Regulators 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 (A) Identification of the genetic components involved, (B) Their classification into pair wise protein-protein and protein-DNA interactomes, followed by (C) 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.

Molecular basis of heterosis (hybrid vigor): 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.