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Genomic Science Program

Systems Biology for Energy and the Environment

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Genomic Science Program

2014 Awardee

A Novel Poplar Biomass Germplasm Resource for Functional Genomics and Breeding

INVESTIGATORS: Luca Comai (PI), Andrew Groover, Isabelle Henry

INSTITUTIONS: University of California Davis, US Forest Service

PROJECT SUMMARY: Interspecific hybridization is the most effective method for producing poplar clones for commercial applications, including biomass production. Previous research has shown that commercial F1 hybrids frequently exhibit dosage variation, i.e. variation in the number of pieces or entire chromosomes, and that these variants can have transgressive phenotypes desirable for biomass production. Poplar is an excellent system for studying and exploiting gene dosage because germplasm is propagated vegetatively for research and production, and advanced genome-enabled tools can be directly employed on the actual feedstock. In the previous funding cycle, we have produced and characterized a population of interspecific hybrids carrying insertions and deletions, which together, tile the entire genome with dosage variation. In this proposal, we will complete the development of this unique resource for the research community and use the germplasm to investigate the role of gene dosage in poplar hybrid performance, and to identify chromosomal regions and genes that contribute to poplar bioenergy traits. Our specific objectives are as follows:

Create and maintain a resource for poplar feedstock functional genomics: We will use next-generation sequencing and bioinformatics pipelines already developed in the previous funding period to catalog dosage variation in ~500 additional and already available P. deltoides x P. nigra F1 individuals and identify the smallest set of lines with the highest information content. We will make germplasm and sequence data available to the research community without IP restrictions.

Investigate the phenotypic effects of dosage change: We will use field trials to characterize variation for traits central to sustainable production of biomass with optimal feedstock properties. We will document correlations between trait values and copy number along each chromosome to associate particular traits with chromosomal regions.

Exploit the indel germplasm for functional genomics: First at genome resolution, then more in depth on specific indel regions, we will describe and analyze dosage-dependent regulation, identify gene modules and candidate genes that influence traits of interest.

Outputs will include a population of interspecific hybrid of poplar carrying well defined dosage variation that spans the majority of the poplar genome at least once, and extensively characterized trait measurements. Additionally, we will identify specific regulatory or functional gene modules underlying phenotypes of interest. Finally, because our dosage variants were produced in a hybrid type that is of interest to the poplar industry, it is possible that our germplasm collection already includes new cultivars directly usable for bioenergy applications. Importantly, the approaches we describe here can be generalized to other poplar hybrid combinations and to germplasm development for other vegetatively-propagated species. Our efforts will add new, useful and unique tools that have both functional and practical applications for poplar breeding and is widely applicable to other biomass crops such as switchgrass, alfalfa, willow, and Miscanthus.

Name: Comai, Luca
Phone: 530-752-8485


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]
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  • 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 »
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