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Sowing the seeds of more genetically advanced conifer breeding

While classical breeding has been used for decades to improve tree characteristics and accelerate their growth, a better understanding of their adaptive response genetics is necessary for enabling breeding programmes to cope with climate change. An EU-funded project has collaborated with scientists from across the world to create the tools and data needed.

As the largest, tallest and longest living non-clonal terrestrial organisms on Earth, conifers have immense ecological importance, dominating many terrestrial landscapes and representing the largest terrestrial carbon sink. They are of great economic importance, as they are key to the production of timber, paper and biomass. But first and foremost, the fact that their genome has diverged from that of angiosperms over 300 million years ago means that they provide a different view of plant genome biology and evolution. Some 30 % of conifer genes have little or no sequence similarity with plant genes of known function, and they have developed very efficient physiological adaptation systems. With this tremendous value in mind, the team from the PROCOGEN project (Promoting a functional and comparative understanding of the conifer genome — implementing applied aspects for more productive and adapted forests) focused on bringing breeding programmes started 50 to 70 years ago to a whole new level, by addressing the genome sequencing of two keystone European conifer species. PROCOGEN specifically addresses the genome sequencing of Scot’s pine and Maritime pine. Why this choice? Carmen Diaz-Sala / Maria Teresa Cervera: PROCOGEN provides information about the genome sequences of Pinus pinaster and Pinus sylvestris. These are two European pine species of important ecological and economical value, with contrasting geographical distribution and adaptive capacities. During the project, we analysed the molecular control of the adaptation processes in different European model conifer species that have developed adaptive mechanisms, such as those related to growth in changing environments, as well as responses to drought stress (Pinus pinaster) and cold acclimation (Pinus sylvestris as well as Picea abies). What would you say are other important goals you achieved during the project? One of the main goals of this project was to establish collaborations with other worldwide initiatives on conifer genomics, so as to be able to increase our knowledge about conifer genome structure, function and evolution. This collaboration effort has been facilitated by the participation of PROCOGEN members in different conifer genome sequencing and characterisation initiatives. Comparative studies based on genomics and transcriptomics provided us with information on unique features of conifer genomes. They allowed us to identify gene families with differentially expanded gymnosperms and angiosperms, to infer a slower evolutionary rate in conifers using ‘Conserved orthologous set’ (COS) markers, as well as to analyse the role of gene expression and natural selection in shaping the evolution of protein-coding genes belonging to conifer gene families (genes related to reproductive biology, stress-related genes, etc.). Additionally, the results of the comparative genetic mapping helped us to reassess the static view of conifer genome evolution, which was inferred essentially from comparisons of Pinaceae species. These results support a new hypothesis of substantial chromosome rearrangements between conifer families: through a different number of fusions, these rearrangements would have shaped the 12 chromosomes of modern Pinaceae species and the 11 chromosomes of modern Cupressaceae species. You mentioned international cooperation. Can you tell us more about the other projects you linked up with and their added value for your research? PROCOGEN linked up with EC-funded projects such as EVOLTREE, NOVELTREE, TREEBREEDEX and FORESTTRAC, as well as other projects on conifer genetics, genomics, breeding and forest management. This quest for synergies also led us to North America and Canada, where other similar projects are ongoing. This cooperation brought benefits at both ends. PROCOGEN gained precious information about conifer breeding populations and experimental trials, research needs, practical issues and challenges related to the implementation of forest tree gene conservation. This collaborative work helped us to identify candidate genes contributing to economically and ecologically important traits. Once we had integrated this information, we provided new reference pine genomes, a vast catalogue of genes involved in adaptive responses, an identification of the adaptive value of allelic variants, and information derived from the comparative genomic studies. This resulted in integrated conifer database generation. In order to further improve the collaboration with other worldwide initiatives on conifer genomics (in Russia focusing on Pinus sibirica and Larix sibirica, New Zealand focusing on Pinus radiata and Japan focusing on Cryptomeria japonica), PROCOGEN participants also organised open meetings for other conifer initiatives. This integrative project greatly contributed to strongly reinforcing the competitive edge of European research on conifer genomics and bioinformatics. Apart from the information database you just mentioned, what kind of tools did you create during the project? Different tools have been developed under PROCOGEN, for example analytical tools for basic and applied research in both breeding and conservation programmes. We also developed a wide range of molecular tools and techniques: Exome capture systems designed for targeted conifer species; a set of conifer COS genes and their associated markers; a reference map of pine tissue transcriptional activity and adaptive responses (including expressed gene catalogue and transcription regulatory elements such as transcription factors, sRNAs and epigenetic elements); dense genetic maps based on orthologous markers; pre-breeding tools (i.e. genotyping arrays for pedigree reconstruction, etc.); as well as different high-throughput SNP genotyping systems. The latter enable us to assess genomic diversity at the natural range scale of the species and redefine core collections. Our bioinformatics tools include a portal for structural and functional expert annotation and data exchange of gymnosperm genomics/transcriptomics information. We also integrated PROCOGEN information into the in-house, online comparative platform PhylomeDB to infer pre-computed phylogenetic trees for each gene. How and when will stakeholders be able to make use of the data and tools you created? Regarding data on genome variability, profiling and regulation of transcriptional activity associated with development and environment, tailor-made molecular tools can already be designed to study growth and adaptation of conifer genetic resources. Pre-breeding arrays are available, and simulation and prediction tools for practical breeding are under development. Simulation tools have been developed to optimise the integration of genomic data into practical breeding, and they have already been tested. Additional tools are still under development, and are in the latest phase before application. Information about tool availability can be found on the PROCOGEN website. What kind of impact do you expect PROCOGEN to have on the effectiveness of tree breeding programmes? Most breeding programmes of conifer species in Europe were implemented in the past so as to improve trees for production and quality traits. PROCOGEN’s tools build upon this tradition with new selection criteria and advanced, faster breeding thanks to four advances. First, we can now identify candidate genes with traits that will be responding to several environmental constraints. We can also determine the breeding potential of their allelic variants, develop pre-breeding arrays for precise selection of conifers showing the best adaptive responses and, finally, ensure high levels of genetic diversity — a key strategy to cope with uncertainty in future risks from climate change. Molecular control of plasticity on woody species has also been addressed. All in all, the outcomes of this project will contribute to the sustainable development and long-term competitiveness of the EU forest sector by providing conifer breeders and managers of forest gene resources with information. Our advanced tools will lead to forest-reproduction material, more tolerant towards expected changes or particularly fit for specific conditions, to be used for forest regeneration and artificial plantations. What are your plans now that the project has been completed? PROCOGEN is strongly committed to advancing knowledge of conifer genomes and their function, as well as technology transfer. Our next priority in this regard is to conduct further functional analysis of conifer genomes and to study the regulation mechanisms of genes controlling economically and ecologically important traits in model conifer species. The technology transfer considers not only the transfer of knowledge and methods generated or validated during the project, but also the enormous effort required to translate basic genomics results into practical applications in order to enable genome-assisted breeding and resource management. PROCOGEN Funded under FP7-KBBE project page on CORDIS PROCOGEN website