Functional & Integrative Genomics

, Volume 12, Issue 2, pp 229–248 | Cite as

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

  • Rita Sharma
  • Pinky Agarwal
  • Swatismita Ray
  • Priyanka Deveshwar
  • Pooja Sharma
  • Niharika Sharma
  • Aashima Nijhawan
  • Mukesh Jain
  • Ashok Kumar Singh
  • Vijay Pal Singh
  • Jitendra Paul Khurana
  • Akhilesh Kumar Tyagi
  • Sanjay Kapoor
Original Paper

Abstract

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.

Keywords

Development Expression Meta-analysis Metabolic pathways Panicle Promoter Seed Transcription factors 

Supplementary material

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Rita Sharma
    • 1
    • 3
  • Pinky Agarwal
    • 1
    • 4
  • Swatismita Ray
    • 1
    • 5
  • Priyanka Deveshwar
    • 1
  • Pooja Sharma
    • 1
  • Niharika Sharma
    • 1
    • 6
  • Aashima Nijhawan
    • 1
  • Mukesh Jain
    • 1
    • 4
  • Ashok Kumar Singh
    • 2
  • Vijay Pal Singh
    • 2
  • Jitendra Paul Khurana
    • 1
  • Akhilesh Kumar Tyagi
    • 1
    • 4
  • Sanjay Kapoor
    • 1
  1. 1.Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
  2. 2.Division of GeneticsIndian Agriculture Research InstituteNew DelhiIndia
  3. 3.Department of Plant PathologyUniversity of CaliforniaDavisUSA
  4. 4.National Institute for Plant Genome ResearchNew DelhiIndia
  5. 5.Biotechnology and Bioresources Management DivisionTata Energy Research InstituteNew DelhiIndia
  6. 6.Plant Molecular Biology and Biotechnology Group, Melbourne School of Land and EnvironmentUniversity of MelbourneParkvilleAustralia

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