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Genomic Science Program

Systems Biology for Energy and the Environment

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Genomic Science Program

2014 Awardee

The Brachypodium ENCODE Project - From Sequence to Function: Predicting Physiological Responses in Grasses to Facilitate Engineering of Biofuel Crops

INVESTIGATORS: Todd Mockler (PI), Todd Michael, Douglas Bryant, Malia Gehan

INSTITUTIONS: Donald Danforth Plant Science Center, St. Louis, MO; Ibis Biosciences, Carlsbad, CA

PROJECT SUMMARY: The goal of this Brachypodium ENCODE (Encyclopedia Of DNA Elements) project is to identify and characterize all of the functional elements associated with progressive drought response in the Brachypodium distachyon genome sequence, and to develop integrated genome feature maps that will enable advanced modeling of complex pathways in plants. Brachypodium is a model organism for grasses, including potential bioenergy feedstocks, and this effort will develop deep knowledge of chromatin dynamics and gene networks related to abiotic stress responses in these plant species. This knowledge is necessary for the improvement of bioenergy grasses, which is needed for economical production of cellulosic biofuels in the US. To accomplish this goal, this Brachypodium ENCODE project will: (1) obtain fundamental information about Brachypodium’s transcriptome, epigenome, chromatin dynamics, and gene regulatory networks; and (2) elucidate the regulatory dynamics of gene networks that can be manipulated to increase energy grass crop productivity.

Physiological analysis will be coupled with drought-focused genomic and transcriptomic profiling in Brachypodium. These assays will include daily measurements of photosynthetic efficiency and membrane damage during drought stress. Drought-treated plants with physiological symptoms of stress will be re-watered, allowed to recover, and then reassessed to determine if they are capable of revival. Periodic sampling of tissue for ‘omics assays will be conducted from just before signs of physiological stress occur until plants can no longer recover with re-watering. Sampling will be conducted at several intervals to ensure that circadian/diel regulation does not confound downstream analysis and interpretation. To capture dynamic genomic features responding to progressive drought, multiple types of whole-genome analysis will be performed including mRNA and small RNA transcriptome profiling, DNA methylation profiling, and profiling of selected histone modifications. We will also leverage natural variation in Brachypodium drought response and previous DOE investments by analyzing progressive drought experiments using three accessions of Brachypodium whose genomes have been sequenced by DOE-JGI: the reference genome accession, Bd21; the drought-susceptible accession Bd3-1; and the drought-tolerant accession Bd1-1.

The information obtained in this project will aid basic and applied research on a wide range of bioenergy grasses and accelerate deployment of improved grass crops, and will also yield genomic data resources useful for the plant research community and valuable for other studies. This project builds upon previous investments in genomic resources for bioenergy and will address several key interests of the program including investigating environmental influences on gene expression and phenotypes and adaptations to abiotic stresses, with an emphasis on water use efficiency in a model bioenergy grass crop. The large experimental datasets generated by this project will be used to develop computational models and approaches to predict plant performance in varying environmental conditions, with the aim of translation to informed breeding programs for bioenergy grass feedstocks.

Name: Mockler, Todd
Phone: 314-587-1694


Genomics-Enabled Plant Biology for Determination of Gene Function Summary of Projects Awarded

Plant Feedstock Genomics for Bioenergy [01/19]

Lignocellulosic Biomass for Advanced Biofuels and Bioproducts: Workshop Report [2/15]

  • Genomics-Enabled Plant Biology for Determination of Gene Function DE-FOA-0002601 [12/16/21]
  • Systems Biology-Enabled Microbiome Research to Facilitate Predictions of Interactions and Behavior in the Environment DE-FOA-0002602 [12/15/21]
  • Biosystems Design to Enable Safe Production of Next-Generation Biofuels, Bioproducts, and Biomaterials DE-FOA-0002600 [12/13/21]
  • SBIR/STTR Funding Call for Climate, Energy and Scientific R&D DE-FOA-0002555 [12/13/21]
  • Quantum-Enabled Bioimaging and Sensing Approaches for Bioenergy DE-FOA-0002603 [11/15/21]
  • NAS Report: Quantum Science Concepts in Enhancing Sensing and Imaging Technologies: Applications for Biology. More »
  • JBEI's Jay Keasling named Office of Science Distinguished Scientist Fellow. More »
  • DOE BER Early Career Research Funding Opportunity Preapplications due Oct. 21. More »
  • Systems Biology of Bioenergy-Relevant Microbes Projects Awarded. [7/21] More »
  • BER Bioimaging Science Program announces new awards. [7/21] More »
  • DOE BER Request for Information – Responses due by 10- 31-21. More »
  • DOE BER Awards $45.5 Million [6/21] More »
  • More News and Announcements »

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