Forest trees are the dominant life form in many ecosystems and contain greater than 90% of the Earth’s terrestrial biomass. Managed and unmanaged forests throughout the United States, and indeed the world, provide recreational and environmental benefits such as carbon sequestration, renewable energy supplies, watershed protection, improved air quality, biodiversity and habitat for endangered species. However, despite the importance of forest trees for natural ecosystems and the world economy, little is known about the biology of forest trees in comparison with the detailed information available for crop plants and model organisms such as Arabidopsis. As a result, the forest science community would derive much benefit from a comprehensive genomics research program, because traditional genetic approaches in forestry are limited by the large size, long generation interval, and outcrossing mating system of most trees. It is, therefore, of considerable importance that a forest tree genome be sequenced, so that forest tree biologists will have the necessary resources to begin a large scale, thorough analysis of genes that produce traits useful in the pursuit of basic science questions, to foster the development of improved plant materials for the forest products industry, and to ultimately select novel phenotypes that could be used to address questions related to the energy-related mission of the Department of Energy.

The genus Populus (including poplars, cottonwoods and aspens) is especially well suited to serve as the model genome for trees because of the following reasons:

• Small genome size; the haploid genome size of Populus is only ca. 550 Mbp, similar to rice, only 4X larger than Arabidopsis and 40X smaller than pine.

• 30⁺ species worldwide; all are diploids (2n = 38) that can be easily crossed, hybrids are fertile and advanced generation pedigrees are available.

• Rapid juvenile growth, allowing meaningful measures of important traits to be taken within a few years after establishment of genetic trials.

• Ease of clonal propagation, allowing manipulations to be evaluated across common genetic backgrounds, destructive sampling (e.g., wood quality assessment) without loss of the genotype, replication of experiments across time and space, and genetic stocks to be archived in clonal nurseries to be shared with researchers around the world.

• High-throughput transformation and regeneration; transgenic trees can be produced allowing detection and characterization of gene function. Populus is unique among tree genera in this regard.

• Extensive genetic maps have been constructed in Populus, including the initial identification of QTLs (i.e., DNA markers associated with) a wide variety of traits.

• Existing collaborative network of scientists around the world who have used poplars as a model organism to study forest tree morphology, physiology, biochemistry, ecology, genetics, and molecular biology.

It was felt that before the forest science community could proceed to solicit the political support necessary to begin a poplar genome sequencing project, it would be vital that forest tree biologists express their enthusiasm for such a project. So far, over 70 scientists have indicated via the website that they acknowledge that a poplar genome sequencing effort should be a top priority of forest genomics research and have expressed their desire to see this activity proceed as quickly as possible toward the ultimate goal of determining the complete sequence of the Populus genome.

The genus Populus, one of two genera in the Family Salicaceae, first occurred in the fossil record around 56 m.y.b.p. Today, the genus consists of five sections, 30 to 40 species and is circumpolar in the Northern Hemisphere. There are approximately eight species indigenous to North America, with four of those having commercial importance. All members of the Populus genus have a genome contained on 19 nearly identical, metacentric chromosomes, a nuclear content of 2C = 1.2 pg and an estimated genetic map length of ca. 2500 cM. The majority of the species are constitutively dioecious, having male and female members of a species. Interspecific hybridization is readily achievable among members within a single section and among members of certain alternate sections. Selection and hybridization began among the aspens in the middle 1950s, followed by selection and breeding in cottonwoods in the 1960s. Heterosis or hybrid vigor is common among interspecific hybrids. Relatively large multi-generation pedigrees exist for those species and their hybrids that have commercial value.

The most commonly produced pedigrees are from P. trichocarpa x P. deltoides, P. deltoides x P. nigra, P. grandidentata x P. alba and P. tremuloides x P. tremula. These species provide a logical choice for a genome sequencing effort. The largest F₁ pedigree [2000⁺ progeny] is between a P. trichocarpa female ‘383-2499' and a P. deltoides male ‘ILL129'. The female, ‘383-2499', has provided the nuclear DNA for the construction of a 10x BAC library that has been distributed around the world. This BAC library was originally constructed by scientists at Texas A&M University. Furthermore, more than 150 simple sequence repeats (SSRs) have been 1) identified from this female, are retrievable from:

and 2) placed on a genetic map. In addition, eight of the BACs have been partially sequenced using shotgun cloning approach. Approximately 1.5 Mb of P. trichocarpa ‘93-968' total genomic DNA has been sequenced from shotgun cloning experiments and SSRs occur about once in every 1 kb; the length and the form of the SSRs vary greatly. There is a 5000⁺ xylem-specific P. tremula x P. tremuloides ESTs available from:

Preliminary efforts to clones genes from alternate genotypes suggest that homology is high among all members of the genus [90%⁺] and that Populus contains multiple, typically two, copies of single genes found in other plant species such as Arabidopsis. As such, we recommend that the female clone ‘383-2499' be used in the genomic sequence effort for all Populus. This P. trichocarpa or black cottonwood female was originally collected along the Nisqually River in Washington, and is replicated in field and nursery plantings presently maintained by Dr. Toby Bradshaw and colleagues, University of Washington and Washington State University.

Once a draft sequence is available for the Populus genome, steps would be taken to annotate the completed genome. This work would be done in collaboration with JGI and ORNL, with the participation of the forest genetics community. We are fortunate to have access to Dendrome, a web-based collection of forest tree genome databases and other forest genetic information resources for the international forest genetics community.

Dendrome is a project of the Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service. It is part of a larger collaborative effort to construct genome databases for major crop and forest species, and the USDA-ARS Center for Bioinformatics at Cornell University, New York maintains this collection of crop databases as part of their ARS Genome Database Resource.

The primary genome database of Dendrome is called TreeGenes. TreeGenes is a database that includes genetic map, DNA sequence, germplasm, and other related information for a large number of forest tree species, including Populus. These same data can also be found at the Dendrome server under Genome Resources or at the USDA-ARS Center for Bioinformatics and Comparative Genomics.