The B4EST project has produced four new videos, explaining some of the concepts behind tree breeding, and why it is important for biodiversity, carbon mitigation and to build the bioeconomy.
Transformative changes in tree breeding for resilient forest restoration
A new publication in Frontiers in Forests and Global Change reviews the work of the B4EST project to show the opportunities from transformative tree breeding in forest restoration schemes .
Ray D, Berlin M, Alia R, Sanchez L, Hynynen J, González-Martinez S and Bastien C (2022) Transformative changes in tree breeding for resilient forest restoration. Front. For. Glob. Change 5:1005761.
Deciding how to establish woodland in forest restoration is not straightforward as different outcomes may be obtained from different establishment approaches, each with cost implications and degree of success limitations attached. Planning restoration requires knowledge of site conditions, including how sites are likely to respond under climate change. For objectives of production and high timber quality it is likely that ground preparation will be used, and planting with forest reproductive material (FRM) of known traits, such as: high survival and growth in establishment, drought tolerance adequate for climate projections, good resistance to pests and pathogens. For objectives associated with biodiversity, carbon sequestration, water supply protection, soil protection, natural regeneration could be a less costly solution with a limited amount of assisted translocation of selected FRM to improve resilience. If objectives are for rewilding forest areas, a degree of natural colonisation perhaps with translocation of some FRM could be a solution. Ignoring site conditions and suitability of available sources of FRM for forest restoration is likely to provide unexpected results with a mix of open ground, scrub and scattered trees resulting from climate, herbivore, and browsing impacts.
The recent B4EST EU Horizon 2020 project examined progress in novel rapid approaches for testing the quality of FRM from existing genetic trials. Here we review the work of B4EST to show the opportunities from transformative tree breeding in forest restoration schemes, including: new climate projection ensembles at high temporal and spatial resolution to develop norms of reaction and transfer models with genetic components; multi-environment genotype-phenotype associations and multi-locus genotype-environment associations in identifying drivers of local adaptation; techniques for genomic selection using single nucleotide polymorphism (SNP) arrays to derive functional traits from polygenic associations; work on seed orchard site and climate specific FRM and zones for deployment; and work on some of the forest ecosystem service benefits derived at a landscape scale. We conclude that tree-breeding will provide robust forest restoration for planting, and rewilding (assisted natural regeneration), and if not “ignoring” but instead assisting natural colonisation processes – tree breeding may improve long-term forest resilience under environmental change.
B4EST policy brief published
The new B4EST policy brief looks at how forest tree breeding can contribute to EU policies, and sets out how forest tree breeding deployment and forest management can be a key tool for reaching the EU Green Deal goals.
The policy brief explores what challenges lie ahead for the future, and makes recommendations as to what policy changes are needed.
This policy brief produced by the B4EST project highlights the importance of forest tree breeding to support the EU Forest Strategy, Green Deal goals and the EU Biodiversity Strategy. The technique, methods and tools of tree breeding are imported from agriculture, and, in forestry, have been actively developed and adapted during the last century. Forest tree breeding has a high potential not only to contribute to mitigating climate change (for example enabling the selection of faster-growing trees), but also assists the adaptation of European forests to climate change. This serves the bioeconomy, ensuring forests continue to provide a wide range of products and services, and also facilitates landscape restoration after major ecological disasters.
Climate change can increase forest vulnerability to damage and disease, reduce forest health and productivity, and cause economic losses. B4EST’s goal is to increase jointly forest survival, health, resilience and productivity under these circumstances, while maintaining genetic diversity and key ecological functions, and fostering a competitive EU bio-based economy.
•What is forest tree breeding, where and how is it used?
•Why is it important in a global change context?
•How does it support EU Green Deal, forest strategy and biodiversity policies?
•What policies regulate its use?
•What challenges lie ahead?
•What policy changes are needed?
Download the policy brief to find out more!
B4EST Nordic policy brief published
The forest sector is of great importance for the economy of the Nordic countries as well as for the supply of wood resources in the EU. Almost 30% of the European forest area and nearly 20% of the growing stock of European forests is in Finland, Sweden, and Norway (State of Europe’s Forests, 2015). Socioeconomic importance of forest is even more significant in Finland and in Sweden. These two countries produce almost 30% of sawn goods, and 60% of pulp for paper and paperboard in the EU and generates over 110 000 direct jobs.
The B4EST Nordic policy brief focuses on specific challenges for the Nordic region, and provides recommendations for FRM management and transnational cooperation.
Three new B4EST leaflets published
The leaflets aim to explain forest tree breeding, where and how it is used, and why it is important!
Download the leaflets:
Where and how is tree breeding used?
How does forest tree breeding support the EU green deal, forest strategy and biodiversity policies?
International conference brings together researchers, stakeholders and policymakers
The B4EST International Conference, Managing Forest Genetic Resources (FGR) for an Uncertain Future, was held on 20-23 June 2022 in Lisbon, Portugal at the Instituto Superior de Agronomia.
It was organised by IEFC and INRAE, with support from the Instituto Superior de Agronomia, and brought together forest researchers, stakeholders and policymakers for two days of in-depth discussions, followed by a field trip to Altriflorestal to learn about eucalyptus.
Discussions focused on:
Accelerating breeding to cope with new challenges and an uncertain future
Forest genetic resources (FGR) and adaptation to climate change
The forests we want: deployment of forest reproductive material (FRM) for forest-based solutions
Science policy interface for mitigation, adaptation and risk management in forestry
Contributions from young scientists within the project were welcomed and featured: they acted as co-chairs for scientific sessions, and gave several flash talks and short presentations.
You can find all presentations from the conference here: https://b4est.eu/b4est-conference/conference-presentations
Conference recordings are available on the session pages, or on the B4EST YouTube channel.
You can find live reporting from the sessions on the B4EST Twitter account:
Using forest genetic resources for climate change mitigation and adaptation
Watch the keynote presentation on forest genetic resources given by Dr Tongli Wang (Associate professor at the University of British Columbia, Canada) on 20 June 2022.
Climate change is causing a mismatch between the climate that trees have adapted to in the past and the climate that the trees will face in the future. Natural migration and evolution may take too long to achieve new local adaptation. Using the available genetic resources created by nature and tree improvement programs will probably be the most effective way to mitigate and adapt to climate change. Nature has created a large number of tree species for different climate conditions and among-population variation along climate gradients within species for local adaptation. Improved genetic materials have been produced through breeding for various objectives, including fast growth and resistance to pests, diseases, and harsh environments. However, challenges remain in making effective use of these genetic resources to fight against climate change.
Dr Wang looks at:
1) using climate niche models to assess the impact of climate change and to assist species in matching their suitable climate;
2) using transfer and response functions to understand the genetic and physiological responses of populations to climate change; and
3) the use of genomic information for delineation of seed and breeding zones.
Title of the PhD thesis:
Improved knowledge and pan-genomic prediction of complex phenotypes using a multi-omic integrative approach in black poplar
Plants are fixed organisms, with continuous development, no pre-established germline, and highly varied life cycles ranging up to hundreds of years in trees. Thus, they are relevant biological models for studying the relationship between development and adaptation to the environment (Mladenov et al., 2021). The woody species Populus nigra, the black poplar, constitutes a reference model where so-called “omics” resources such as phenomics, transcriptomics, genomics and epigenomics have been accumulated for more than 20 years in collaboration between BioForA and the LBLGC.
Genome-wide evaluation is an innovation in the way genetic progress is managed and generated in breeding programs. However, like traditional genetic evaluation, it relies on very little consideration of the underlying genetic architecture of traits of interest. However, new resources from omics approaches are bridging the gap between the phenotypes studied and the DNA sequence, paving the way for systems approaches to integrative biology. Recently, systems biology approaches allow, through the integration of different types of data (genomic, transcriptomic), to better understand the interaction of functional factors that condition the expression of phenotypes (Chateigner et al 2020).
Epigenetics is involved in phenotypic plasticity (Maury et al., 2019), stress memory, and even transgenerational transmission and is of interest in plant breeding (Kakoulidou et al., 2021). Epigenomic data thus offer a new and innovative perspective for improving phenotypic predictions through the integration of information from heterogeneous omics data. The challenge will therefore be to decipher the complexity of quantitative traits of interest using explicit predictive models, while maintaining the predictive qualities necessary for operational selection.
This thesis project is thus placed at the interface between 2 teams (LBLGC and BioForA) for which it reinforces the synergies by developing an integrative and ambitious subject.
New genomic tool for Scots pine research and breeding
In a recently published study, we developed a new genomic tool, PiSy50k, for use in Scots pine evolutionary research and forestry applications. It is anticipated the tool will be important in tree breeding applications, such as when aiming to improve the important growth traits of the species via genomic selection, as well as for many other evolutionary and breeding purposes.
PiSy50k is a genotyping array that gives information on almost 50 000 single nucleotide polymorphisms (SNPs) spread around the genome. SNPs are nucleotide positions in DNA with more than one nucleotide variant in the species. SNP arrays have the big advantages over previously existing genomic tools that individual level genotype data can be gained quickly and handling of the data does not require a lot of bioinformatics work.
Scots pine is a dominating species in the Northern Eurasian boreal forest ecosystem. It is also a major source of wood-based products. Conifer trees commonly have very large genomes, and the Scots pine is not an exception. The genome of Scots pine consists of 24 million base pairs (Gbp), which is about eight times the size of, e.g., the human genome. A large genome with a lot of repetitive regions is challenging to study. The new array is a great advance for Scots pine research, because it allows an easy and quick way of studying genome-wide variation in a large sample of trees. These genotyping results are very useful, for example, in exploring population differences and relatedness between individuals.
Generally, individuals from the same population share the same SNP variant more often than individuals from different populations. However, the Scots pine populations are genetically very similar. The similarity is caused by the species’ very wide distribution range and long-distance wind pollination that connects the populations through gene flow. Despite small genetic differences between the Scots pine populations, our new array has such a high resolution that we were able to separate tree individuals from Finland and Scotland using the genotyping results. We also used the array results to recognize parent-offspring relationships and build pedigrees in the Finnish breeding population.
You can read more about this research in the following paper:
Chedly Kastally, Alina K. Niskanen, Annika Perry, Sonja T. Kujala, Komlan Avia, Sandra Cervantes, Matti Haapanen, Robert Kesälahti, Timo A. Kumpula, Tiina M. Mattila, Dario I. Ojeda, Jaakko S. Tyrmi, Witold Wachowiak, Stephen Cavers, Katri Kärkkäinen, Outi Savolainen, Tanja Pyhäjärvi. Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research. The Plant Journal. (2021) https://doi.org/10.1111/tpj.15628
Top image: Scots pine. Credit: Tanja Pyhäjärvi
Researcher in quantitative genetics
A position as a researcher in quantitative genetics of forest trees is available at the Department of Ecology and Genetics, Plant Ecology and Evolution, Uppsala University.
The Department of Ecology and Genetics is an international environment with staff and students from all over the world. Our research spans from evolutionary ecology and genetics to studies of ecosystems. For more information, see www.ieg.uu.se.
Project description: Our group works on plant population genetics and evolutionary biology with a special emphasis on local adaptation and related questions. We study primarily two groups of plants: the tetraploid weed Capsella bursa-pastoris and its close relatives and forest trees (spruces, birches, larches and poplars). The present position is associated with the EU-funded H2020 B4EST project and more specifically with the development of new breeding strategies and the evaluation of the potential of group selection in forest tree breeding.
Duties: The candidate will be responsible for gathering available data in breeding programs and analyzing them. Population and quantitative genetics data analyses, computer simulations and publishing articles.
Qualifications required: A doctoral degree, or a foreign degree equivalent to a doctoral degree, in within population or quantitative genetics. The applicant is expected to have a solid background in quantitative and population genetics and be familiar with UNIX environments and have experience in standard statistical methods. We attach great importance to personal qualities such as good collaboration skills. Candidates must be able to express themselves very well in spoken as well as written English.
Qualifications desired: Proficiency in relevant programming languages (e.g. bash, Perl, Python, C) will be a strong advantage.
More information and to apply: https://www.uu.se/en/about-uu/join-us/details/?positionId=437204
Closing date: October, 25 2021
For further information about the position please contact: Professor Martin Lascoux, Martin.Lascoux @ ebc.uu.se , +46 18 471 64 16.
The Impact of Drought Stress on the Height Growth of Young Norway Spruce Clonal Trials in Sweden and Finland
Climate change is increasing the frequency of droughts in many areas and particularly in the Northern hemisphere. It has been evidenced that drought is becoming a more significant factor in the decline of forests. Drought affects trees either directly by decreasing their growth or indirectly by increasing their susceptibility to wildfires, and to insect pests and diseases.
Deciduous trees tend to resist drought periods better than conifers as they can drop leaves to reduce their need for water. Among conifers, Norway spruce (Picea abies L. Karst.), one of the most economically and ecologically important forestry species in Europe, has been recognized as being highly sensitive to drought events.
The summer drought of 2018 was one of the most climatically severe events in Europe with record‐breaking temperatures and wildfires in many parts of Europe. In Sweden only, a unique outbreak was recorded as up to four million cubic metres of Norway spruce were killed by the spruce bark beetle triggered by the hot summer of 2018. The infestation even continued in 2019 and 2020. Therefore, drought tolerance can be considered as an important trait for successful regeneration and high productivity of Norway spruce.
A recently published study assessed the impact of the 2018 drought on the height growth of Norway spruce using measurements obtained from about 6000 young clones in Sweden and Finland. Results showed that the hot summer of 2018 had negatively influenced height growth of trees in 2018 and also their recovery in 2019, particularly in the Southern Swedish trials. However, we have identified some resistant genotypes having both good growth and drought tolerance capacities.
In conclusion, given the predicted occurrence of more frequent and severe drought events as well as the high sensitivity of Norway spruce to drought, the resistant genotypes should be selected and incorporated in the future breeding programs of Norway spruce.
Hayatgheibi, H.; Haapanen, M.; Lundströmer, J.; Berlin, M.; Kärkkäinen, K.; Helmersson, A. The Impact of Drought Stress on the Height Growth of Young Norway Spruce Full-Sib and Half-Sib Clonal Trials in Sweden and Finland. Forests 2021, 12, 498. https://doi.org/10.3390/f12040498
Norway spruce seedlings face increased frost risks in the future – towards better decision support
In Sweden, Norway spruce is one of the most widespread and important tree species for the provision of economic and ecological benefits. It is a secondary tree species and regenerates naturally under the shelter of larger surrounding trees. However, current forest practices predominantly involve even-aged stands where regeneration is commonly carried out by planting seedlings after final felling of clear-cut stands. Given these practices, late spring frosts have been identified as a major risk to newly replanted Norway spruce forests in southern Sweden, causing damage to the newly exposed shoots which in turn has detrimental effects to the growth, quality and vitality of the trees.
The growth rhythm of Norway spruce is adapted to seasonal changes in day length and temperature, with substantial variation across different regions. Consequently, the timing of bud burst and shoot exposure is clearly related to provenance origin and is under strong genetic control. Thus, to avoid damages of late spring frosts, a general recommendation in southern Sweden is to select forest regeneration material (FRM) with a late bud burst on planting sites which are considered to be frost prone. Suitable FRM for such conditions are stand seed from Eastern Europe and seed orchards with clones specifically selected for late bud burst.
However, these recommendations are very coarse as: (i) it is very difficult to classify the frost risk at a specific planting site; (ii) there is a continuum of FRM available, each with a unique growth rhythm property; (iii) climate change will affect both frost events and growth rhythms. There is therefore a need to develop models that can predict a FRM specific bud burst and associated risk of frost damages, both in the current and future climate.
In this study we used gridded climate data combined with data from 18 Swedish and East-European Norway spruce provenances grown at three different sites in southern Sweden to develop models that can predict timing of bud burst, frost events and the risk of associated damages. Results corroborated that accumulated temperature above a certain threshold value, called temperature sum, is a main determinant for timing of bud burst and that this trait is correlated with the provenance origin along latitudinal and longitudinal gradients. Furthermore, early bud burst was found to be associated with a higher risk of frost damage, but this also depends on the site specific conditions. The importance of local site conditions was highlighted by comparing gridded climate data with data from temperature loggers at ten sites spread across southern Sweden. In particular, gridded climate data often underestimated daily minimum temperatures at 0.5 meters above ground. This indicates that frost risk of young trees that are particularly vulnerable is underestimated in the models developed on gridded data only.
The developed models were used to predict outcomes in a future climate for the periods 2021-2050 and 2071-2100 using the RCP8.5 scenario. There are four RCP-scenarios used to project future climate conditions which represent different greenhouse gas concentrations. In RCP 8.5, emissions continue to rise throughout the 21st century and is generally considered the “worst-case” scenario with respect to temperature increase. As the climate gets warmer the total number of frost events in southern Sweden will decrease. But as bud burst will occur earlier in the year, the number of frost events after bud burst will instead increase as will the associated risk of frost damages. Thus, adapting growth rhythm properties of FRM in future Norway spruce stands will continue to be a highly important task.
The models developed in this study can be used predict a provenance specific risk of frost damage at an arbitrarily selected site if the provenances can be properly characterized with regards to temperature sum requirements for bud burst. Given these features, the models could be included into deployment recommendation tools like Plantval, to improve decision support to forest owners and managers. However, the majority of seedlings planted in Sweden originate from seed orchards, which also have a higher expected areal production than provenances. Thus, to make full use of the models suggested here, a link between the growth rhythm (mainly bud burst) of seed orchards and provenances are needed.
A fuller description of this work is available in: Svystun, T., Lundströmer, J., Berlin M., Westin, J., and Jönsson, A.M. 2021. Model analysis of temperature impact on the Norway spruce provenance specific bud burst and associated risk of frost damage. Forest Ecology and Management, 493, 16p. doi:10.1016/j.foreco.2021.119252
Application of Transfer Effect Models for Predicting Growth and Survival of Genetically Selected Scots Pine Seed Sources in Sweden
Image: Scots pine trial located in the north of Sweden, comparing plants from a selected cross representing stand seed (on the left) versus plants obtained from advanced-generation seed orchards (on the right). Credit: Ulfstand Wennström, Skogforsk.
Commercial forest stands or plantations are often regenerated artificially, usually by the transfer of forest reproductive material (FRM) in forms of seeds, seedlings, or cuttings, from somewhere else. With the progression of climate change, one important practical challenge for forest managers or forest owners is to select material that will thrive now, under the present climate, and also be able to withstand predicted climate. In order to ensure good general adaptation combined with good growth, the climatic condition of the targeted plantation site (deployment site) should be similar to that of the FRM’s origin, from which they are selected.
Provenance trials are a special type of plantation experiment that helps us understand how trees are adapted to different environmental conditions. However, with advancing tree breeding programs, deployment recommendations, as well as seed transfer models, developed on provenance trials, need further testing.
Scots pine (Pinus sylvestris L.) is the most widely distributed conifer in the world and is of considerable importance as a timber producing species, particularly in the Nordic countries. Transfer effect models for growth and survival of Scots pine in Sweden and Finland were recently developed, using unimproved seedlots available in provenance and progeny trials of both countries. However, the validity of these models for the transfer of improved seeds, e.g., seed obtained from advanced generation seed orchards, remained unknown.
Results of our study, which was a collaborative project between Sweden (Skogforsk) and Finland (Luke), and built on a 40 years of Scots pine improvement activities in the north of Sweden, revealed that the recently developed transfer models can even predict performance of Scots pine elite seeds, obtained from 1.5-generation seed orchards and which have undergone an intensive genetic selection.
Additionally, based on our result, “Plantval”, which is an operational breeding database for common deployment recommendations of Scots pine in Sweden and Finland, can be further utilized for transfer of genetically improved materials.
A fuller description of this work is available in: Hayatgheibi, H., Berlin M., Haapanen M., Kärkkäinen K., and Persson T. 2020 Application of Transfer Effect Models for Predicting Growth and Survival of Genetically Selected Scots Pine Seed Sources in Sweden. Forests, 2020, 11, 1337. doi:10.3390/f11121337
Climate-EU: Scale-free climate normals, historical time series, and future projections for Europe.
Marchi, Castellanos-Acuña, Hamann, Wang, Ray, Menzel
Newly published research in the journal Nature Scientific Data, describes how new climate data for Europe are downscaled to high resolution and accessed by users in a useful format for further analysis.
The data repository contains the scripts and the databases required to provide scale-free (i.e. for a specified latitude and longitude) monthly seasonal and annual user specified climate data from 1901 to 2019.
The repository additionally includes gridded climate projections (CMIP5-RCP scenarios) for 30-year climate normal periods (climate baseline [1961-1990]; 2020s [2010-2039], 2050s [2040-69] and 2080s [2070-2099]) for Europe from multiple published GCM and RCM sources.
The quality of ClimateEU estimates was evaluated against weather station data for a representative subset of climate variables. Dynamic environmental lapse rate algorithms employed by the software generate scale free climate variables for specific locations made a 10 to 50% improvement in accuracy compared to other gridded data sets.
ClimateEU was initially developed by two of the authors (Hamann and Wang). Ray and Marchi wished to use ClimateEU to access past and present climate data and future projections for their work in the B4EST project.
In B4EST ClimateEU data are used with tree trait data (e.g. relating to tree height and survival) from common garden provenance and progeny trials.
This enables calculation of the genetic adaptation and plasticity components of forest reproductive material under varying environmental conditions. The calculations will be used to understanding the extent to which it is possible to control the tolerance of trees to climatic and biological change through tree breeding.
The database and downscaling tool produces 48 monthly variables (monthly precipitation, minimum, maximum, and average temperature), as well as 36 derived bioclimatic variables useful in ecology forestry and agriculture.
The new B4EST Downscaling Tool for scale-free downscaling of climatic time series, indices and climatic normals from 1901 to 2098
In a previous post we explained how B4EST is working to quantify the potential impacts of climate change on forests in Europe by understanding how trees with different genetic characteristics are likely to perform under different projected future climates.
To achieve this, in B4EST we use models to analyse the effect of historical mean and extreme climatology on a range of provenances and seed orchards to derive information on how the progeny may respond to the future climate in different parts of Europe. Selected progeny forming new forest stands will need to cope with climate change, e.g. milder and wetter winters and/or episodes of drought in the summer, or late spring frosts.
Our models will assess how well the genetic diversity and phenotypic plasticity of material will allow selected material to respond to climatic extremes in the future. Climatic change may also influence pest and disease threats to trees and so this factor also requires consideration when selecting forest reproductive material (FRM).
A serious drawback of many climate data portals is that they lack the temporal resolution researchers need to analyse extreme events. For this reason statistical downscaling methods and downscaling tools such as ClimateEU were developed.
Our solution has been to prepare climatic data for Europe with a monthly time series for the B4EST project. The dataset has been firstly generated combining the CRU-TS for the period 1901-current and the high emissions scenario representative concentration pathway (RCP8.5) provided by UKCP18. This UKCP18 pathway (RCP8.5) makes no assumptions about green-house gas emissions reductions being effective; in other words it provides an extreme view of the climate future in Europe.
This dataset has been selected as candidate for our Climate Downscaling Tool, known as ‘ClimateDT’. The monthly time series of both CRU-TS and UKCP18 allows the calculation of certain projected extreme events, such as: drought, extreme high and low temperature, monthly and seasonal precipitation extremes, predictions of the beginning and end of the frost-free period. These projections are simulated, so the extreme climatology calculations should best be offered as a frequency above or below a threshold value at a decadal time scale. The results will allow the calculation of probabilities that can be used to convert the climatic vulnerability of FRM into a risk of damage or mortality. Additional climatic dataset will be then added in future.
ClimateDT provides scale-free climate data for historic climates and future projections and is currently hosted on CNR-IBBR servers. Raw monthly temperature (minimum and maximum) and total monthly precipitation for the period 1901-current are downscaled from CRU-TS while future scenarios derive form UKCP18 layers.
The downscaling is performed to user defined locations of latitude, longitude and elevation to provide many climatic variables and indices. The available time span for derived data is January 1901 to December 2098 with a monthly time step. The system is based on a website for data uploading and a virtual machine for data processing in R environment. The data transfer between the machines occurs using a Secure Shell (SSH) cryptographic network protocol and an email alert is scheduled when uploaded data has been processed.
Downscaling is performed following the method of the ClimateEU software with some modifications:
- The local lapse rate is calculated for every year and month by month and the adjustment to be applied to the climatic variable is multiplied times the r-squared of the regression in order to avoid over-adjustments;
- Both temperature and precipitation variables are adjusted using the dynamic lapse rate if the regression is statistically significant;
- Additional R packages such as dismo and SPEI are currently integrated in the process to provide additional well-referenced climatic indices often used in ecology and environmental science;
The calculation engine is totally open-source and new development could be integrated easily in the script thanks to the modular structure.
Planned additional features include the use of a different interpolation method (Inverse Distance Weighted) as well as additional climatic indices or nonlinear function for dynamic lapse rate calculation.
In the current form 42 climatic indices are available for the Europe and North Africa. However, any other region of the globe is available upon request. An extension of ClimateDT on the whole globe is under development but not yet available in the B4EST portal.
Enhancing the value of productive tree species in Europe: new tool ‘4TREE’ to help tree breeders select trees with desirable characteristics.
An important goal of the B4EST project is to produce a tool for tree breeders to enable them to access to the genomic information that distinguish individual forest trees at a low cost.
This would allow breeders to evaluate trees at an early stage of growth rather than having to wait many years until they have grown and they can observe a tree’s characteristics. In turn this enables them to react promptly to new considerations like those related to global changes, such as those in our climate, which need to be accounted for when selecting tree material for forest establishment.
The genotyping tool ‘4TREES’ has been developed by B4EST for four economically important forest species: maritime pine, stone pine, ash tree and poplar. Similar arrays were also developed within B4EST for Norway spruce and Scots pine.
The 4TREES array is based on regions of the genome where a single nucleotide (one of the building blocks of DNA) varies between individuals of the same species. These regions are called Single Nucleotide Polymorphisms or SNPs. Except for the stone pine, a pine species with extremely low levels of genetic variation, all of the SNPs used for this array come from existing genomic resources.
Having obtained hundreds of thousands SNPs per species, the first step was to use these resources for the production of a screening array, on which a set of approximately 137K SNPs per species (36K SNPs for stone pine) were tested on a representative panel of individuals of each species.
From this screening, 13,5K (6K SNPs for stone pine) highly informative SNPs were selected for each species to be on the 4TREE array. The most important criteria for these selections were to incorporate SNPs known to be in candidate genes or regions linked to traits of interest for breeders, such as resistance to dieback disease that ravages the ash tree populations. A good coverage of the genome was also important, as it has been shown to improve the predictions.
The 4TREE array will be a highly valuable genome-assisted breeding tool, made commercially available for cost effective genotyping for four important tree species in Europe.
Climate Matching Tool to help forestry practitioners understand future climate conditions for forests in Europe.
Developing visualisation techniques to communicate to practitioners the urgency and impact of climate change on forests is a challenge. This is because the longer rotation lengths of trees compared to crops requires consideration of the projected climate change over periods of time that can be difficult to comprehend, for example 50 years into the future.
To help forest practitioners understand the anticipated future climate, we developed a Climate Matching Tool (CMT) in B4EST, with additional support from the Forestry Commission. The CMT is a web-application that can be used on a computer or mobile device. It aims to enable:
- forest planners to better understand the changes in future climatic conditions that new forests will experience;
- tree breeders to identify material that is better suited or matched to future climate conditions;
- forest managers to select material that is resistant or tolerant of environmental impacts e.g. extremes of frost, drought and heat; and/or biological impacts e.g. changes in the range of pests and pathogens due to climate change that could impact on future managed forests;
- the range of products from well-managed resilient forests to increase in society and help mitigate climate change.
These issues are particularly important considerations for forest decision makers given the need to make European forests more resilient to the direct and indirect impacts of environmental change and the focus in policy on forest expansion.
The CMT includes two modes of operation, a basic mode for quick analyses (Figure1), and an advanced mode for more complex or detailed enquiries (Figure 2). Both the basic and advanced modes allow the user to:
- locate and assess where the projected climate of a selected location currently exists (find an analogue of the future climate) or,
- find and locate in time and space where the climate of selected location will be in the future.
In Europe there is a rich legacy of introduced tree species from the Pacific North West, the first version of the CMT therefore focuses on these two areas.
The CMT uses a method of matching published in 2005 (Broadmeadow et. al. 2005). It is based on three climatic variables:
- mean monthly temperature;
- mean monthly diurnal temperature range;
- and monthly precipitation.
The data used in the CMT is from the monthly time series of UKCP18 (RCP8.5) that is available at 12 km resolution for Europe, and 60 km globally. This is a high emissions scenario the earth is currently tracking, and makes no assumptions about emissions reductions being effective. We have downscaled the global data for the Pacific North West to 12 km – the same resolution as Europe.
Basic mode climate matching can be based on 10-year or 30-year climate normal periods from 2001 to 2079, whereas the advanced mode offers 10-year or 30-year climate periods from 1981-2079. Both operating modes allow the selection of precipitation, temperature or both variables on which to match. In advanced mode, climate data for the months or seasons to use in a match can be selected, as may the number of pixels to match. The advanced mode allows the user to switch between Europe and the Pacific North West or both regions to calculate a match, if both regions are selected 10,000 pixels are available to be matched.
A results box is presented following a calculation. The results show the distribution of the ‘best match’ units for the number of pixels selected, and the position of the selected location in the distribution. The result colour rendering can also be switched. Help instructions are available and ‘tool tips’ are shown for each selectable drop-down box.
Broadmeadow, M.S.J., Ray, D., Samuel, C.J.A., 2005. Climate change and the future for broadleaved tree species in Britain. Forestry 78, 145–161. doi:10.1093/forestry/cpi014
New COST Action in epigenetics/epigenomics
A new COST Action relevant to the B4EST community, EPI-CATCH “EPIgenetic mechanisms of Crop Adaptation To Climate cHange” has begun.
Its objective is to define, develop, generate and share new breaking knowledge and methodologies for the investigation of epigenetic mechanisms modulating plant adaptation to environmental stresses driven by climate change. So far, no international network has been created with the aim of standardizing methodology in plant epigenetics/epigenomics and better integrate these data with other “omic” approaches. EPI-CATCH will create a pan-European framework for networking in this under-investigated research field.
More information can be found on their website https://www.cost.eu/cost-action/epigenetic-mechanisms-of-crop-adaptation-to-climate-change
Briefly: EPI-CATCH has been designed to address the following issues:
- the scarce research investment in developing methods and infrastructure for plant epigenetics/epigenomics,
- the heterogenous and complex nature of epigenetic mechanisms,
- the significant impact derived by new epigenetic discoveries.
EPI-CATCH has 3 main challenges in epigenetics/epigenomics: 1) improving lab methodology. 2) improving in silico data analysis and 3) better integration of epigenomic data with other “omic” data.
For each country, persons interested in the project could contact the member of the Management Committee representing their country – you can find the full list here: https://www.cost.eu/cost-action/epigenetic-mechanisms-of-crop-adaptation-to-climate-change/#tabs|Name:management-committee
Research Scientist in integrative genomic prediction of complex phenotypes for poplar selection purposes
INRAE is offering a permanent position for a research scientist interested in integrative genomic prediction of complex phenotypes for poplar selection purposes. The successful candidate will be involved in B4EST WP3 activities.
– Deadline for applications: March 5, 2020
– Pre-selections: April-May 2020
– Final selections: May-June 2020
– Starting date for appointments: from September 2020
Open to candidates with a doctorate (or equivalent). A specialization in quantitative genetics and a solid experience in functional genomics are expected. Any experience in statistical modelling and bioinformatics will also be appreciated. Fluency in English is desirable, as well as long-term international research experience.
Detailed information about the position, and how to apply is available on the INRAE portal.
Further information: Leopoldo Sanchez Rodriguez (email@example.com)
Post-doc scientist sought to work on ‘Genetics, Adaptation and Breeding’ for European Ash.
Do you have a PhD in quantitative, population genetics or statistical geonomics, with experience in genetic analysis and programming?
We are looking for a highly motivated and creative scientist to join the B4EST team based at BioForA Research Unit at INRA Val de Loire in Orléans, France.
The successful candidate will be working in the ‘Genetics, Adaptation and Breeding’ team on European Ash, Fraxinus excelsior and Hymenoscyphus fraxineus, an invasive fungus causing ash dieback. It’s a one year post, starting ideally, in March 2020.
A selection program has been set up by INRA with the aim of creating seed orchards to produce superior seed material combining tolerance to the fungus and superiority for selection criteria for Ash, such as vigor and straightness.
As part of the B4Est European project coordinated by INRA, a 12k SNP chipset is currently being developed in order to conduct Genome Wide Selection (GWS). Both INRA and Wageningen University Research (WUR) contributed to this tool by providing genotypes from diverse geographic origins with contrasted phenotypes. The successful candidate will contribute to the implementation of the GWS approach.
The deadline for applications is 31st January 2020.
What will tomorrow’s tree breeding sector look like? An economic analysis
The genetic selection of trees (breeding) and associated production of improved forest reproductive material (FRM) have a long history in many European countries. Looking forward, the tree breeding sector plays a strategic role in ensuring the resilience of forests under climate change, but its evolution is difficult to predict as it results from the complex interactions of technology, institutional actors, regulatory environment, market developments and the research and development sector.
An objective of B4EST is to understand this complexity in order to develop solutions and recommendations that fit the broader context within which tree breeding operates. As the organisation of breeding and production and diffusion of FRM is organised quite differently depending on the species and countries, the analysis is based on four cases capturing this diversity (Maritime Pine, Norway Spruce, Eucalyptus and Poplar).
The project will investigate the economic potential of the genomic revolution, which has transformed selection in many sectors (e.g., animal production) but, to date, has had little impact in the forest sector. Genomic selection has the potential to accelerate the breeding process and improve the assessment of genetic value, but it also involves significant costs and requires new knowledge. Inevitably, the relative newness of the technology also introduces uncertainty, and the specificities of tree biology – for instance the length of the production cycle or time to sexual maturity – introduce constraints that are not present in other natural resource sectors.
The project will compare the relative efficiency of genomic-based and traditional breeding methods for three species (Maritime pine, Norway spruce and Populus sp.). This part will be based on the collaboration between tree geneticists familiar with the comparison of different methodologies for the selection of trees and economists familiar with cost-benefit analysis. The work will complement the analyses that have already been made in the literature by better taking into account the costs of the different basic operations related to tree breeding and the possible substitutions among those costs when modifying the structure of the breeding programs. The results will inform private and public breeders about when and why one type of selection is economically preferable to another, and under which conditions genomic selection is likely to be broadly adopted by the forest sector in the future.
B4EST will also investigate the broader innovation systems to which tree breeding activities belong, with the aim of anticipating the evolution of the sector and how that evolution may be influenced, for instance through the use of public policies or regulatory changes. The task will analyse the organisational structure of the breeding sector by mapping the main public and private organisations involved and their relationships, defining the key aspects of the regulatory framework and identifying the salient market forces shaping the sector. Drawing on case studies of three species (Maritine Pine, Eucalyptus, Norway Spruce) and five countries (France, Spain, Portugal, Finland, Sweden), the project will highlight the main drivers of change in tree breeding in Europe. Stay tuned!
Institut National de la Recherche Agronomique (INRA), Grenoble Applied Economics Lab (GAEL): Stéphane Lemarié, Aline Fugeray-Scarbel, Eve Audoin
Natural Resources Institute Finland (Luke), Bioeconomy and Environment Research Unit: Xavier Irz
Identifying eucalypts with increased tolerance to biological and climate threats
Eucalyptus globulus and hybrids are important non-native tree species with a high production capacity. They also have a potential to grow on marginal lands and thereby provide an income for depressed rural areas in Southern Europe.
B4EST aims to identify and develop eucalypt trees well adapted to growing in rapidly changing environments, and those more tolerant to biological and climate threats. To do this it is first necessary to evaluate the amount of genetic variation amongst eucalypt trees for tolerance to cold (freezing temperatures) and to water stress. Tolerance to snout beetle (Gonipterus platensis), today’s eucalyptus pest with highest impact in Iberian Peninsula, is also being evaluated.
Trees’ growth and survival performances in these conditions will be assessed in a variety of circumstances:
- in a field trial with contrasted water availability,
- in controlled conditions for drought and cold tolerance,
- in breeding trials with contrasted drought and/or cold exposure, and
- in fields and laboratory for resistance to Gonipterus.
B4EST field trial with contrasted water availability
A field trial was established in June 2018 in central Portugal with thirty clones (genetically identical individuals) of Eucalyptus globulus and Eucalyptus spp. Hybrids are distributed in three blocks: 1) without irrigation, 2) with irrigation and additional fertilization, 3) without irrigation and on a soil with seasonal waterlogging.
The trial has a weather station on site to monitor daily climate variables (Figure 1a). It also has sensors monitoring the soil water and the amount of water supplied by irrigation (Figure 1b). The trees are also equipped with sensors to monitor daily micro-fluctuations in the trunks. This monitoring will provide measures of the extent to which the trees are adjusting in the short-term to site conditions, and of specific responses to drought by trees.
So far, the heights of the Eucalyptus clones have been assessed ten times. The results show that faster growth occurred as expected in the irrigated block and that clones which already have adult leaves show a faster early growth.
Assessing drought and cold resistance in controlled conditions
An experiment to test the tolerance of trees to cold (freezing) temperatures by 15 clones, including forest reproductive material being used in operational forestry, has been carried out and the damage to the foliage and survival rates of the trees are being evaluated from one week to one month after the stress.
Two eucalyptus clones with contrasting tolerance to drought were selected and used in a pilot study of drought tolerance carried out in the Toulouse Plant Microbe Phenotyping Platform in Toulouse (Figure 2). The results are being analysed to set up a larger experiment in the near future using the same trees as was used in the assessment of tolerance to cold.
Selecting clones with drought and cold resilience from field trials for further analysis
The breeding trials more exposed to cold and/or to drought were identified and split into four classes: 1) trials exposed to cold, 2) trials exposed to drought; 3) trials exposed to cold and drought; 4) trials less exposed to cold and drought.
An analysis was carried out ranking existing eucalyptus clones for growth and survival. This allowed the identification of 163 eucalyptus clones as a training population for genomic selection (a form of genetic selection using DNA markers). Leaves and wood samples from 160 clones have already been collected and have been sent for DNA extraction and micro-densitometry, respectively.
Assessing the susceptibility of eucalyptus to eucalyptus snout beetle
Laboratory tests are being carried out to assess the susceptibility of different eucalyptus trees to eucalyptus snout beetle (Gonipterus platensis). Twelve different trees of eucalyptus have already been tested – with the extent of foliage consumption by the Eucalyptus snout beetle and amount of egg laying in the leaves being evaluated. Field assessments have also been undertaken evaluating eucalyptus snout beetle attacks in eucalyptus breeding trials. Field work is still under way to evaluate the susceptibility to this beetle of more eucalyptus trees.
This work is carried out within the B4EST project as a collaboration between Altri Florestal (Portugal), CIRAD (France) and UPS (France) using the genetic material and field trials of Altri.
Postdoctoral researcher vacancy to work on forest genetics
Do you have a doctoral degree and a recorded scientific expertise and interest in population, evolutionary and quantitative genomics? The University of Oulu, Department of Ecology and Genetics is recruiting a postdoctoral researcher to work on various aspects of Scots pine genetics. The successful applicant will contribute to evolutionary focused combined analysis of gene expression and nucleotide diversity data of Scots pine and analysing the performance and data from recently developed SNP chips for multiple European tree species in B4EST project in collaboration with French National Institute for Agricultural Research (INRA).
The University of Oulu is one of the biggest and most multidisciplinary universities in Finland. It is an international science community working in close cooperation with research institutes, companies, and the public sector. Together it forms a globally significant research hub, relentlessly pushing the boundaries of known for a more sustainable and intelligent future. The postdoctoral researcher will be part of Pyhäjärvi Lab (oulu.fi/pyhajarvilab) which collaborates closely with other European forest geneticists via the Horizon 2020 projects GenTree and B4EST.
The applicant should have a doctoral degree, recorded scientific expertise and interest in population, evolutionary and quantitative genomics. Experience in bioinformatics and gene expression analysis is an advantage. The deadline for applications is Friday, 29 November 2019 at 23:59 (Finnish local time). Further information and to apply for the post.
Downscaling climate data for the scientific community: the B4EST R Shiny web app
Climatic data is an important component of ecological models. In B4EST we want to quantify the potential impacts of climate change on forests in Europe by understanding how different tree phenotypes (trees of different characteristics) are likely to perform under different projected future climates. To do this we will be reanalysing existing European growth trials of tree provenance (geographic seed origin) and progeny (genetic/family origin) using data on historic and projected future climate.
As part of our work we will need to deal with biases in climate projections as both global and regional climate models include some interpolation errors which need be known and understood. In B4EST, we will be quantifying these errors, or discrepancies, between different data sources so we can better understand the uncertainties in our ecological models.
A particular challenge to our task is that whilst a wide range of climatic data is now available from web portals, time series data (data indexed in time order) are rarely available at high resolution (5 km or less).
Frequently used time-series databases include:
- the Climate Research Unit (CRS) data TS.4.02 from the University of East Anglia, UK,
- the Copernicus climate data portal (EU), and
- the UKCP18 data from the Centre for Environmental Data Analysis (CEDA).
The data provided at these portals are too coarse for site sensitive scientific studies, such as those used in B4EST. For this reason, many groups have developed different downscaling methods, which increase the resolution of the data enabling it to be used at smaller spatial scales.
Climate data software ClimateWNA and the ClimateEU (https://sites.ualberta.ca/~ahamann/data.html) provide an interface in the form of a standalone MS Windows application, enabling users to extract and downscale PRISM 1961-1990 monthly normal climate data (1.25 x 1.25 arcmin, 4 km approximately) to scale-free point data based on latitude, longitude and elevation.
The climatic time series data availability for ClimateEU is unfortunately not suitable for the requirements of B4EST. In order to overcome this time limitation, as well as additionally replicating and controlling the downscaling process, B4EST (Work Package One) has followed the main steps developed by the ClimateEU team, to migrate the ClimateEU method into R programming language (for more detail, see the explanation below).
The testing procedure is currently under development. Once the statistical process has been defined, CRU time series, UKCP18 surfaces and other climatic surfaces with historical data and future projections will be made freely available to enable scientists to develop a range of climate data for ecological and genetic studies in a user-friendly R-shiny web app (https://shiny.rstudio.com/). In this way scientists working in B4EST will be able to access reliable climatic time series data to characterize the historic and future climate of their provenance trials and experiments.
Migrating the ClimateEU method into R programming language – the process
Using Worldclim ver 1.4 as a test climatic surface (representing the 1961-1990 climatic normal period) with 30 arc-second of spatial resolution and other data obtained from meteorological stations across Europe, a scale-free bi-linear interpolation process with a dynamic local lapse rate adjustment has been completed. Other spatial interpolation techniques such as inverse distance weighting have been tested to increase the range of interpolation methods with which to compare results.
Planter’s guide – new tool for choosing Scots pine plant material in Sweden and Finland
A new web-based tool developed with support from the B4EST project provides recommendations of the best available Scots pine seedlings from seed orchards in Sweden and Finland. It allows the user to select a planting site and compare plant material from both countries.
The tool builds on a new model framework developed in spring 2019, which allows Swedish and Finnish seed orchard crops to be ranked and compared on the same scale in either of the countries. This has now been implemented in a freely available web-based decision support tool (Planter’s Guide) which covers both countries in each language, and also as an English version.
The user can select an arbitrary planting site, either by clicking on a map or by providing coordinates. The tool then produces a list of seed orchards ranked according to a performance index, by growth or by survival. The deployment recommendations are climate adapted: the performance index is based on survival ability in the current climate, but simultaneously taking advantage of the improved growth conditions in the future climate.
Additional information about each seed orchard (e.g. ownership, clonal origin, establishment year, size) is available by selecting and clicking on it in the list. A map of the suitable deployment area for each seed orchard is shown, and the deployment maps for different seed orchards can be compared.
Use the Planter’s Guide in Swedish (SE)
Use the Planter’s Guide in Finnish (FI)
Contact: Mats Berlin (firstname.lastname@example.org)
Survey results show positive perceptions of adaptive tree breeding
A European survey carried out by the B4EST project shows that improved forest reproductive materials are perceived positively by the forest sector, and are considered important in forest regeneration and afforestation to adapt to climate change.
The survey wanted to understand the experiences and expectations of different groups in the forest sector towards adaptive tree breeding, and the usage and uptake of improved forest reproductive material (FRM). FRM refers to all parts of a tree that can be used for reproduction, for example fruits, seeds and cones. Improved FRM which result from selection on a combination of adaptive and production performances can provide specific benefits, for example better resilience to climate conditions, pests and diseases.
The survey received 565 responses from nine European countries (Finland, France, Germany, Italy, Norway, Portugal, Spain, Sweden and the United Kingdom). The online survey was open to all stakeholders of the forest-based bioeconomy, and received the highest number of responses from public administrators as well as public and private forest managers. Eight species were investigated – six native (Norway spruce, Scots pine, maritime pine, poplar, common ash, stone pine) and two non-native (Douglas-fir, Eucalyptus).
The results show that negative effects of climate change are increasingly expected by 2050, with regional difference between Scandinavia and Southern Europe. There is some confidence by the European forest sector that future climatic changes will be manageable, and that improved forest reproductive material will be an important management strategy to adapt to climate change. Respondents said their three most important forest management strategies to adapt to climate change will be:
- Diversification of tree species
- Artificial regeneration with improved forest reproductive material combined with revision of guidelines towards optimal adaptation to future climate
- Enrichment of natural regeneration with forest reproductive material better adapted to future climate changes
To successfully adapt to climate change, the use and importance of improved forest reproductive material is expected to increase and at the same time, more research is needed to find solutions to the biggest threats like droughts, windstorms and pests. This may indicate that breeding programs for a larger number of species are required, to reach an expected level of diversification.
- The Executive Summary of the survey results
- Zusammenfassung (DE)
- Resumen ejecutivo (ES)
- Résumé de l’analyse (FR)
- Utvidet sammendrag (NO)
- Sammanfattning (SE)
Contact: Dennis Roitsch (email@example.com)
Image: Norway spruce seedlings, Landbruks- og matdepartementet, Wikimedia
A greenhouse seed orchard to improve maritime pine seed production
Major difficulties face those seeking to produce improved Maritime pine seed. These include invasive pests and climate change which are leading to a decrease in seed production. Another challenge is pollen contamination from surrounding non-improved stands which is having a negative impact on the genetic value of the produced seeds. In the B4EST project, we are testing on a small scale, whether the use of a greenhouse seed orchard can improve the quality and quantity of seed production.
Tree breeding programmes aim to produce improved plant material to use for afforestation. The best performing trees for climate adaptation, productivity or resistance to pest or pathogens, are selected and planted or grafted in a seed orchard managed to produce seeds. These seeds from selected parents are then used to produce seedlings to be planted in the forest. In this way the genetic gain from the breeding program is deployed in the forest so as to better provide wood and forest services.
Maritime pine is the first planted species in France: more than 50% of commercialized seedlings each year are maritime pine seedlings, all issued from improved material. The breeding program has led to several generations of open pollinated and extensively managed seed orchards that are used to produce enough seedlings for 15, 000 to 20, 000 hectares of plantation each year. However, the conditions of seed production are changing. Invasive pests (Leptoglossus occidentalis) perhaps combined with climate change (summer drought) are drastically decreasing seed yields. Already this is forcing orchard managers to harvest former generation seed orchards to reconstitute their stocks. Moreover, pollen contamination (estimated to be over 90% in some cases – Bouffier et al, 2017) induces heavy losses in seed genetic value.
A greenhouse seed orchard would allow for a more intensive management of seed production, with a good control of environmental conditions. For the first time in the Maritime pine breeding programme, we tested mass pollination under greenhouse conditions. We want to evaluate the technical feasibility of this method, the potential of seed yield per cone and the pollen contamination rate. Twenty grafted trees in 100 litre pots were placed in a greenhouse during flowering time and mass pollinated, then transferred outside for cone maturation. In the absence of an authorised efficient chemical control, bags were placed on young cones for protection against seed bugs. After harvest, the seeds will be analysed for their molecular marker (sections of DNA) profiles to check their pedigrees.
This part of B4EST research is being led by INRA, France.
Bouffier L., Debille S., Alazard P., Pastuszka P., Raffin A., Harvengt L., Lelu-Walter M.-A., Musch B., Trontin J.-F. (2017). Pollen contamination and mating structure in maritime pine clonal seed orchards. IUFRO Seed Orchard Conference 2017 (2.09.01 Unit), 04-06 sept. 2017, Bålsta (Suède). Poster, pp. 65.
How to genotype hundreds of trees in a blink of an eye?
Dr Tanja Pyhäjärvi , University of Oulu, Finland
All breeding is based on genetic differences among individuals. In traditional breeding, the similarity of genetic background and the relatedness among individuals is predicted from pedigrees. Pedigrees have been an important part of breeding for a long time. All of us have that friend who has a pure bred dog with a fancy pedigree on some database or on paper. Mom, dad, mom’s mom, mom’s dad etc., you know it.
In modern breeding, the exact pedigree information is not always needed. Why? Because we can use information from DNA level variation to figure out relatedness among individuals. On top of that, it is also possible to follow which of the thousands of variable sites in a genome are linked to a certain desired or unwanted characteristics. DNA level information also tells us directly about the amount of genetic diversity and extent of inbreeding within a given individual.
Many breeding methods that use DNA level information have one problem. They need a lot of it! Often information is needed from tens of thousands of DNA locations and from thousands of individuals. So, what do you do when you want to peek into DNA level differences among thousands of trees? One of the goals of B4EST project is to develop new high throughput methods for easier and cheaper genotyping to tackle this issue.
Luckily there are multiple technological options to achieve this goal. In B4EST, we have chosen a method called genotyping arrays. These postcard size arrays have 384 wells, and each well contains 50 000 different type of small DNA pieces that are designed to capture a different variable site in a tree’s genome. Short, sticky custom designed pieces of DNA are attached to a glass surface and form microscopic clusters. Then the sample genome’s DNA is fragmented in small pieces and allowed to find a matching sticky piece on the surface. And that’s not all: samples are also labeled with fluorescent dyes. With a special light conditions and a very good camera, an image of the array can be obtained.
Just add some image processing and algorithms and voilá!, different genotypes (heterozygotes and homozygotes) can be identified. And that is how you can genotype hundreds of trees and tens of thousands genetic markers in one go.
Of course making all this to work smoothly requires a lot of existing genetic and technical knowledge. The arragys that we intend to design in B4EST project will be publicly available for anyone who needs efficient genotyping of Norway spruce, Scots pine, poplars, maritime pine, ash and stone pine.
PhD position available exploring ‘Demo-genetic tipping points in forests facing disturbance’
A PhD position is available at INRA Avignon, exploring ‘Demo-genetic tipping points in forests facing disturbance: an integrative modelling approach to support the design of adaptive management strategies’.
The PhD will address two general questions:
– what is the adaptive capacity of the forests facing changes in disturbance regime?
– how far can the choice of genetic resources and silvicultural treatments increase this adaptive capacity?
Deadline for applications: June 30th 2019
Further information http://bit.ly/2KLO97E
Contact for more information: François Lefèvre (firstname.lastname@example.org) INRA, URFM – Mediterranean Forest Ecology, Avignon (France)
1st B4EST annual meeting
B4EST partners gathered in Edinburgh from 21-23 May for the first Annual Meeting. The meeting was a chance for an update on the progress of the project, and to work together with colleagues on the project’s objectives: proposing options to manage and help forests adapt to climate change.
B4EST works with eight of the most economically, ecologically and socially important tree species in Europe, and the focus for this meeting was Scots pine.
Guest speaker Richard Ennos from the University of Edinburgh looked at how Dothistroma septosporum was affecting pine trees in Scotland and the pathogen’s evolutionary potential. The pathogen affects 82 species of pine, and spreads by spores to infect the tree crown, causing growth reduction. Currently there are a number of epidemics worldwide, in Europe, North America and New Zealand, and it was first recorded on native Scots pine in the UK in 2010.
There have been previous breeding programmes for resistance in New Zealand, which has only a single asexually reproducing Dothistroma genotype. But the UK situation is different – three genetically distinct clusters of Dothistroma septosporum have been found in Scotland, confirmed by genome resequencing. Of interest to B4EST, is how is this likely to affect breeding for durable resistance. The resequencing showed the genetic diversity, sexual reproduction within races and hybridisation between races of D. septosporum in the UK, meaning that there is high evolutionary potential, much greater than in New Zealand. Breeding for durable resistance is therefore more difficult, because you are breeding against something which is changing. Richard concluded there is a need to rethink traditional tree breeding programmes to integrate continuous natural selection driven by changing composition of evolving pest and pathogen populations.
Matti Happanen from LUKE gave an overview of the current panorama of Scots pine breeding and the potential uses of genomic information. There are some constraints – an economic rotation of 70-100 years, difficult clonal propagation, late sexual maturity and fairly small seed yield. Accurate genomic relationships are the most useful new information for operational breeders, while possible additional gains will arise from higher accuracy and selection intensity, rather than from faster breeding. Genotyping costs are still far too high for largescale operational breeding applications, but further reduction of the costs will open new ways to implement genomics in tree breeding.
Making the management of genetic diversity in forest tree breeding efficient, flexible and fast
The use of genomic information for tree selection has the potential to identify more accurately individual trees carrying favorable genes and at earlier stages of their development than we had ever done before. This innovation, known as genomic selection, is possible as soon as trees are big enough to provide the small amount of tissue (for example, a leave or a needle) that is required for DNA analyses. Young plants can be selected for their future performance or by their resistance or tolerance to environmental stresses at the nursery, well before their evident characteristics (definite phenotypes) are available in the field. It is thought the technique will be revolutionary for forest trees.
The most revolutionary benefit comes from the shortening of the generally long time required to assess phenotypically a candidate to selection, usually 10 to 15 years in the best of the cases and dependent on the species. Making things faster is not just a question of return of investment; early evaluation brings promptness and flexibility when facing challenging demands, especially those associated to the suitability of existing varieties to global change. One good example in B4EST is that of selecting Ash trees that are tolerant to a rapidly expanding wave of a destructive fungus.
B4EST has made a strategic choice of the most economically, ecologically and socially important tree species in Europe for innovative breeding, covering a wide range of current and potential habitats, industrial uses and societal values, with three broadleaf (hardwood) and four conifer (softwood) species. Some are the object of advanced breeding programs (Norway spruce, Scots pine, maritime pine and poplar), and are therefore the ideal candidates to adopt further breeding innovations. Some represent highly productive non-native species of great potential in Europe (Eucalyptus), while others species like Stone pines provide sustainable high value non-wood products or are highly threatened like Ash. These species can also be considered as pioneer models for all 48 forest tree species listed in EU directives regulating forest reproductive material trade.
Genomic selection requires screening genomes with thousands of genetic markers. Such tools are typically expensive to develop for a single partner, or for a single species, unless high demands can be guaranteed over a long period. B4EST represents the ideal framework to gather partners and species to a level of demand that opens up the door to extremely competitive rates, within the consortium and for external partners.
B4EST is developing three genotyping arrays, highly miniaturized devises able to screen up to 50,000 markers each, for six of the species lacking such resources (Norway spruce, Scots pine, maritime pine, stone pine, ash and poplar). They will be available in September 2019. It will also develop genomic selection at an operational level on all the above species (including Eucalyptus), in different contexts and for different objectives. By doing so, new statistical tools able to handle massive data will be tested over relevant collections of more than 2,000 individuals per species, paving the way for further implementations in other species in the future.
This article explains research that will take place in B4EST Work Package 3 which is led by Dr Leopoldo Sanchez Rodriguez, INRA (Orleans).
New research fellow starts with B4EST
Abdou Rahmane Wade has just started his PhD within the INRA team in Orléans. He will study the ways to incorporate gene network information (information about which genes interact and with what effect) into mathematical models for predicting tree phenotypes (trees with the same characteristics).
So far prediction models used information contained in the gene sequence (polymorphisms) to predict directly the tree phenotype. Abdou’s project aims at including an intermediary step between polymorphisms and phenotypes that accounts for the way genes interact with each other. This, it is believed, will increase the performance of the predictions.
Abdou’s research is part of B4EST Work Package 3 and Vincent Segura and Leopoldo Sanchez will supervise his thesis.
Abdou has recently finished his training on genetics, evolution and plant breeding at SupAgro Montpellier.
Take our survey on adaptive tree breeding!
The B4EST project is launching a European survey on adaptive tree breeding, open to people working in the forest sector such as forest managers and owners, tree breeders, and representatives of forest associations and industry.
B4EST is an EU Horizon 2020 project which has a focus on fostering productive, sustainable and resilient forests under climate change. The survey aims to identify a realistic picture of the experiences and expectations of different groups in the forest sector towards adaptive tree breeding and the usage and uptake of improved forest reproductive material (FRM). FRM is used in regeneration and afforestation, and refers to all parts of a tree that can be used for reproduction, for example fruits, seeds and cones. Improved FRM provides specific benefits, for example better resilience to climate conditions, pests and diseases.
By taking the survey, you will have the opportunity to influence future FRM developments, and inform policy makers.
It takes about 15 minutes to answer the questions, and you can choose whether to answer anonymously or leave contact details if you wish to receive an executive summary of the key findings.
The deadline for answering the survey is 10 March 2019.
Take the survey in English here: https://www.surveymonkey.de/r/VT5W8T6
It’s also available in:
|German (DE) ||https://www.surveymonkey.de/r/VQK2TFX|
What plant materials should we use and how should they be managed to provide Europe with healthy and productive forests in a future climate?
The Ålbrunna Norway spruce seed orchard. Currently the main provider of improved plant material in central Sweden. One of many seed sources that need to be characterized in detail in the B4EST project. Picture courtesy of Almqvist, Skogforsk
The selection of plant materials, for example seedlings and saplings, is one of the most important decisions that a forest manager will make when establishing or regenerating a forest. The decisions made will have a fundamental influence on the performance of the trees and will have consequences over the entire life of a forest stand. If chosen correctly, used at suitable sites and managed properly, genetically improved plants combine higher rates of growth, improved stem and wood quality and will be better adapted to cope as our climate changes.
In B4EST we are combining new scientific advances in forest genetics, silviculture, molecular biology and climate research with the needs of forest owners and other stakeholders to develop guidelines and decision support tools to enable greater and more informed use of genetically improved plants in forestry. An important feature of our work is that the information and tools we create will be applicable to contemporary genetically improved plant material like seed orchard crops and clones or clonal mixes.
To develop the guidelines and tools we will make use of mathematical models developed in B4EST which describe how trees of different genetic make-up react to climatic conditions (like drought, heat, precipitation and frost) as well as damaging biological agents such as insects and fungi. The models will be used to predict the performance of genetically improved plant material in future climatic conditions to understand ‘deployment zones’.
To inform the development of our models and tools, we will also be working with for example, forest owners and forest owner associations, forest managers, larger forest companies to explore and create a generic definition of tree ‘performance’. We will explore for example if it should include tree growth and survival, increased stem and wood quality, as well as the ability to avoid damages from climatic events (like frost or drought) and attacks from biological agents such as insects and fungi.
As we discussed earlier, the performance of a forest stand results from the combination of the plant material used and the way in which it is managed once planted. A major aim of the project will be to improve existing models which estimate tree growth and stand dynamics (how the trees as a group or a stand develop over time given for example, silvicultural actions and the properties of a site) to take account of the genetic gains that may be achieved from using genetically improved plant material and other important factors identified by B4EST, like group performance, genetic diversity and adaptive properties. These will be used to simulate different silvicultural practices at both forest stand and landscape scales and enable us to compare, evaluate and recommend alternative ways of managing forest stands as well as optimizing the genetic gain.
Finally, we will also develop a framework for providing deployment recommendations for genetically improved plants that are based on biological constraints rather than administrative ones. In other words the information will be categorised over regions with similar biological backgrounds and climatic conditions and a common characterization of plant material. In this way we hope to facilitate cross-border collaboration in the use of plant materials. We will also be identifying and discussing with relevant stakeholders any national and EU rules that may restrain or prevent the use of new clones and varieties.
This article explains the research that will take place in B4EST Work Package 4 which is led by Mats Berlin, Skogforsk, Sweden.
Investigating how tree characteristics interact to help us produce ‘good’ trees in a changing environment.
Although in tree biology we often study single characteristics or ‘traits’, we know that in reality natural selection has acted on all traits at the same time. The tree we see in the forest is the outcome of maximising different essential functions of the tree under pressure from the living and physical environment. Tree breeders have typically focussed on improving some traits, like growth rate or productivity, at the expense of other potentially valuable characteristics. But in a changing world, where future environments are uncertain, we need to find ways to make forests resilient, and making more use of a wider range of the traits of a tree is key.
In the B4EST project, we will use specially selected populations of trees to study how different traits, like growth rate, pest and disease resistance, drought tolerance and seed production, work together. For example, a tree that invests a lot of resources in disease resistance might not grow as tall as others; in this case we would try to find good combinations of these characteristics that mean we have productive trees that are also able to tolerate disease.
We will study how these interactions change when the trees are planted in different environments and how they work in different species. We will try to find the genes that control these combinations of traits and use the knowledge we gain to find ways to breed trees that are diverse, resilient and productive at the same time. In this way, we hope to help secure our forests against the uncertainty of environmental change.
The work described above is being completed within B4EST Work Package 2 which is led by Ricardo Alia from CIFOR-INIA.
Assessing the biological and climatic factors affecting the productivity and resilience of trees.
B4EST began in May 2018, and is a Horizon2020 EU funded project led by Dr Catherine Bastien from INRA in Orleans, France. The project aims to enhance the role of forests in Europe in providing for biodiversity, carbon storage, and the provision of renewable raw materials for the expanding bio-based economy, under climate change. B4EST will also identify new opportunities for wood and non-wood (e.g. nuts, seeds and fruits) products based on forest-based raw materials that could also stimulate the European bio-economy.
The bio-based economy currently utilises 50-60% of the harvested wood from 161 million hectares of forest (38% of land area) in Europe. This forest industry and the European industries dependent on wood products represents 7% of the EU manufacturing GDP which together support 3.5 million jobs. Rapid climate change is a current cause of uncertainty in the sector and numerous studies predict impacts to European forest production that would have a knock-on impact on the industrial sector and jobs.
The project is using eight study species to demonstrate novel techniques in the identification, assessment, and deployment of environmentally and genetically tested and improved trees that will be better suited to a future climate. The B4EST project study species are: Scots pine, Norway spruce, maritime pine, stone pine, Douglas-fir, eucalyptus, ash and poplar. All these species have high importance from an economic, ecological, and/or social perspective.
An important part of the project will be to use trials in Europe of trees of selected provenance (region of tree or seed origin) and/or progeny (descendancy) to identify and assess the combined resistance of trees to climatic and biological stresses, for example drought, heat, frost, pests and diseases. We’ll also be assessing how trees of selected progeny are better able to adapt to these stresses.
How will we do this? We’ll be studying existing genetic trials in what are known as ‘common garden experiments’. These are trials designed to test a range of genotypes – trees with the same genetic makeup. These could be trees of different provenances that have undergone natural selection, or trees of known progeny. In some cases the trials also test selected clonal material.
Common garden experiments test all the selected trees across a range of environmental conditions. This enables us to measure important characteristics (‘traits’ such as height growth, timber straightness, disease resistance) to understand the different ways a genotype performs and responds to a range of environmental conditions (‘phenotypic’ variation).
We aim to model several important responses simultaneously, combining measures of characteristics such as tree height, tree form, wood quality, disease/pest resistance and consider trade-offs between characteristics. The models will be used to predict how genotypes will perform in parts of Europe as our climate changes, and under pressures of certain pests and diseases. The genetic variation of tree material will be studied to understand and predict to what extent it is possible to control the tolerance of trees to climatic and biological disturbances through tree breeding. This will help define the suitable regions for future deployment of tree breeding material under climate change.
The research described will be undertaken by B4EST’s Work Package 1 which is led by Forest Research in the UK, and involves fourteen partners: INRA (France), INIA (Spain), Skogforsk (Sweden), LUKE (Finland), EFI (Europe), SLU (Sweden), NERC-CEH (UK), WR (Netherlands), CIRAD (France), CREA (Italy), NIBIO (Norway ), UPS (France), ALTRI (Portugal).
Adaptive breeding for productive, sustainable and resilient forests under climate change
Climate change can increase forest vulnerability to damage and disease, reduce forest health and productivity, and cause economic losses.
The EU project B4EST was recently launched with the aim of providing forest tree breeders, forest owners, managers and policy makers with better scientific knowledge to deal with these issues.
B4EST will combine expert knowledge from forest actors with the generation of new scientific information on tree species sensitivity and capacity to adapt to climate change. It aims to provide new, flexible and resilient tree breeding strategies and tools, which take into account old and new pests and diseases currently threatening European forests. B4EST will match the already available and newly identified forest genetic resources to the environments where they will perform best, and provide recommendations for policy makers and forest managers.
The project focuses on 8 of the most economically, ecologically and socially important tree species in Europe, covering a wide range of current and potential habitats, industrial uses and societal values. The goal is to increase forest survival, health, resilience and productivity, while maintaining genetic diversity, key ecological functions and fostering a competitive EU bioeconomy.
The project consortium includes 19 partners from Finland, France, Italy, Netherlands, Norway Portugal, Spain, Sweden and the UK, as well as the European Forest Institute. The EU is funding the project with about EUR6 million over a four-year period.
Postdoctoral researcher vacancy
Postdoctoral researcher, Tandem Forest Value project FutureGenes
We are searching for a post doc researcher to work on Tandem Forest Value Project FutureGenes. It is a two-year position starting in December, 2018.
Tandem Forest Values is a bilateral (Finland-Sweden) research program within forestry and the forest products industry. FutureGenes project combines four teams: National Resources Institute Finland, Luke (prof. Katri Kärkkäinen) SLU (Prof. Harry Wu) UOulu (Dr. Tanja Pyhäjärvi) and Skogforsk (Dr. Mats Berlin) to study genetics of adaptation to climate and possibilities to mitigate the effects of climate change to forests via breeding and optimal seed deployment. In the project, we will analyse data on Scots pine and Norway spruce obtained in national projects on local adaptation and genomic selection, and in an ongoing H2020 project B4EST (Adaptive tree breeding strategies and tools for forest production systems resilient to climate change and natural disturbances).
We are searching for a post doc researcher to work with us e.g. in analyses of genetic variation, differentiation and genomic prediction (e.g., quantitative genetic and sequence variation analyses, genomic selection methods), and in defining optimal deployment models for future climates.
Closing date: 9 November 2018
Image credits: Daiga Ellaby, Unsplash