Genomic Mechanisms of Carbon Allocation and Partitioning in Poplar |
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Princiapl Investigator |
Matias Kirst |
University of Florida |
Co-Investigators |
Gary Peter |
University of Florida |
Tim Martin |
University of Florida |
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Mark Davis |
DOE/NREL |
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William Berguson |
NRRI/University of Minnesota in Duluth |
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Agency |
DOE |
3 years |
Project Overview:
Anthropogenic carbon dioxide (CO2) emissions have increased from insignificant levels in the pre-industrial era to over twenty-four billion tons in 2003 (DOE 2004). Carbon sequestration by the “enhancement of the uptake of CO2 by plants” is considered by the Department of Energy (DOE) as desirable tool for reduction of CO2 and other greenhouse gases (DOE 2004). This effort is part of a global strategy for reduction of greenhouse gases, formalized by the ratification of the Kyoto Protocol (UN, 1997). The protocol states that the parties shall “elaborate policies and measures such as protection and enhancement of sinks and reservoirs of greenhouse gases” and “research on, and…development…of carbon dioxide sequestration technologies” (UN, 1997). The completion of shotgun sequencing of the Populus trichocarpa clone Nisqually-1 by DOE’s Joint Genome Institute (JGI) in December of 2003 (Wullschleger et al. 2002; Brunner et al. 2004) created the genomic tools that were essential for the enhancement of CO2 sequestration through biotechnology.
We propose to identify the molecular basis of natural variation in carbon allocation (C translocation from source to sink organs) and partitioning (C distribution into chemical structures) in poplar. Identification of these molecular mechanisms can lead to rational strategies for using genetic approaches to increase terrestrial C sequestration by enhancing C flow into sink organs and chemical forms that are favored for long term storage.
The allocation of carbon from source to sink organs and the partitioning of C-compounds to the various chemical constituents is largely under genetic control in poplar. Methods of quantitative genetic analysis (QTL) have identified genomic regions that regulate carbon allocation and partitioning in poplar and other woody species (Wu et al. 1994; Wu et al. 1998; Sewell et al. 2002; Brown et al. 2003; Kirst et al. 2004; J. Tuskan, personal communication). Quantitative genetic studies demonstrated that these traits are frequently controlled in specific families by few loci with large effects. In spite of unprecedented advances in quantitative genetic methods, the molecular basis of QTLs for most traits remains largely unknown. Now the poplar genome sequence and the novel genomic tools provide new approaches to go from QTL to genes. Integrating traditional quantitative genetic approaches with novel genomics methods made available by the poplar genome sequence creates an unprecedented opportunity to identify and characterize genes, pathways and networks that control carbon allocation and partitioning traits.
In this proposal, will be to merge genetic markers, transcript abundance, and quantitative carbon allocation and partitioning phenotypes, collected from a segregating interspecific Populus pedigree, with the sequence of the Populus genome. We will carry out:
1. Genome-based carbon partitioning and allocation QTL characterization. Quantitative trait loci for carbon partitioning and allocation traits, under limiting and luxuriant nitrogen availability, will be identified and candidate genes underlying these QTLs will be defined based on the genome sequence.
2. Genomic regulation of transcription for carbon allocation/partitioning. Genome sequence will be applied to design and construct a QTL/C-metabolism targeted long oligonucleotide DNA chip, to contrast transcript abundance between progeny sets that inherited alternative alleles for target QTLs.
3. Genome identification of target genes for functional characterization. Differentially regulated genes in target organs, located in the QTL interval (cis-regulated) whose predicted function and expression are correlated with carbon allocation and partitioning will be candidates for direct functional analysis. Genes will be down regulated in transgenic poplars by gene silencing and unregulated with select tissue specific promoters.