Cross-talk among components of drought tolerance and sugar signaling in Sweet Sorghum. 

For biofuel purposes, large scale plantings of sweet sorghum will be done on marginal lands that are prone to environmental stresses especially drought stress, affecting the sugar yield. To be able to fully harness the potential of sweet sorghum as a biofuel crop and ensure optimum supply of biomass and ethanol, it is imperative to assess the yield and brix degree (sugar level) of sorghum cultivars under diverse environmental conditions and develop improved cultivars that are tolerant to environmental stresses. Recent studies suggest a positive correlation between drought tolerance and carbohydrate metabolism in sweet sorghum. In severe drought conditions, genotypes that are drought tolerant have been found to perform better as compared to less tolerant cultivars, as they can avoid premature senescence and perform photosynthesis for longer period of times. Therefore, it is conceivable to increase stem sugars by manipulating genes involved in drought tolerance.

Development of Genomic Resources for Bio-energy crop (Switchgrass) and feedstock improvement.
Switchgrass is a potential bio-energy crop and its genome is under sequencing using next-generation technologies. An accurate estimate of genome structure and composition prior to full genome sequencing is helpful. Generation and sequencing of BAC libraries is an efficient strategy to obtain this information and support assembly of the large and complex underlying genomes. In order to gain insight into the genome structure and organization, initiate functional and comparative genomic studies, and assist with its genome assembly, inRonald lab, we have constructed and characterized switchgrass BAC libraries, in collaboration with CUGI. A collection of 330K high-quality BAC-end sequences was generated at HudsonAlpha Institute of biotechnology, from both the libraries that provided the basis for a genome-wide survey of switchgrass genome structure and organization. Comparative mapping of full-length BACs and BES onto other grass genomes reveals high levels of synteny and micro-collinearity between them. The work was described in an article published April 12, 2012 in PLoS One. As one of the best-studied grasses, rice has an accumulated wealth of knowledge that makes it an attractive candidate as a reference for other important staple crops and emerging biofuel grasses. Its compact genome size, completed genome sequence, availability of high-density genetic maps and whole-genome expression data, all make rice a model system for studies of switchgrass. Based upon biofuel traits i.e. release of sugars from cell wall upon saccharification, we have prioritized several rice cultivars that includes IR64, Dular, Minghui, N22, SHZ-2 and Pokali, and sequenced at Joint Genome Institute. We also sequenced Kitaake rice, that has a short life cycle.
 Micro-collinearity between switchgrass BAC clones and orthologous regions from Brachypodium (Bd), rice (Os), sorghum (Sb) and maize (Zm). 
Comparative genome analysis based upon large genome fragments reveals that the order, transcriptional orientations, and gene structure of switchgrass genes is significantly conserved with rice. At JBEI we are using information from rice and other grasses for prioritizing genes for BAC library screening. We have established a qPCR-based BAC library screening strategy. We are specifically interested in glycosyl transferease, glycosyl hydrolase, Transcription factors, Kinases, transporters and genes involved in lignin biosynthesis pathway. We are screening BAC libraries for these potential cell wall, biomass or stress-specific sequences and selected more than 350 BAC clones. In Rice, a cluster of CslF genes was identified from corresponding region of a mojor QTL for (1,3; 1,4)-B-D-glucan content in Barley. I have identified their orthologs from switchgrass and now we are working towards functional characterization in switchgrass.  

Stress Biology

Plant stresses, together with the growing population, threaten stable global food availablity. in an estimate, up to 60% of global grain production is lost because of environmental stresses. Progress in our understanding of the plant stress responses has largely relied on dissection of a limited number of generic networks that have been worked out independently. The advent and widespread availability of modern data acquisition techniques have enabled high-throughput and quantitative investigations, and we are now beginning to understand sharing of components between biotic and abiotic stress signaling pathways.

Ethylene Responsive Transcription Factors (ERFs) play a vital regulatory role in variety of developmental processes and stress responses in plants. In fact, several of them (e.g. Sub1, OsERF922, BrERF4, SiERF3, GmERF3) have already been shown to confer tolerance to multiple stresses indicating that these encode multifunctional factors that play dual role in response to abiotic/biotic stresses. Therefore, ERF family genes are ideal candidates for engineering stress tolerance to multiple stresses. I performed a comprehensive phylogenomic analysis of ERFs in tomato to identify key genes regulating abiotic stress and fruit development. In collaboration with Dave Mackill, Ronald lab has isolated Submergence tolerance 1 (Sub1), which is a complex locus carrying three genes that encode putative AP2/ERF regulators. Based upon expression profiling of submergence tolerance rice variety and rice stress response interectome, we have prioritized several genes for further analysis. A Genome-scale gene network, RiceNet, can accurately predict gene function in rice and other monocot plants, and thus enables the identification of genes regulating important crop traits and their engineering. My research focus seeks to understand biology of ERFs during biotic and abiotic stress, and use this information for development of stress tolerant crops. We are trying to understand how information generated for rice can be transferred to bioenergy crop "switchgrass". 

Plant-Based Biopharmaceuticals

Plants are our best friends since our existence and are backbone of all the life on earth as they convert sun's energy to chemical energy that feeds the world. Thousands of years ago, human societies began to understand gathering by agriculture. In those ancient times, human beings could not read or write, even then they started a scientific discipline "Plant Domestication" i.e. genetic modification of plants to create new forms of plants, which transformed human life.

Spectacular progress has been made in genetic engineering since the recovery of the first transformed plants in the early 1980s and infect, today the manipulation of plant genome has become a core tool in plant biology. A relatively new bioscience "Plant Molecular Farming" has emerged and is gaining momentum. It involves the genetic modification of the host plant through the purposeful addition of a gene or group of genes (that hold the information for synthesizing a bio-molecule) to plant genome. For this purpose, genes of interest and nucleotide sequences required for its expression are stitched together as transcriptional units and inserted in the target genome. Plants have been engineered for variety of purposes that includes germplasm improvement and molecular farming.

Vibrio cholerae is one of the pathogens infect gastrointestinal tract and results in severe diarrhea. The pathogen colonizes intestine and secrete cholera toxin thereby causing the disease cholera. Cholera toxin B subunit (CTB) is non-toxic and is a component of a widely licensed oral cholera vaccine. For my doctoral research at DPMB, university of Delhi South Campus, I worked towards development of plant-based vaccine against V. cholera. We demonstrated for the first time that antigenic determinants from Vibrio cholerae can be produced as chimeric product, a step towards development of plant-based combinatorial vaccine. To screen useful transformants with desired level of transgene expression and copy number, a large number of transformants are required for screening and therefore, an efficient transformation protocol. I have keen interest to understand plant transformation process. Earlier, I worked to optimized an efficient Agrobacterium-mediated tomato transformation protocol. At present I am working to understand and optimize transformation process for perennial grass "Switchgrass" and M202sub1, a rice cultivar which is recalcitrant for DNA uptake. Whereas switchgrass is a potential bioenergy crop, M202sub1 is tolerant to submergence stress.

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