Forest Tree Genomics Research Articles

Progress in physiological and genetic research concerning forest tree response to low temperature

Abstract Forest trees are a great model for physiological and genetic studies of plant resistance to unfavourable environmental conditions, since the same species can successfully acclimate at different latitudes. Modern biology, such as genomics, transcriptomics, proteomics, etc., significantly facilitates these studies and accelerates the acquisition of new knowledge. This allows for a more effective implementation of conservation measures and the renewal of forest ecosystems. This review contains information on the latest scientific achievements in the field of acclimatization and tolerance to abiotic stresses, such as cold and frost, of forest trees. There is no doubt that in the course of evolution forest trees developed a complex and dynamic mechanism for controlling the entry into the winter dormancy stage, which allows woody plants to successfully survive in cold and freezing conditions and is initiated long before the beginning of winter. Studying the function of individual genes in forest tree species, however, remains an incredibly difficult task due to large genomes, specific development as well as the lack of standard techniques and routine procedures. In recent years, similarities between the well-studied genetic response to low temperatures of the model plant Arabidopsis thaliana and forest trees have been identified, which produced meaningful analogies and allows for issues of functional genetics to be addressed more effectively. The main goal of this work was to show that findings from forest tree genomics can be effectively used as a tool for the reproduction and protection of important tree species through the identification of the predisposition of specific populations to climate change and their adaptive capacity.

Using CRISPR as a Gene Editing Tool for Validating Adaptive Gene Function in Tree Landscape Genomics

Anthropogenic activities have substantially modified natural forested ecosystems around the world through species exploitation, land-use changes, soil degradation, pollution and introduction of exotic species. The impacts of these activities are being exacerbated today by climate change that is expected to become more severe over the coming decades. Modern landscape genomics has made advances in identifying genes that are associated with phenotypic expression, but they have been unable to prove that the associations are more than correlative. The threats to biological diversity raised by climate change, underscore the need to have an improved understanding of the genetic basis of phenotypic traits. In sedentary, long-lived tree species this becomes of utmost importance, as the success of populations is likely to depend, in large part, on existing standing genetic variation. The most recent technologies of gene editing (CRISPR/Cas9) promise to be an elegant approach that will move forest tree genomics to the next level, by allowing the rigorous testing of gene function and its role in the adaptation of trees to their environment. This perspectives paper looks at how genome editing technologies can be used to advance our understanding of the role genes play in adaptation to climate change in woody plants. We discuss the different CRISPR modes than can be used in studies of adaptive traits in perennial species.

Forest tree genomics: 10 achievements from the past 10 years and future prospects

Key message This review highlights some of the discoveries and applications made possible by “omics” technologies over the last 10 years and provides perspectives for pioneering research to increase our understanding of tree biology.

Sprucing up forest tree genomics

Sprucing up forest tree genomics

IUFRO Tree Biotechnology 2011: "From genomes to integration and delivery"

Forest trees have unquestionably entered the genomic era. The updated version of the Populus genome, the recently released Eucalyptus grandis genome and the concerted efforts towards the generation of genome sequences for spruces (Picea sp.) and pines (Pinus sp.) by several groups worldwide, are fueling a multitude of inter-disciplinary studies and applications in sustainable forest production and conservation. Time now calls for the integration of scientific fields with an increased sense of urgency for delivery of effective biotechnologies. The IUFRO (International Union of Forestry Research Organizations) Tree Biotechnology biannual conference has established a solid tradition for over 20 years as the official meeting of the IUFRO working group 2.04.06 – Molecular biology of forest trees. This conference has convened scientists and foresters interested in the genetics, genomics, molecular biology and physiology of forest trees, and the application of this knowledge to tree improvement and conservation. The Tree Biotechnology Conference has undoubtedly been the premiere international forum where the most cutting edge research in tree biotechnology developed both in academia and industry is presented. “From genomes to integration and delivery”, this was the theme chosen for the 2011 edition of the IUFRO Tree Biotechnology Conference, first time to be held in South America. Our intention was to promote a more integrated and applied dialogue on tree biotechnology and genomics, beyond the mainstream discussion of the fundamental advances on the genetic mechanisms that underlie tree phenotypes. In nine scientific sessions some of the current advances of genomics applied to forest conservation, tree physiology, stress response, molecular breeding, in vitro and propagation technologies, wood development and genetically modified (GM) trees were highlighted. With 340 registered participants, the Conference brought to Brazil most of the world’s brain power in forest tree genomics and biotechnology. An outstanding team of international scientists shared their results and visions on the present and future of this fast moving area of forest science, while a brilliant group of young scientist and students delivered a very energetic and diverse collection of high-quality scientific presentations. Forty two countries were represented at the Conference with almost 100 different laboratories from tens of Universities, research institutions and private companies. During the seven days of the Conference 26 invited lectures, 63 oral and 185 poster presentations were delivered, totaling 274 papers made available as extended abstracts into this BMC Proceedings supplement. The special workshop on the hot topic of “Genomic Selection in tree breeding” and the several reports on whole-genome studies, made this conference edition inaugurate a deliberate effort towards a better integration between the quantitative genomics, the “single-gene” and the system biology approaches to more efficiently unravel the complex relationships between genotypes and phenotypes in forest trees. A field trip to the forest plantations, nurseries and mill of VERACEL Cellulose was a definite highlight and a welcome break from the scientific sessions, providing an overview of some of the advances and challenges facing the translation of research into plantation forestry. In closing this introductory statement, acknowledgements are due to the outstanding financial support provided by the competitive grants of the Brazilian Ministry of Science and Technology through the National Research Council (CNPq) and the Ministry of Education through its agency for graduate studies (CAPES). Major support was also provided by EMBRAPA (Brazilian Corporation of Agricultural Research), and VERACEL Cellulose, the host organizations, together with an exceptional suite of private sponsors. Besides the organizations that backed this conference and an active Scientific Committee involved in abstract review a number of people were involved in the organization and logistics. The conference would not have been possible without the valuable contributions of all these players. Given the rewarding feedback received after the Conference, the original goal of providing an exceptional mix of science, social activities and field exploration in a relaxed atmosphere was truly accomplished. The IUFRO Tree Biotechnology Conference 2011 made a significant contribution to advance the forest biotechnology research community one step ahead on the challenging task of moving from gene and genome discoveries to the delivery of valuable technologies into sustainable forestry.

The Eucalyptus grandisGenome Project: Genome and transcriptome resources for comparative analysis of woody plant biology

Background The International Year of Forests 2011 [http://www. un.org/en/events/iyof2011/] will be a milestone for forest tree genomics. The draft genome sequence of Eucalyptus grandis was released in January 2011 in the USA (Phytozome [http://www.phytozome.net]) and in Belgium (BOGAS, [http://bioinformatics.psb.ugent.be/webtools/bogas/]). The genome sequencing was funded by the US Department of Energy (DOE) and performed at the DOE Joint Genome Institute (JGI) in collaboration with members of the Eucalyptus Genome Network (EUCAGEN, [http://www.eucagen.org]) who contributed genetic materials, linkage maps, EST resources and bioinformatics support. The E. grandis genome together with that of Populus trichocarpa[1]and other woody plant genomes recently completed (e.g. Vitis, Cacao, Prunus, Citrus and Malus)will provide excellent opportunities for comparative studies of the unique biology of woody plants. Eucalypts are currently the most widely grown hardwood fibre crop in the world and eucalypt breeding programs will benefit greatly from the new genomic resources. The reference genome sequence of Eucalyptus, a foundation tree genus in Australia comprising more than 70% of the native forest estate, will also offer important benefits for ecological and evolutionary biology studies. We report the sequencing, assembly and annotation of the E. grandis genome. Genome sequencing and assembly Whole-genome (8X) shotgun sequencing was performed for a partially inbred (S1), 17-year-old tree of E. grandis (est. genome size 640 Mbp, n = 11), BRASUZ1 (Suzano, Brazil). A total of 7.7 million Sanger reads (5.4 Gbp) were produced from plasmid, fosmid and BAC libraries. An inbred genotype was selected to circumvent perceived problems with the assembly of a highly heterozygous eucalypt genome. However, microsatellite genotyping showed that BRASUZ1 was much less homozygous than expected, with large parts of the genome remaining heterozygous presumably due to viability selection. This finding was confirmed during the assembly of the S1 genome approximately 25% of the assembly occurred in two haplotypes of 3-4X coverage, while the remainder of the genome assembled into a single haplotype of 6-7X coverage. Linkage maps with over 2400 DArT and microsatellite markers were subsequently used as a framework for the assembly of 11 large chromosome scaffolds. The chromosome scaffolds contained 88% (605 Mbp) of the draft assembly, with the remainder of the assembly sequence (85 Mbp) in 4941 smaller scaffolds. Based on similarity searches with 1.6 million ESTs from BRASUZ1, it was estimated that 96% of expressed gene loci were included in the 11 chromosome assemblies.

Forest tree genomics: growing resources and applications

Over the past two decades, research in forest tree genomics has lagged behind that of model and agricultural systems. However, genomic research in forest trees is poised to enter into an important and productive phase owing to the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees and the need to mitigate the effects of climate change. Research on long-lived woody perennials is extending our molecular knowledge of complex life histories and adaptations to the environment - enriching a field that has traditionally drawn biological inference from a few short-lived herbaceous species.

TreeGenes: A Forest Tree Genome Database

The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the Pinaceae family. The primary data types curated include species, publications, tree and DNA extraction information, genetic maps, molecular markers, ESTs, genotypic, and phenotypic data. There are currently ten main search modules or user access points within this PostgreSQL database. These access points allow users to navigate logically through the related data types. The goals of the Dendrome Project are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species, (2) develop interfaces that encourage the submission and integration of all genomic data, and to (3) centralize and distribute existing and novel online tools for the research community that both support and ease analysis. Recent developments have focused on increasing data content, functional annotations, data retrieval, and visualization tools. TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange.

Transcriptome Analysis of Ozone-Responsive Genes in Leaves of European Beech (Fagus sylvatica L.)

Suppression subtractive hybridization (SSH) was performed to isolate cDNAs representing genes that are differentially expressed in leaves of Fagus sylvatica upon ozone exposure. 1248 expressed sequence tags (ESTs) were obtained from 2 subtractive libraries containing early and late ozone-responsive genes. Sequences of 1139 clones (91 %) matched the EBI/NCBI database entries. For 578 clones, no putative function could be assigned. Most abundant transcripts were O-methyltransferases, representing 7 % of all sequenced clones. ESTs were organized into 12 functional categories according to the MIPS database. Among them, 12 % (early)/15 % (late) were associated with disease and defence, 19/11 % with cell structure, 4/10 % with signal transduction, and 9/6 % with transcription. The expression pattern of selected ESTs (ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit [rbcS], WRKY-type transcription factor, ultraviolet-B-repressible protein, aquaporine, glutathione S-transferase, catalase, caffeic acid O-methyltransferase, and pathogenesis-related protein 1 [PR1]) was analysed by quantitative real-time RT-PCR (qRT-PCR) which confirmed changed transcript levels upon ozone treatment of European beech saplings. The ESTs characterized will contribute to a better understanding of forest tree genomics and also to a comparison of ozone-responsive genes in woody and herbaceous plants.

Analysis of 70,000 EST sequences to study divergence between two closely related Populus species

The Populus genus has evolved as the model organism for forest tree genomics, which has been further emphasised with the sequencing of the Populus trichocarpa genome. Populus species are widely spread over the Northern Hemisphere and provide a great source of genetic diversity, which can be used for mapping of quantitative trait loci, positional cloning, association mapping and studies in environmental adaptation. Collections of expressed sequence tags (ESTs) are rich sources in studies of genetic diversity. Here, we report on an in-depth analysis of 70,000 ESTs from two Populus species, Populus tremula and Populus trichocarpa. We present data on the level of conservation in transcript sequences and supply a collection of potential single nucleotide polymorphisms.

Advances in forest tree genomics

Advances in forest tree genomics

Cryopreservation in Populus functional genomics.

The release of the first tree genome sequence for Populus tricocarpa, along with continuing rapid development of Populus EST, microarray and metabolomic technologies, promises to advance forest tree genomics. High throughput transformation by knockout or other gene manipulation strategies to generate large numbers of transgenic Populus for functional elucidation of the estimated 36000 genes will soon follow. The efficacy of large-scale transformation approaches for advancing Populus genomics will ultimately depend on the availability of properly maintained transgenic germ lines for distribution. The Arabidopsis community has already demonstrated the value of shared genetic resources, especially mutant and transgenic seed stocks, in functional genomics research. Seed bank will not work for the Populus research community. Instead, a stock distribution center for transgenic Populus research will have to be based on long-term preservation of clonal germplasm. This review presents recent progress in applying cryogenic techniques for clonal preservation of long-lived trees and discusses the challenges facing Populus molecular geneticists in germplasm preservation.