PROCOGEN

Promoting a functional and comparative understanding of the conifer genome- implementing applied aspects for more productive and adapted forests

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 Obiettivo del progetto (Objective)

'In the midst of a climatic change scenario, the genetics of adaptive response in conifers becomes essential to ensure a sustainable management of genetic resources and an effective breeding. Conifers are the target of major tree breeding efforts worldwide. Advances in molecular technologies, such as next-generation DNA sequencing technologies, could have an enormous impact on the rate of progress and achievements made by tree breeding programmes. These new technologies might be used not only to improve our understanding of fundamental conifer biology, but also to address practical problems for the forest industry as well as problems related to the adaptation and management of conifer forests. In this context, ProCoGen will address genome sequencing of two keystone European conifer species. Genome re-sequencing approaches will be used to obtain two reference pine genomes. Comparative genomics and genetic diversity will be closely integrated and linked to targeted functional genomics investigations to identify genes and gene networks that efficiently help to develop or enhance applications related to forest productivity, forest stewardship in response to environmental change or conservation efforts. The development of high-throughput genotyping tools will produce an array of pre-breeding tools to be implemented in forest tree breeding programmes. ProCoGen will also develop comparative studies based on orthologous sequences, genes and markers, which will allow guiding re-sequencing initiatives and exploiting the research accumulated on each of the species under consideration to accelerate the use of genomic tools in diverse species. ProCoGen will integrate fragmented activities developed by European research groups involved in several ongoing international conifer genome initiatives and contribute to strengthening international collaboration with North American initiatives (US and Canada).'

Introduzione (Teaser)

Conifers are the main target of tree breeding initiatives worldwide. New 'omics technologies promise to improve problems related to conifer forests including adaptation to a changing climate in Europe and North America.

Descrizione progetto (Article)

The EU-funded http://www.procogen.eu (PROCOGEN) project is aiming to unravel the genome sequence and organisation of ecologically and economically important conifer species. The next step will be to integrate the genomic information underlying economic and ecological traits - related to growth, drought and cold stress -into existing forest management and breeding programs for more precise selection of trees in a wide range of growing conditions.

The PROCOGEN team have de novo sequenced and re-sequenced the genomes of P. sylvestris and P. pinaster selected trees to recover the innate variability in each species.

Transcriptome libraries have been constructed to identify genes functionally involved in the expression of important traits related to growth and response to stress conditions. Functional analysis and characterization of the transcriptional regulatory network, such as the identification of regulatory sequences in gene promoters interacting with specific transcription factors, or the epigenetic dynamic associated with growth and adaptive responses, are in progress.

Comparative mapping evaluates the level of synteny and conservation of orthologous sequences among Pinus and Picea species. In the frame of ProCoGen, an exome capture has been designed based on conifer orthologous sequences, which may be applied to other non-model species. Additionally, a small number of orthologous genes on the same chromosome (micro-synteny) and in the same sequence (collinear) have been used to isolate orthologous genes harboured in specific regions on chromosomes. Finally, comparative conifer and conifer versus angiosperms genome-wide studies are in progress to determine content and distribution of different elements as well as to infer gene and sRNA function based on comparative transcriptomics.

Bioinformatic tools for the analysis of the immense amount of data generated by the sequencing of genomes, whose size is significantly higher than the human genome, have been improved or developed .

Strategies for applying basic scientific knowledge in applications in different case studies have been identified. The identification and quantification of associations in the variation at the genomic and phenotypic levels will enable genome-assisted breeding and resource management. To maximise PROCOGEN work, the project team integrates groups involved in other conifer genome analysis initiatives worldwide to integrate data, develop synergies and create added value to the research overall.

Efficient dissemination activities include workshops, the project website and numerous scientific and stakeholder events, as well as publications.

PROCOGEN has made a start in the ambitious combination of high-throughput technologies, advanced bioinformatics and application of basic scientific knowledge into practical applications. The results will improve forest adaptation and, consequently, forest productivity in the wake of climatic change threat. Project data will be a source of information and tools for conservationists, forest managers and forest breeders.