Plant Molecular Biology

, Volume 69, Issue 1, pp 133-153

First online:

Open Access This content is freely available online to anyone, anywhere at any time.

Expression profiling of rice cultivars differing in their tolerance to long-term drought stress

  • Thomas DegenkolbeAffiliated withMax-Planck-Institut für Molekulare Pflanzenphysiologie
  • , Phuc Thi DoAffiliated withMax-Planck-Institut für Molekulare Pflanzenphysiologie
  • , Ellen ZutherAffiliated withMax-Planck-Institut für Molekulare Pflanzenphysiologie
  • , Dirk RepsilberAffiliated withMax-Planck-Institut für Molekulare PflanzenphysiologieForschungsinstitut für die Biologie landwirtschaftlicher Nutztiere (FBN)
  • , Dirk WaltherAffiliated withMax-Planck-Institut für Molekulare Pflanzenphysiologie
  • , Dirk K. HinchaAffiliated withMax-Planck-Institut für Molekulare Pflanzenphysiologie Email author 
  • , Karin I. KöhlAffiliated withMax-Planck-Institut für Molekulare Pflanzenphysiologie


Understanding the molecular basis of plant performance under water-limiting conditions will help to breed crop plants with a lower water demand. We investigated the physiological and gene expression response of drought-tolerant (IR57311 and LC-93-4) and drought-sensitive (Nipponbare and Taipei 309) rice (Oryza sativa L.) cultivars to 18 days of drought stress in climate chamber experiments. Drought stressed plants grew significantly slower than the controls. Gene expression profiles were measured in leaf samples with the 20 K NSF oligonucleotide microarray. A linear model was fitted to the data to identify genes that were significantly regulated under drought stress. In all drought stressed cultivars, 245 genes were significantly repressed and 413 genes induced. Genes differing in their expression pattern under drought stress between tolerant and sensitive cultivars were identified by the genotype × environment (G × E) interaction term. More genes were significantly drought regulated in the sensitive than in the tolerant cultivars. Localizing all expressed genes on the rice genome map, we checked which genes with a significant G × E interaction co-localized with published quantitative trait loci regions for drought tolerance. These genes are more likely to be important for drought tolerance in an agricultural environment. To identify the metabolic processes with a significant G × E effect, we adapted the analysis software MapMan for rice. We found a drought stress induced shift toward senescence related degradation processes that was more pronounced in the sensitive than in the tolerant cultivars. In spite of higher growth rates and water use, more photosynthesis related genes were down-regulated in the tolerant than in the sensitive cultivars.


Abiotic stress Expression profiling Gene × environment interaction QTL Water use efficiency Water potential