Original Paper

Functional & Integrative Genomics

, Volume 11, Issue 1, pp 157-178

Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice

  • Swatismita RayAffiliated withInterdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus
  • , Prasant K. DansanaAffiliated withInterdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus
  • , Jitender GiriAffiliated withInterdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus
  • , Priyanka DeveshwarAffiliated withInterdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus
  • , Rita AroraAffiliated withInterdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus
  • , Pinky AgarwalAffiliated withInterdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus
  • , Jitendra P. KhuranaAffiliated withInterdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus
  • , Sanjay KapoorAffiliated withInterdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus
  • , Akhilesh K. TyagiAffiliated withInterdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South CampusNational Institute of Plant Genome Research, Aruna Asaf Ali Marg Email author 

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Abstract

Water-deficit stress is detrimental for rice growth, development, and yield. Transcriptome analysis of 1-week-old rice (Oryza sativa L. var. IR64) seedling under water-deficit stress condition using Affymetrix 57 K GeneChip® has revealed 1,563 and 1,746 genes to be up- and downregulated, respectively. In an effort to amalgamate data across laboratories, we identified 5,611 differentially expressing genes under varying extrinsic water-deficit stress conditions in six vegetative and one reproductive stage of development in rice. Transcription factors (TFs) involved in ABA-dependent and ABA-independent pathways have been found to be upregulated during water-deficit stress. Members of zinc-finger TFs namely, C2H2, C2C2, C3H, LIM, PHD, WRKY, ZF-HD, and ZIM, along with TF families like GeBP, jumonji, MBF1 and ULT express differentially under water-deficit conditions. NAC (NAM, ATAF and CUC) TF family emerges to be a potential key regulator of multiple abiotic stresses. Among the 12 TF genes that are co-upregulated under water-deficit, salt and cold stress conditions, five belong to the NAC TF family. We identified water-deficit stress-responsive genes encoding key enzymes involved in biosynthesis of osmoprotectants like polyols and sugars; amino acid and quaternary ammonium compounds; cell wall loosening and structural components; cholesterol and very long chain fatty acid; cytokinin and secondary metabolites. Comparison of genes responsive to water-deficit stress conditions with genes preferentially expressed during panicle and seed development revealed a significant overlap of transcriptome alteration and pathways.

Keywords

Oryza sativa L. var. IR64 Microarray Transcriptome analysis Water-deficit stress Metabolic pathways Transcription factors