Perennial challenges and opportunities

The remarkable expansion of tree genomics resources over recent years has now culminated in the release and publication of the first annotated tree genome, that of a poplar tree (Populus spp.) from the Pacific North-West of the USA (Tuskan et al., 2006). The increased interest and investment in tree genomics research is not coincidental. The importance of tree biotechnology for understanding ecosystems at various levels of organization, offsetting carbon emissions via long-term carbon sequestration, and providing sources of renewable and recyclable bioenergy are now well recognized and appreciated. The biennial International Union of Forest Research Organizations (IUFRO) Tree Biotechnology meeting (http://www.unl.pt/unl/eventos/reitoria/iufo-tree-biotechnology-2007) gathered a diverse community of scientists poised to face the new research challenges. ‘... loss of biodiversity in keystone species as a result of climate change or human activity could lead to extinction of hundreds of dependent microbial and/or insect species.’ Perennial species are subject to life-long continua of biotic and abiotic stresses that will be faced under the cloud of potentially consequential climatic and atmospheric change in the near future. Molecular dissection of stress responses in forest trees is thus of significant economic as well as ecological relevance to long-term forest health, plantation and ecosystem productivity, and biodiversity. One pressing threat is the large-scale outbreak of mountain pine beetle (Dendroctonus ponderosae) in western North American pine forests, from Canada to Mexico (Mock et al., 2007). The epidemic is projected to destroy over half of the merchantable pine in the central and southern interior of British Columbia by the end of this summer (http://www.for.gov.bc.ca). As part of a concerted effort to cope with this catastrophic natural disaster, Natalia Kolosova (University of British Columbia, Canada) presented functional genomics approaches undertaken in the Treenomix (http://www.treenomix.ca) project to decipher natural defense and resistance mechanisms of conifers. Microarray analyses revealed common as well as specific transcriptomic responses by hybrid spruce (Picea glauca × engelmannii) and lodgepole pine (Pinus contorta) to fungus inoculation, and by spruce to insect challenge. Phenylpropanoid and terpenoid pathway genes were among the most strongly up-regulated in all interactions, consistent with the involvement of some of these genes in conifer defense against insects and bark beetle-vectored fungal pathogens (Keeling & Bohlmann, 2006; Ralph et al., 2006). Responses to multiple, simultaneous stresses, such as drought and mechanical bending (Gilles Pilate, INRA, France), as well as metabolic costs of defense (Chung-Jui Tsai, Michigan Technological University, USA) in Populus are also being dissected using functional genomics approaches. A familiar yet stimulating perspective on the cornerstone importance of genetics in forest-dominated ecosystems was presented by Thomas Whitham (Northern Arizona University, USA). He summarized over 20 yr of research on genetic variation, multitrophic interactions and environmental stresses in cottonwood (Populus fremontii, Populus angustifolia and their hybrids) riparian communities and ecosystems. Ecological fitness traits, such as foliar chemistry, and their underlying quantitative trait loci (QTL) affect not only primary productivity but also plant–herbivore interactions, decomposition and nutrient cycling. The consequences for dependent communities and associated ecosystems comprise ‘extended phenotypes’ (Whitham et al., 2003). Thus, loss of biodiversity in keystone species as a result of hundreds of dependent microbial and/or insect species (Whitham et al., 2006). Genetic diversity of foundation species therefore warrants consideration in habitat restoration, as well as in clonal forestry with conventionally bred or genetically modified varieties. The prospect of broadening community and ecosystem genetics research to the genomics scale brought about by the nearly completed poplar genome sequence (Tuskan et al., 2006), the ever-growing number of sequenced microbial genomes (Martin et al., 2004; http://www.ncbi.nlm.nih.gov) and advanced genomics technologies will encourage more cross-talk between ecological and molecular research. One of the defining features of trees as a life form is the extravagant and perennial secondary growth resulting in production of wood. Because wood is a valuable and renewable commodity, modification of wood properties has been the focus of intensive research for years. In addition to its utilization in the more conventional structural lumber and paper industries, woody lignocellulosic biomass is now of great interest as a feedstock for the bioenergy sector. Because of its dominant role in shaping wood physicochemical properties, lignin has long been the focus of intensive research. As reviewed by Wout Boerjan (University of Ghent, Belgium), research on lignin biosynthesis and transgenic modification has already demonstrated the feasibility of engineering trees with altered lignin quantity and composition. Although these modifications were originally targeted to improving pulping efficiency, many of the advances are readily applicable to improving wood bioenthanol conversion (Himmel et al., 2007). An ambitious systematic investigation of genes expressed during secondary growth has been initiated in Sweden using the model tree taxon Populus. Björn Sundberg (Swedish University of Agricultural Sciences, Sweden) presented the FuncFiber project (http://www.funcfiber.se/), a multidisciplinary and multi-institutional effort aiming to isolate genes that affect important commercial wood properties in trees. The project builds on extensive transcription profiling of differentiating xylem using thin cryogenic sectioning (Hertzberg et al., 2001; Schrader et al., 2004). A combination of anatomical and chemical phenotyping approaches, including Fourier transform infrared (FTIR) imaging, nuclear magnetic resonance (NMR), pyrolysis mass spectroscopy and chemometrics, was used to identify more than 30 transgenic lines with altered wood properties for in-depth characterization. Several presentations and posters from the Arborea project (http://www.arborea.ulaval.ca) reported on identification of regulators of wood formation in spruce. Groups of regulatory genes isolated via expressed sequence tag (EST) sequencing and microarray analysis are being tested in transgenic plants for roles in the regulation of various wood properties. Modifications resulting in phenotypic responses are further intensively studied by microarray analysis for identification of suites of candidate genes that regulate the traits of interest. The genomics resources in species of commercial importance are rapidly expanding. Zander Myburg (University of Pretoria, South Africa) announced at the meeting that the Eucalyptus genome has been approved for sequencing by the Joint Genome Institute's (JGI, http://www.jgi.doe.gov/CSP), Community Sequencing Program because of its value as a woody energy crop. New sequencing technologies are promising to rapidly expand our knowledge of the organization of megagenomes such as that of gymnosperm conifers and to assist in the annotation and assembly of the Eucalyptus genome. Comparative genomics approaches have been tremendously enabled in recent years by the development of tree genomic resources. Investigations in Arabidopsis are revealing new insights into the function of transcription factors such as the no apical meristem, ATAF, cup-shaped cotyledon (NAC) domain proteins during vascular differentiation (Masatoshi Yamaguchi, RIKEN, Japan), into the roles of specific classes of peroxidases during lignin polymerization (Lise Jouanin, INRA, France), and into the differential roles of phenylpropanoid biosynthetic enzymes in reproductive biology (Carl Douglass, University of British Columbia, Canada). Detailed analysis of gene family structure combined with comparative expression analysis will lead to better hypotheses for identification and functional analysis of the orthologs in tree species. Tools are being developed for gene to wood trait associations circumventing some of the traditional difficulties associated with genetic studies in trees (long generation cycles, long times to expression of commercially important traits, large size, etc.). Results from a technique called ‘induced somatic sector analysis’ (ISSN) were presented by Gerd Bossinger (University of Melbourne, Australia) and in several related presentations and posters from the same group. ISSN creates transgenic somatic wood sectors transformed with candidate genes with putative roles in xylogenesis. Comparison of the sectors with untransformed neighboring wood sectors offers a new dimension in assessing gene effects on wood formation. Development of biotechnological products is a lengthy and expensive process. Are biotechnological innovations of wood properties economically justifiable? A case study presented by Gary Peter (University of Florida, USA) quantified the potential economic value of biotechnology for the forest products industry. Multidimensional cash flow modeling showed that genetic improvements of growth and wood properties in loblolly pine have the potential to improve the profit margin of an integrated kraft pulp and linerboard mill by 5–50% under conservative scenarios (Peter et al., 2007). Vegetative bud dormancy is another perennial trait unique to trees from temperate, boreal, and subtropical climates. Bud formation and associated signaling and physiological events represent developmental programing that allows trees to cope with freezing and dehydration stress during winter months. This process is not available in annual plants and can only be molecularly dissected in trees. An improved understanding of the genes that control dormancy could provide new tools for assessment, molecular breeding, and genetic engineering of dormancy characteristics. One significant message this year was the involvement of circadian clock machinery in regulation of the dormancy cycle. Presentations from Maria Eriksson (Swedish University of Agricultural Sciences, Sweden) and Isabel Allona (Polytechnic University of Madrid, Spain) point to involvement of LATE ELONGATED HYPOCOTYL (LHY) and TIMING OF CAB EXPRESSION 1 (TOC1) in poplar and chestnut (Castanea spp.) bud set and possibly in other stages of dormancy. Transgenics with RNAi down-regulation of poplar ortholog PttLHY under short days stopped growth later and under long days resumed growth earlier. In chestnut, both CsTOC1 and CsLHY orthologs show diurnal cycling similar to that found in Arabidopsis during active growth. However, their diurnal oscillation is disrupted during winter months and under low temperatures, suggesting a unique regulation of the circadian clock in trees associated with vegetative bud dormancy and cold acclimation (Ramos et al., 2005). It appears that these oscillators might receive input from phytochrome receptors such as PHYTOCHROME A and the response mediated by the CONSTANS/FLOWERING LOCUS T gene module (Bohlenius et al., 2006). These findings suggest that vegetative bud dormancy may employ similar signaling cascades as the short-day-induced flowering in Arabidopsis. An integrated approach involving transcription, metabolic profiling and QTL genetic analysis was presented by Antje Rohde (University of Ghent, Belgium). A number of candidate genes isolated from transcription profiling will be subjected to association studies with several dormancy-related traits. Integration of the QTL and physical genetic map in poplar is underway for identification of dormancy-associated genes. Studies in spruce bud burst seem to challenge our traditional view of slow evolutionary changes in response to changing environment. The presentation by Oystein Johnson (Norwegian Forest and Landscape Institute, Norway) and related posters showed that temperatures during embryo development have extended, multiyear effects on the phenological characteristics of the resulting progeny. Zygotes developed at warmer than normal temperatures produced plants that had delayed bud set, and vice versa. It appears that this might be associated with epigenetic changes induced by the warmer temperatures, and studies are underway to identify the targeted genes. Acceleration of the slow pace of conventional tree improvement using marker-assisted selection has been discussed for a long time. David Neale (University of California-Davis, USA) presented candidate gene-based association approaches for dissection of complex traits, such as disease resistance, stress tolerance and wood properties, in conifers. With current genomic technologies, it is now possible and cost-effective to resequence large numbers of candidate genes for single nucleotide polymorphism (SNP) discovery and large-scale genotyping. SNPs exhibiting strong genetic associations with wood property traits in loblolly pine (Pinus taeda) include allelic variations of key lignin biosynthetic genes (e.g. cinnamoyl CoA reductase and 4-coumarate:CoA ligase), supporting the effectiveness of the approach (Gonzalez-Martinez et al., 2007). Expansion of the loblolly pine program to SNP genotype all commercial clones (c. 50 000 SNPs in 10 000 trees), along with similar efforts for white spruce (Picea glauca) in the Arborea project (Janice Cooke, University of Alberta, Canada), will provide unprecedented resources to advance conifer biology and breeding. A synergistic EST sequencing project for pines and other conifers, led by Jeffrey Dean (University of Georgia, USA) and sponsored by JGI's Community Sequencing Program, promises to more than triple the number of publicly available ESTs from loblolly pine, and facilitate SNP discovery. It will soon become clear if the long-awaited promise of marker-assisted breeding for long-lived forest trees may finally become reality. Tree biotechnology research is becoming more diversified, transecting levels of organization ranging from community and ecosystem studies to cellular and subcellular biology. Novel systems biology approaches are needed to capture, interpret and use this information. Foundations enabling such holistic approaches are already being laid out. The mere fact that scientists of such diverse backgrounds can meet and find common language and interest is very promising. What better focal point for systems biology than trees? Biomass-dominant trees are a driving force of ecosystem dynamics and promise to be in the driver's seat toward a more energy-sustainable, cleaner economic future. The prospect of channeling tree biomass into renewable and carbon-neutral biofuels is a motivation and a serious challenge. Finding solutions for these challenges can put tree biotechnology research on the map of the most significant scientific endeavors and accomplishments. Special thanks to Margarida Oliveira and Cristina Marques for organizing the meeting and to Scott Harding for his comments on this report.

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