More sustainable pine forests in the making
Conifers, the genus of trees that includes pine, spruce and fir, play a very important role in regulating forest dynamics and the climate in Europe. They have a major impact on the health of ecosystems, in addition to boasting great economic significance thanks to their wood and non-wood products. The EU-funded PROCOGEN (Promoting a functional and comparative understanding of the conifer genome - implementing applied aspects for more productive and adapted forests) project conducted genomic research in conifers to advance breeding and forest management. To achieve its aims the project brought together researchers, academics and industry stakeholders from Europe and North America under one multidisciplinary team. It worked on genome organisation, conifer genotyping and identification of genes that govern key traits related to growth and adaptation to environmental changes, as well as to ecological and economic benefits. The latest genomic tools and tests were employed on the genetic material obtained, with focus on four European species: Maritime pine, Scots pine, Norway spruce and Sitka spruce. Pioneering developments have been achieved in different fields of basic research, such as structural genomics of large and complex plant genomes, providing new reference pine genomes, genome variability based on Single Nucleotide Polymorphism (SNP) discovery, and a vast catalogue of genes involved in adaptive and productive responses. Functional analysis provided information not only about the genetic control of adaptive and productive traits, but also information about the potential role of epigenetic mechanisms in the molecular control of the phenotypic plasticity, which is a crucial issue when boosting resilience to climate change. Comparative analysis allowed studying macro and micro-synteny of conifer species at different levels. The resulting information has impact not only on the knowledge of their evolution when comparing with angiosperms, but also on accelerating the use of genomics tools in other conifer species. Impacts in translational genomics, based on multiple-goal breeding modelling and case studies, are crucial to select basic results to apply in molecular-assisted breeding and conifer resources management. Pre-breeding tools (i.e. genotyping arrays for pedigree reconstruction), exome capture and Genotyping By Sequencing (GBS) approaches for high-throughput SNP genotyping have been used to assess genomic diversity at the natural range scale of the species and redefine core collections. Impact in bioinformatics has been mainly associated with new developments required to analyse such large and complex genomes. Some other key activities included the review of existing methodologies and the assessment of key population parameters, the proof-of-concept studies on the feasibility of genomic selection for model conifer species in Europe or the development of simulation tools and their application to a series of typological breeding scenarios. Data is being provided to the scientific community and to the general public through user-friendly and highly integrated environments. Once the research completed, the project team published the results and paved the way to future research areas. It advanced strategies to improve forest productivity and adaptation to climate change, contributing to a more sustainable paradigm for European forests. This research can be useful for forests within the EU’s frontiers as well as beyond (i.e. Russia, New Zealand, Japan and the Americas), advancing sustainability and climate change on a global scale.
Keywords
Pine, conifer, PROCOGEN, genome, forest management, genomics
