Conifer genomes present challenges for successful sequencing, mainly due to their large size and complexity. To address these challenges, we have assembled a research team with the requisite expertise and experience having elicited and productively used prior federal support for research on loblolly pine genetic diversity, development of conifer genetic and genomic resources, development of molecular markers for complex traits, development of the bioinformatics and database infrastructure used by a majority of conifer genetics researchers today, development and extension of marker-informed conifer breeding, and development of many of the bioinformatics data display, analysis, and storage software and algorithms in use today.
Development of a high quality reference genome sequence for loblolly pine, Douglas-fir and sugar pine by means that can serve as a model approach for sequencing other large, complex genomes and empower the forest tree biology research community and the broader biological research community in the practical use and application of this resource.
- High-quality reference genome sequences of loblolly pine, Douglas-fir and sugar pine
- Transcriptome sequencing for gene discovery, reference building, and aids to genome assembly
- Dendrome and TreeGenes databases: Annotation, data integration, and distribution
Impact and Outcomes
- EMPOWERMENT. Our goal is to develop the technologies, platforms and bioinformatics infrastructures to rapidly and inexpensively sequence large and complex genomes of coniferous forest trees. This will allow the forestry community to begin sequencing the many genomes of economic and ecological importance without a dependence on centralized genome centers.
- ADAPTIVE. We recognize the sequencing technologies are developing rapidly and that we must have the expertise and flexibility to rapidly adopt new approaches into our overall sequencing strategy.
- COMPARATIVE. We recognize the power of comparative genomics approaches in assembling and annotating genome sequences and will use this approach throughout the project.
- OPEN ACCESS. We have a policy of sharing all data generated from this project with the research community
Our project will achieve broad community empowerment through the development of a reference conifer genome sequence. Short-term impacts include facilitating genomic-based breeding for wood products and energy, developing diagnostic tools to estimate risk and impacts caused by changing environments, and facilitating genome sequencing in other conifers. Additional outcomes and longer-term impacts include more complete integration of forest and horticultural tree genome projects and integration with other areas of tree biology (e.g., via the NSF iPlant Tree Biology Cyberinfrastructure initiative
- USDA FS: Douglas-fir Transcriptome Observatory for the Pacific Northwest
Richard Cronn, USFS PNWRS, Corvallis OR
- USDA FS: Sugar pine transcriptome project
Jessica Wright, USFS PSWRS, Davis CA
- Sweden: Norway Spruce Genome Project
Par Ingvarsson, Umea Plant Science Centre
- Canada: SMarTForest: Spruce Marker Technologies for Sustainable Forestry
Kermit Ritland, University of British Columbia, Vancouver BC
- Canada: AdapTree: Assessing the Adaptive Portfolio of Reforestation Stocks for Future Climates, Genome Canada
Sally Aitken, University of British Columbia, Vancouver BC
- Europe: ProCoGen
Carmen Diaz-Sala, University of Alcala, Madrid, Spain
Maria-Teresa Cevera, INIA-CIFOR, Madrid, Spain
- Russia: Siberian Conifer Genome Project
Siberian Federal University, Krasnoyarsk 660036, Russia
Funding for the Loblolly Pine Genome Project is provided by: USDA/NIFA #2011-67009-30030