A Functional Genomics Approach to Altering Crown Architecture in Populus: Maximizing Carbon Capture in Trees Grown in Dense Plantings
Principal Investigator: Gerald A. Tuskan
Co-investigators: Udaya C. Kalluri, Stan D. Wullschleger, Glenn T. Howe, Stephen P. DiFazaio, Gancho T. Slavov

Abstract

Recent increases in energy costs have led to a heightened interest in growing hybrid poplar (Populus spp.) for ethanol production. Available commercial clones, however, represent only one or two generations of genetic improvement over their wild ancestors. Alteration of plant architecture (i.e., canopy form) was a major component of the striking gains in agronomic productivity achieved during the green revolution. In particular, the development of plants that are unresponsive to limited light availability via an altered phytochrome response has been an effective strategy for maximizing productivity in high-density stands. Therefore, the objective of this project is to gain a molecular understanding of phytochrome-mediated responses to competition in Populus and then use that knowledge to maximize carbon capture per unit land area. Photochromes are a well-studied family of photoreceptors that is responsible for how plants perceive their light environment. Specifically, we will use a functional genomics approach to assess the shade-avoidance syndrome in black cottonwood (P. trichocarpa). Poplar are unique in that they possess a limited subset of PHY compared to other model organisms, so the precise mechanisms of photoreception are sure to differ from those model organisms like Arabidopsis. Our intent is to focus on the 3 poplar phytochrome genes (PHYA, PHYB1 and PHYB2) and characterize light signaling pathways, cross-talk among genes, and transcriptional cascades in shade-modulated plants. Gene expression profiles will be assessed using microarrays and qRT-PCR for cisgenic mutants over- and under-expressing each of the three phytochrome genes. Expected phenotypes include plants with narrow crowns, prolific branching, and minimal self-thinning in densely-planted stands. This work will lead to a conceptual model of phytochrome-mediated responses to competition in Populus. Specific predictions of this model will be tested by assaying variation in phytochrome gene sequences and expression along a gradient of crown architecture in wild Populus accessions from the Pacific Northwest. The ultimate goal of this project is to facilitate the development of a renewable bioenergy resource that will have high yields and reduced harvest and transport costs. This will be a collaborative project among scientists at Oak Ridge National Laboratory, Oregon State University,West Virginia University, and ArborGen, LLC .

For more information contact: Gerald Tuskan

Environmental Influences on Wood Chemistry and Density of Populus and Loblolly Pine
Principal Investigator: Gerald A. Tuskan

Abstract:

Environmental factors confound our estimates of genetic parameters, complicate gene discovery, and impact product quality. A multivariate model will be establish an empirical relationship between climatic + silvicultural variables and chemical + physical wood property traits in Populus and loblolly pine in an effort to develop a framework for understanding the environmental influences on wood quality. Two new high-throughput techniques, NIR and CT scan, will be applied to genetically stratified increment samples from each species grown under intensively managed and monitored experiments. Spatial resolution provided by NIR and CT scan, together with the temporal resolution provided by the experimental design, should allow us to define the relationship between fluctuating environmental conditions and subsequent wood properties. The specific objectives of the study are to: 1) determine the degree to which physical and chemical wood properties vary in association with environmental and silvicultural practices in Populus and loblolly pine and 2) develop and verify species-specific empirical models in an effort to create a framework for understanding environmental influences on wood quality.

For more information contact: Gerald Tuskan

Genetic and Environmental Controls on Carbon Allocation and Chemical Partitioning in Woody Plants: Implications for Terrestrial Ecosystems.
Principal Investigator: Stan D. Wullschleger

Abstract:

The genetic and environmental mechanisms that control 1) whole-plant allocation of biomass above- and below-ground, and 2) cellular partitioning of photosynthate to long-lived pools for ultimate carbon sequestration in soils will be examined in a 3-year field study. We argue that the carbon sequestration potential of terrestrial ecosystems can be enhanced by managing for increased carbon allocation below-ground and by genetically selecting plants for increased lignin concentration as a recalcitrant chemical constituent of both leaves and roots. A series of hypotheses will be examined using two three-generation segregating F2 hybrid poplar families from which biomass samples will be collected for identifying clonal differences in cell wall chemistry and carbon allocation above- and below-ground. Pyrolysis molecular beam mass spectrometry (pyMBMS) will be used to quantify the lignin, hemicellulose, cellulose and extractive content in leaves and fine-root samples from 375 individual progeny within each family. Co-linear genetic maps will be combined with phenotypic data on carbon allocation and partitioning as part of a quantitative trait loci (QTL) analysis. Moreover, a mechanistic model will be developed as an investigative tool to assess the potential benefits of clonal selection for vegetative and soil carbon sequestration based on observed chemical composition of leaves and fine-roots, and whole-tree patterns of carbon allocation. Data generated in the first two years of this study will be used to define a subset of hybrid poplar clones contrasting in chemical composition and carbon allocation (e.g., high vs. low lignin and high vs. low allocation to roots) that will subsequently be incorporated into a replicated field trial designed to address 1) the contribution of these whole-plant and cellular traits to carbon sequestration, and 2) the genetic plasticity of these traits to the manipulation of soil water and nutrient regimes. Once these traits are understood, it should be possible to apply traditional and/or advance genetic techniques for customizing woody plants for the specific purpose of carbon sequestration. Our findings will have direct implications for natural and managed ecosystems, including understanding the genetic and environmental plasticity of critical processes (carbon allocation and partitioning) involved in carbon sequestration and the consequences of this plasticity to carbon management in terrestrial ecosystems.

For more information contact: Stan Wullschleger

Genome-Enabled Discovery of Carbon Sequestration Genes in Poplar
Principal Investigator: Gerald A. Tuskan

Abstract:

The fate of carbon belowground is likely to be a major factor determining the success of carbon sequestration strategies involving plants. We propose a large-scale, multi-institutional effort to identify and characterize poplar genes that play key roles in belowground processes: 1) the allocation of carbon to structural, coarse, and fine roots; 2) the partitioning of carbon into various chemical fractions within the cell walls of roots; and, ultimately, 3) the deposition of carbon into long-term soil pools. We seek to enhance carbon allocation to roots by altering the auxin and cytokinin signaling pathways, because these two growth regulators have strong, interacting effects on root proliferation and development. We will also explore the effects of altering poplar homologs of genes that affect carbon allocation in model species. These include the invertase family, which controls sucrose metabolism, and transcription factors and activators that affect cell division and expansion. Finally, we will initiate two major gene discovery efforts aimed at identifying novel genes that control carbon allocation and partitioning in Populus: 1) isolation of genes controlling metabolite production in poplar and 2) isolation of genes affecting carbon allocation in Arabidopsis. All of these genes will be tested in transgenic poplar using advanced tools to confer root-predominant and inducible suppression and overexpression of target genes. This broad, integrated approach is aimed at ultimately enhancing the quantity and longevity of soil carbon stores derived from tree plantations. Preliminary calculations indicate that this dual strategy could result in up to an additional 1.27 gigatons of carbon per year stored globally in belowground systems.

For more information contact: Gerald Tuskan

Genomic Characterization of Belowground Ecosystem Responses to Climate Change.

Abstract:

Most analyses of terrestrial ecosystem response to atmospheric and climatic perturbations inevitably conclude that belowground processes are key to predicting the trajectory and effects of global change. However, belowground processes remain poorly understood because antiquated and cumbersome methodologies are being applied to highly complex and heterogeneous biological and geochemical systems. Genomics approaches promise to revolutionize the study of belowground communities, ultimately contributing to a mechanistic understanding of ecosystem responses to climatic change. We will develop quantitative, species-specific molecular assays to analyze the plant root composition of soil cores, thereby characterizing belowground competitive interactions with unprecedented precision. We will also assess functionally significant changes in plant-associated microbial communities by assaying the relative abundance and expression of nitrogen-cycle genes using microarray technology. Finally, we will develop advanced statistical and computational techniques, including artificial neural networks, to identify key drivers of this exceedingly complex and heterogeneous system. We will apply these tools in a new ORNL facility to study the effects of carbon dioxide concentration, temperature, and moisture on a community of early successional plant species with contrasting characteristics. This research will provide a unique view into the obscure-yet-important world of belowground biota, thus contributing to a mechanistic understanding of responses of entire plant and microbial communities to climate change. The developed tools could subsequently be applied to increasingly complex systems, thus positioning ORNL to attain a leadership role in the emerging field of ecosystem genomics.

For more information contact: Lee Gunter


Ecosystem Genomics - An Emerging Opportunity for Environmental Research

Abstract:

The rapid pace of genomics research has energized the entire community of biologists, and genomics techniques and information are being applied in an increasing number of fields. One emerging field is ecosystem genomics, which promises substantial breakthroughs in ecology and environmental science. We have undertaken a research program that capitalizes on the poplar (Populus spp.) genome sequence as an entry point for studying the molecular bases of ecologically significant processes such as flowering, drought adaptation, and response to perturbations such as elevated carbon dioxide. As the technologies and analytical methods mature, these poplar-centered studies will logically lead into wider ecosystem-scale investigations involving carbon and nitrogen cycling. We have embarked upon a pilot project to study the molecular bases of a qualitative trait: gender determination. This proof-of-principle study involves sequencing portions of floral homeotic genes from a variety of male and female trees, with the goal of identifying molecular polymorphisms associated with gender. The project has the added benefit of providing the first estimate of single nucleotide polymorphism (SNP) for a forest tree, thus paving the way for studies of quantitative adaptive traits in natural populations.

For more information contact: Stan Wullschleger

Metabolic Profiling: A Required Element in Functional Genomics
Principal Investigator: T. J. Tschaplinski1; G.J. Van Berkel 2
1Environmental Sciences Division
2Chemical Sciences Division

Abstract

The emerging science of metabolomics or metabolite profiling offers tremendous potential to discover novel genes and assign function to those genes. Metabolic profiling determines the consequences of a targeted change in gene activity, and has the potential to provide information on gene function and how it affects the complex biochemical network. The creation of a comprehensive gas chromatography-mass spectrometry (GC-MS) library of trimethylsilyl (TMS)-derivatives of organic constituents is essential for the near-term development of metabolic profiling in poplar (Populus), by using time-compressed GC-Time-of-Flight (ToF) MS analyses. A proof-of-principal study was initiated to prove that high throughput rates of broad-spectrum metabolite analyses can be achieved, with derivatization protocols effective at reproducibly silylating the 300-450 metabolites. The research is organized around three tasks that include 1) optimization of gas chromatography-mass spectrometry (GC-MS) derivatization and analytical protocols for high throughput, 2) creation of a mass spectral library of known Populus metabolites, including the characterization of unknown compounds and establishment of deconvolution strategies to separate overlapping compounds, and 3) extension of analyses to the liquid chromatography-mass spectrometry (LC-MS) platform to further increase the number of metabolites analyzed and improve characterization of unknowns.

For more information contact: Tim Tschaplinski