Journal of Biosciences

, Volume 31, Issue 1, pp 69–74 | Cite as

Candidate genes for drought tolerance and improved productivity in rice (Oryza sativa L.)

  • M. S. Vinod
  • Naveen Sharma
  • K. Manjunatha
  • Adnan Kanbar
  • N. B. Prakash
  • H. E. Shashidhar


Candidate genes are sequenced genes of known biological action involved in the development or physiology of a trait. Twenty-one putative candidate genes were designed after an exhaustive search in the public databases along with an elaborate literature survey for candidate gene products and/or regulatory sequences associated with enhanced drought resistance. The downloaded sequences were then used to design primers considering the flanking sequences as well. Polymerase chain reaction (PCR) performed on 10 diverse cultivars that involvedJaponica, Indica and local accessions, revealed 12 polymorphic candidate genes. Seven polymorphic candidate genes were then utilized to genotype 148 individuals of CT9993 × IR62266 doubled haploid (DH) mapping population. The segregation data were tested for deviation from the expected Mendelian ratio (1:1) using a Chi-square test (<1%). Based on this, four candidate genes were assessed to be significant and the remaining three, as non-significant. All the significant candidate genes were biased towards CT9993, the female parent in the DH mapping population. Single-marker analysis strongly associated (<1%) them to different traits under both well-watered and low-moisture stress conditions. Two candidate genes,EXP15 andEXP13, were found to be associated with root number and silicon content in the stem respectively, under both well-watered and low-moisture stress conditions


Candidate gene mapping population polymerase chain reaction single marker analysis 

Abbreviations used


Absiscic acid


absiscic acid responsive element


candidate gene


doubled haploid


low-moisture stress


maximum root length


number of panicles


number of tillers


polymerase chain reaction


plant height


panicle length


polyvinyl chloride


quantitative trait loci


randomized complete block design


root number


root volume


shoot dry weight




silicon content in stem


total silicon content in stem


stem weight


The Institute for Genomic Research


total plant length




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Copyright information

© Indian Academy of Sciences 2006

Authors and Affiliations

  • M. S. Vinod
    • 1
  • Naveen Sharma
    • 2
  • K. Manjunatha
    • 1
  • Adnan Kanbar
    • 3
  • N. B. Prakash
    • 4
  • H. E. Shashidhar
    • 1
  1. 1.Marker-Assisted Selection Lab, Department of Genetics and Plant BreedingUniversity of Agricultural SciencesBangaloreIndia
  2. 2.Biometrics and Bioinformatics UnitInternational Rice Research InstituteLos BanosPhilippines
  3. 3.Department of Agronomy, Faculty of AgricultureUniversity of DamascusDamascusSyria
  4. 4.Department of Soil Science and Agricultural ChemistryUniversity of Agricultural SciencesBangaloreIndia

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