Sanjay Kapoor


E-mail: ;
Tel: +91-11-2415-7192
SPECIALIZATIONFunctional Genomics - Plant Reproduction - Heterosis - Gene Regulation -Rice

Research Interests:

Functional Genomics of Reproductive Development in Rice: Molecular events that follow the establishment of floral organ primodia, ultimately culminate into development of male (pollen) and female (embryo sac) gametophytes in specialized sex organs known as the androecium and gynoecium. The gametes thus formed undergo fertilization and develop into seeds. Understanding the underlying gene regulatory networks that control the development of reproductive floral organs, and the male and female gametophytes therein, involves

  • Identification of the genetic components involved,
  • Their classification into pair wise protein-protein and protein-DNA interactomes, followed by
  • Construction of biologically realistic gene regulatory networks.

Our lab aims to unravel these networks to understand developmental mechanisms in terms of mechanistic models and, thus, pave the way for translating genetic interactions into phenotypic traits. In this regards, we have carried out whole genome microarray-based transcriptome analysis of more than twenty tissues/stages of rice vegetative and reproductive development, which has helped in the identification of several co-expressed groups of genes. These groups either show similar up-regulation profiles or express in a tissue or developmental stage specific manner and, thus, forming putative interactomes. The transcriptomic analysis has been refined to include subtractive logic in order to shortlist genes that express specifically in individual tissues/stages of development for validation of function and/or promoter activities. For gene function validation RNAi/miRNA based silencing and ectopic expression strategies in transgenic rice and/or Arabidopsis are being followed. Moreover, promoter activities are being determined by driving expression of GUS and/or GFP reporter gene in transgenic systems.

Analysis of Methylome Dynamics: During of Reproductive Development: We are also involved in determining the role of epigenetic components in controlling flower development at the whole genome level. We have profiled rice genome for methylated cytosines signatures by microarray based as well as New Generation Sequencing based methodologies at various stages of reproductive development. The data generated from this work is being correlated with the differential expression patterns of transcription factors and signal transduction components obtained from the first component to reveal the underlying connectivity between the genic and epigenetic regulatory processes in a holistic manner.

Understanding Molecular Basis of Heterosis: The molecular basis of heterosis has been a matter of debate for about a century now. At genetic level, both dominance and overdominance along with epistatic interactions have been proposed to be responsible for the manifestation of heterosis. Several attempts have been made, though with limited success, to predict heterotic potential of the hybrids based on associations between phenotypes and the causative molecular event like RFLPs, SSRs and SNPs. A number of studies attempting to link changes in gene expression with heterosis have demonstrated a shift in gene expression patterns in hybrids, but they fall short of identifying the causal factors resulting in this shift. Today, in the post-genome era, with the availability of technologies like whole genome microarrays and NGS, we are in a better position to categorize all the genes that show association with heterotic phenotypes and search for molecular basis of heterosis. Not only can the gene identities be determined, but also, their relative contributions to heterosis in terms of quantitative changes in expression be assessed. In this project, we have initiated work on identification and comprehensive cataloguing of genes associated with heterosis, based on high-density microarray analysis. The data generated from transcriptome analyses are being exploited to identify genes that are associated with heterosis and link this information to already identified molecular markers and/or QTLs in the designated parents and their F1 hybrids. By these strategies we hope to develop insights into the molecular basis of manifestation of heterosis and use this information to, one day, predict heterosis.


(Click here for complete list of Publications)

  1. Nayar, S., Sharma, R., Tyagi, A.K. and Kapoor, S. 2013. Functional delineation of rice MADS29 reveals its role in embryo and endosperm development by affecting hormone homeostasis. Journal of Experimental Botany (doi:10.1093/jxb/ert231)
  2. Baranwal V, Mikkilineni V, Zehr-Barwale U, Tyagi AK and Kapoor S. 2012. Heterosis: Emerging ideas about hybrid vigour. Journal of Experimental Botany doi:10.1093/jxb/ers291.
  3. Sharma R, Agarwal P, Ray S, Deveshwar P, Sharma P, Sharma N, Nijhawan A, Jain M, Singh AK, Singh VP, Tyagi AK and Kapoor S. 2012. Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice. Functional & Integrative Genomics. doi: 10.1007/s10142-012-0274-3.
  4. Deveshwar P, Bovill WD, Sharma R,  Able  JA and Kapoor S. 2011. Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice. BMC Plant Biology 11:78.
  5. Kapoor, M., Arora, R., Lama, T., Nijhawan, A., Khurana, J.P., Tyagi, A.K., and Kapoor, S. 2008. Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics 9.
  6. Arora R, Agarwal P, Ray S, Singh AK, Singh VP, Tyagi AK Kapoor S. 2007. MADS-box gene family in rice: Genome wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 8:242.
  7. Kapoor S., Kobayashi T. and Takatsuji H. 2002. Silencing of Tapetum-specific Zinc-finger Gene, TAZ1, Causes Premature Degeneration of Tapetum and Pollen Abortion in Petunia. Plant Cell 14:2353-2376.
  8. Kapoor S. and Sugiura M. 1999. Identification of Two Essential Sequence Elements in the Nonconsensus Type II PatpB-290 Plastid Promoter by Using Plastid Transcription Extracts from Cultured Tobacco BY-2 Cells. Plant Cell. 11: 1799–1810.
  9. Kapoor S., Suzuki J.Y. and Sugiura M. 1997. Identification and functional significance of a new class of non-consensus type plastid promoters. Plant J. 11:327-337.
  10. Kapoor S., Maheshwari S.C.  and Tyagi A.K. 1993. Organ-specific expression of rice plastid genes.  Plant Cell Physiol. 34: 943-947.


  1. 'Method of lowering pollen fertility by using tapetal layer-specific zinc finger transcription factor gene’ 
    • Inventor; Hiroshi Takatsuji, Sanjay Kapoor, Akira Kobayashi.
    • Australlia patent, No. 779285, 2005.1.13, 
    • Korea Patent No.455620, 2004.10.26., 
    • China Patent, No. CH0261275P, 2005.9.9.
  2. ‘Method of making sterile petunia plants by transformation with a nucleic acid encoding a zinc finger transcription factor’ 
    • Inventor; Hiroshi Takatsuji, Sanjay Kapoor, Akira Kobayashi.
    • Australlia patent, No. 779284, 2005.1.13, 
    • Korea Patent No.455621, 2004.10.26., 
    • US Patent, No.6,989,473, 2006.1.24.
  3. 'Rice Nucleic Acid Sequences Associated With Panicle Development and Uses Thereof' 
    • Inventors: Kapoor Sanjay, Tyagi K. Akhilesh and Arora Rita
    • India Patent No. 157/DEL/2007 (Pending)
  4. 'Nucleic Acid Sequences Form Rice Involved in Seed Development and Uses Thereof'
    • India Patent No. 160/DEL/2007 (Pending)
    • Inventors: Tyagi K. Akhilesh, Kapoor Sanjay and Agarwal Pinky
  5. 'Tissue-specific promoter and uses thereof'
    • India No. 1146/DEL/2011 (Pending)
    • Inventors: Kapoor Sanjay, Tyagi K. Akhilesh and Deveshwar Priyanka
    • 'Tissue-specific promoter and uses thereof'
  6. Abiotic and Heavy Metal Stress-inducible BLEC-Str8 Promoter from Rice.
    • Indian Patent Application no.1403/DEL/2011(Pending)
    • Inventors: Tyagi K. Akhilesh, Kapoor Sanjay and Dhar Swatismita