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Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice

  • Sharma, Rita1, 2
  • Agarwal, Pinky1, 3
  • Ray, Swatismita1, 4
  • Deveshwar, Priyanka1
  • Sharma, Pooja1
  • Sharma, Niharika1, 5
  • Nijhawan, Aashima1
  • Jain, Mukesh1, 3
  • Singh, Ashok Kumar6
  • Singh, Vijay Pal6
  • Khurana, Jitendra Paul1
  • Tyagi, Akhilesh Kumar1, 3
  • Kapoor, Sanjay1
  • 1 University of Delhi South Campus, Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi, 110021, India , New Delhi (India)
  • 2 University of California, Department of Plant Pathology, Davis, CA, 95616, USA , Davis (United States)
  • 3 National Institute for Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India , New Delhi (India)
  • 4 Tata Energy Research Institute, Biotechnology and Bioresources Management Division, Lodhi Road, New Delhi, 110003, India , New Delhi (India)
  • 5 University of Melbourne, Plant Molecular Biology and Biotechnology Group, Melbourne School of Land and Environment, Parkville, Victoria, 3010, Australia , Parkville (Australia)
  • 6 Indian Agriculture Research Institute, Division of Genetics, New Delhi, 110012, India , New Delhi (India)
Published Article
Functional & Integrative Genomics
Publication Date
Mar 31, 2012
DOI: 10.1007/s10142-012-0274-3
Springer Nature


Carefully analyzed expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the spatial and temporal expression profiles of rice genes in 19 stages of vegetative and reproductive development. We could verify expression of 22,980 genes in at least one of the tissues. Differential expression analysis with respect to five vegetative tissues and preceding stages of development revealed reproductive stage-preferential/-specific genes. By using subtractive logic, we identified 354 and 456 genes expressing specifically during panicle and seed development, respectively. The metabolic/hormonal pathways and transcription factor families playing key role in reproductive development were elucidated after overlaying the expression data on the public databases and manually curated list of transcription factors, respectively. During floral meristem differentiation (P1) and male meiosis (P3), the genes involved in jasmonic acid and phenylpropanoid biosynthesis were significantly upregulated. P6 stage of panicle, containing mature gametophytes, exhibited enrichment of transcripts involved in homogalacturonon degradation. Genes regulating auxin biosynthesis were induced during early seed development. We validated the stage-specificity of regulatory regions of three panicle-specific genes, OsAGO3, OsSub42, and RTS, and an early seed-specific gene, XYH, in transgenic rice. The data generated here provides a snapshot of the underlying complexity of the gene networks regulating rice reproductive development.

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