U.S. National Science Foundation awards grants to seed plant systems biology - biofuel and bioeconomy-centered projects

The U.S. National Science Foundation (NSF) has made 26 new awards totaling $85.8 million during the tenth year of its Plant Genome Research Program (PGRP). These awards - which cover two to five years and range from $400,000 to $7.9 million - support research and tool development to further knowledge of genome structure and function. They will also increase understanding of gene function and interactions between genomes and the environment in economically vital crop plants. The new awards - made to 45 institutions in 28 states - include international groups of scientists from Asia, Australia and Europe.

The wealth of genomics tools and sequence resources developed over the past ten years of the PGRP have opened up exciting, new comparative approaches in plant biology. PGRP researchers continue to uncover gene networks that regulate plant development and growth in concert with environmental signals, such as temperature, light, disease and pests.

Amongst the projects of immediate interest to the emerging biofuels and bioeconomy are:

A four-year, $5.5 million project to make a comparative analysis of C3 and C4 leaf development in rice, sorghum and maize, led by Timothy Nelson, which involves Yale University, Boyce Thompson Institute, Cornell University and Iowa State University:
C4-type plants such as maize, sorghum and several promising biofuel feedstocks possess a set of complex traits that greatly enhance their efficiency of carbon-fixation, water and nitrogen use, and performance in high temperatures and light intensities, in comparison to C3-type plants such as rice and many temperate grasses. The key C4 traits are (1) specialization and cooperation of two leaf photosynthetic cell types (mesophyll and bundle sheath) for carbon fixation and photosynthesis, (2) enhanced movement of metabolites between cooperating cells, and (3) very high density of leaf venation. These C4 traits appear to be regulatory enhancements of features already present in less-efficient C3 plants, but regulated in different patterns. Although C4 plants have evolved at least 50 times independently in various taxonomic groups, the molecular basis of key C4 traits is insufficiently understood to permit their introduction into important C3 plants to enhance their performance as agricultural or biofuel feedstocks.

This project will compare the leaves of rice (a C3 grass), maize (a moderate C4 grass) and sorghum (an extreme C4 grass). The abundance and spectrum of gene transcripts, proteins and metabolites will be compared along a developmental gradient from immature tissues at leaf base to mature tissues at the leaf tip. To align the gradients of the three species, markers for developmental time points in gene expression, protein accumulation, sink-source transition and cell wall specialization will be employed. Mesophyll and bundle sheath cells will be obtained from each leaf stage by laser microdissection, and their whole genome RNA transcripts, proteomes (including modifications), and selected metabolites (related to photosynthesis) will be profiled and compared. Two hypotheses will be tested by the comparative analysis of the corresponding C3 and C4 plant datasets: (1) To produce C4 traits, plants use networks of genes, proteins, and metabolites that are already present in C3 plants, and (2) C4 features are plastic and expressed in a degree that depends on environment and developmental stage. This analysis should identify the regulatory points that are potential targets for the production of C4 traits in C3 species.

A four-year, $4.6 million grant to a project led by John Browse at Washington State University to continue research that uses biochemical genomics to reveal components of biosynthesis pathways necessary to produce novel fatty acids in oilseeds:
The goal of this project is to use genomics to access the network of genes and proteins that operate chemical factories to synthesize and accumulate novel fatty acids in seeds. Evolution of new enzyme functions, together with the co-evolution of additional biochemical and cell biological traits, has provided hundreds of potentially useful chemicals in seed oils, including the hydroxylated, conjugated and cyclopropane fatty acids to be studied in this project.

Providing a detailed description of genes and proteins required for optimal pathway function will require the integrated deployment of four strategies: a) Investigate and optimize the activities of enzymes for unusual fatty acid synthesis using bioinformatics and protein engineering. b) Carry out extensive sequencing of seeds sampled through the period of oil synthesis, and use functional genomic screens to identify co-evolved enzymes (and other protein functions) required for incorporation of the novel fatty acid into the oil. c) Perform biochemical analysis of the identified proteins and quantify their contributions to the accumulation of unusual fatty acids through expression in transgenic plants. d) Analyze protein-protein interactions in membranes to gain insight how these pathways are physically organized. Finally, the accumulated knowledge will be tested through experiments to reconstruct the native pathways in transgenic plants using expression of multiple genes and pathway engineering. The discoveries that result from this project will yield an understanding of the underlying principles of how pathways evolved for the synthesis of novel seed oils.

The basic knowledge from this project will enable the design of a new generation of specialty crops that will become the green factories of the future, providing for the production of industrial lubicants, solvent oils and biodiesel.


A four-year, $1.7 million grant to a University of Alaska Fairbanks and University of Minnesota-Twin Cities project led by Matthew Olson to study population genomics of cold adaptation in poplar:
Populus species are economically, ecologically, and environmentally important; they are harvested for paper pulp and particle board production, and hold potential for playing important roles in CO2 biosequestration and biofuel production:
energy :: sustainability ::biomass :: bioenergy :: biofuels :: bioproducts :: bioeconomy :: energy crops :: systems biology :: genomics ::

Populus also is the model organism for hardwood tree genomics and physiology. Population genetic tools are increasingly useful for identifying genes that underlie variation in ecologically and economically important traits, but are not presently available in Populus. This project will develop these tools for Populus balsamifera, use them to identify the genetic basis for phenotypic variation in bud set (an important determinant of cold adaptation and growth rate). This research also will test whether the same genes responsible for variation and adaptive evolution of bud set in North American P. balsamifera and European P. tremula.

These objectives will be accomplished through collaboration with Canadian researchers who are establishing long-term common gardens of P. balsamifera. These common gardens will be maintained as a long term resource and are available to the wider scientific community; therefore, the data we generate will greatly facilitate future genotype-phenotype association analyses on additional economically and ecologically important traits (wood density, drought tolerance, etc.). The comparative population genomic analyses of adaptation to northern latitudes will be accomplished through collaboration with colleagues at the University of Umea, Sweden, who are conducting complementary research in European aspen (P. tremula).

A three-year, $2.5 million grant to The Grass Regulome Initiative which will focus on integrating control of gene expression and agronomic traits across the grasses; the project is led by Erich Grotewold and involves the Ohio State University and the University of Toledo (earlier a similar project led by Gronewold - "Engineering phenolic metabolism in the grasses using transcription factors"- received a grant from the U.S. Department of Energy):
An emerging theme in plant systems biology is establishing the architecture of regulatory networks and linking system components to agronomic traits. The goal of this project is to provide a concerted effort to perform comparative transcriptional genomics across several grass crops (maize, sorghum, sugarcane and rice), combining the development of experimental tools and bioinformatic resources to discover and display regulatory motifs. The Grass Regulatory Information Service (GRASSIUS) will be implemented as a public web resource that integrates sequence and expression information on transcription factors (TFs), their DNA-binding properties, TF binding sites in the genome, the genes that TFs target for regulation and the regulatory motifs in which they participate.

A method for the in vivo identification of direct targets for TFs, which should be applicable even in the absence of a complete genome sequence, will be developed and applied towards the identification of direct targets for a small subset of maize, rice, sorghum and sugarcane TFs. Together with the generation of a large centralized collection of plasmids harboring open reading frames for several TFs and antibodies to a subset of them, this project will facilitate the community-wide identification of protein-DNA interactions, essential for establishing the grass regulatory map. The experimental and computational integration of regulatory motifs with QTLs will provide an accelerated translation of findings derived from these studies to issues of agronomic relevance.

Benefiting from the increasing amount of genome sequence available, this proposal integrates genetics, molecular biology, biochemistry, statistics, bioinformatics and computer sciences in establishing the architecture of the regulatory networks that control plant gene expression, in a pioneering effort to launch the comparative transcriptional genomics field to important grass crops.

And 4 major projects on maize genomics (maize artificial chromosomes; functional genomics of maize gametophytes; construction of comprehensive sequence indexed transposon resources for maize; cell fate acquisition in maize).

Plant biologists continue to exploit genomics tools and sequence resources in new and innovative ways. It's exciting to see research involving biologists and mathematicians, computer scientists and engineers, all working to address major unanswered questions in plant biology. These latest projects will also have a significant impact on how we train the next generation of plant scientists to carry out research at the cutting edge of the biological sciences. - James Collins, NSF assistant director for biological sciences.

PGRP is also continuing to support the development of tools to enable researchers to make breakthroughs in understanding the structure and function of economically important plants - from the gene level to the whole plant. Example projects include:

• A multidisciplinary team of investigators at the University of Wisconsin-Madison will develop cutting-edge technology using cameras, robotics and computational tools to enable high-throughput analysis of traits in mutant or naturally varying plant populations.
• A project led by the Dana-Farber Cancer Institute is using Arabidopsis and rice genomic resources to produce a plant "interactome," a map of all protein-protein interactions. This map will provide scientists with testable predictions of how genes and the proteins they encode interact to carry out complex functions within a plant cell.

The PGRP, which was established in 1998 as part of the coordinated National Plant Genome Initiative by the Interagency Working Group on Plant Genomes of the National Science and Technology Council, has the long-term goal of advancing the understanding of the structure and function of genomes of plants of economic importance.

References:
National Science Foundation: NSF Awards 26 New Grants to Seed Plant Systems Biology - October 11, 2007.

National Science Foundation: overview of 2007 PGRP Awards.