibuUSA
  7. 7.Health Science CenterTexas Tech UniversityLubbockUSA

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