U.S. Department of Energy, Office of Science
Poplar Genome Based Research for Carbon Sequestration in Terrestrial Ecosystems
Links of interest:
The DOE Poplar Genome Based Research for Carbon Sequestration in Terrestrial Ecosystems program conducts basic research to obtain scientific understanding to help select, breed, or manage trees to meaningfully enhance long-term biological carbon sequestration in forested ecosystems. Both trees and soils are appropriate targets for long-term carbon storage.
Mechanisms being studied by the program that have the potential to enhance carbon sequestration include:
The program's research builds on the documented genomic sequence of a black cottonwood tree. The program also supports research using genomic sequences of microbes important to carbon cycling in the rhizospheres under trees.
The program is managed by the Office of Biological and Environmental Research (BER), within the DOE Office of Science.
Atmospheric carbon dioxide concentration has been increasing steadily for about two centuries. The chief causes are fossil fuel combustion for energy production and clearing of land for agriculture. The present rate of increase is about 1.8 ppm/year, against a present background of about 380 ppm.
In the future, society may want to slow, or perhaps even stop, the atmospheric carbon dioxide concentration increase because it is a major greenhouse gas contributing to global climatic change (including warming) and sea-level rise. It is therefore important to increase understanding of potential mechanisms, available now or in the future, to slow the rate of atmospheric carbon dioxide concentration increase. For example, DOE is interested in possible uses of trees, such as those in the genus Populus, as vehicles for removing carbon dioxide from the atmosphere and storing the carbon in long-lived and safe forms. To facilitate basic research on this topic, DOE/BER---through the DOE Joint Genome Institute---sequenced the nuclear genome of a female genotype ("Nisqually-1") of black cottonwood (P. trichocarpa Torr. & Gray), eight times over for high quality (see table at left; Tuskan et al. 2003, 2006). This was the first, and presently only, woody plant whose nuclear genome has been sequenced.
The genus Populus (including aspen, poplar, and cottonwood species) has advantages both as a model for basic research and as a potential system for carbon sequestration. It is easily mutated, has facile transgenesis, and is easily cloned. Its physiology is relatively well characterized and it has a relatively small, compact nuclear genome of about 485 Mbases (four times larger than Arabidopsis thaliana but less than 1% the size of red pine). In addition to the full sequence of the nuclear genome of a specific black cottonwood clone, much is known about the genomes of Populus species in general, and extensive genetic tools exist for Populus research, including genetic linkage maps, BAC (bacterial artificial chromosome) libraries, EST (expressed sequence tags) libraries, and QTLs (quantitative trait loci) for mapping of physiological traits in Populus (Yin et al. 2004). Research on Populus genomics is rapidly advancing (Strauss and Martin 2004).
Populus species can be highly productive in many environments, and the genus has a wide ecological range or distribution. For example, one or more Populus species is native to each state except Hawaii, eastern cottonwood (P. deltoides) is native to 43 states, quaking aspen (P. tremuloides) is native to 39 states, and white poplar (P. alba) has been introduced to 45 states (see the Plants Database link to the left). Moreover, Populus trees produce products and services of considerable value to humans in addition to the potential for enhanced carbon storage.
Strauss SH, Martin FM (2004) Poplar genomics comes of age. New Phytologist 164:1-4
Tuskan GA, DiFazio SP, Teichmann T (2003) Poplar genomics is getting popular: the impact of the poplar genome project on tree research. Plant Biology 5:1-3
Tuskan GA, DiFazio SP, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen G-L, Cooper D, Coutinho PM, Couturier J, Covert SF, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, dePamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai C-J, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596-1604
Yin TM, DiFazio SP, Gunter LE, Riemenschneider D, Tuskan GA (2004) Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map. Theoretical and Applied Genetics 109:451-463