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Genomic Science Program

Pilot Project: Brookhaven National Laboratory (BNL)

Quantitative Plant Science Initiative (QPSI)

The Quantitative Plant Science Initiative (QPSI) is a multidisciplinary, team-based project aimed at accelerating the development of biodesign strategies towards improvement of current and emerging bioenergy/bioproduct crops. Our overarching goal is to integrate and coordinate experimentation with computational approaches to address the knowledge gap that exists between plant genomes and the function encoded within. Towards this goal, QPSI leverages genomic and post-genomic data for the capture and integration of functional inferences and hypothesis-driven, targeted experimentation to gain sequence-to-function knowledge. 

Sustainable bioproduction crops that thrive in marginal soils and maintain performance in diverse and fluctuating environments are needed. Understanding and predicting biosystem productivity in diverse environments remains a challenge in systems biology and is hindered by a lack of information about those systems. Post-genomic resources have accelerated our ability to achieve systems-wide information as to how plants respond and adapt to biotic and abiotic stresses. Capitalizing on this cascade of genome-based data, the QPSI capability is developing approaches that combine the scalability of functional genomics with protein function characterization to generate the foundational knowledge needed for the redesign of target plant processes. This project is leveraging cross-kingdom ‘omics-derived functional extrapolations and quantitative gene-to-phenotype knowledge at the single-cell level to discover novel niche-specific and lineage-wide processes as targets for crop improvement. Emerging from these platforms, protein function predictions will be used to guide characterization via genetic, biochemical and molecular imaging techniques. We are also developing approaches that combine target-specific experimentation with computational platforms for the accurate propagation of experimentally grounded functional characterization across sequence space.

This synergistic, mission-driven project will provide the means to gain the fundamental sequence-to-function understanding that is critical for advancing biodesign and genome-wide engineering of current and emerging crops. Furthermore, the results of this work will advance our understanding of plant adaptation and acclimation to stress, with transformative applications to DOE mission in energy security.

Principal Investigator: Crysten E. Blaby-Haas1
Technical Co-manager: Ian K. Blaby1
Imaging Lead: Qun Liu1,2
Collaborators: Steven Almo3, Sean McSweeney2, Daifeng Wang4, Shinjae Yoo5
 
Participating Institutions: 1Biology Department, Brookhaven National Laboratory, Upton, NY; 2National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY; 3Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY; 4Department of Biomedical Informatics, Stony Brook University, Stony Brook, USA; 5Computational Science Center, Brookhaven National Laboratory, Upton, NY

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