The microbiomes of Swedish forest trees under the influence of environment and different nitrogen fertilisation.

Student: Andreas Scheneider

Brief description:
To ensure increasingly sustainable and efficient forestry practices, an understanding of how forest trees interact with their environments is crucial. This includes abiotic factors as well as biotic components such as microorganisms. Microbial lifeforms associated with plants can have beneficial effects on growth, health and fitness of individual plants. Through the rapid development of high-throughput sequencing technologies, it is now possible to get a full picture of microbial communities in all environments, including plants and their surroundings. Through so called amplicon sequencing, where a specific region of the genome of interest is amplified and sequenced, it is possible to get a profile of the microbial community in the original sample. This microbial count data can then be correlated with environmental parameters. This PhD will focus on the dynamics of the above-ground microbiomes of spruce and aspen; and the changes the below-ground microbiome of spruce and pine undergo depending on different nitrogen fertilisation.
Main supervisor: Nathaniel Street
Co-supervisor: Vaughan Hurry and Torgny Näsholm.
Industrial partner is Holmen Skog (contact person Daniel Hägglund)

Cold stress responses of Norway Spruce in warming climate

Student: Tuuli Aaro

The project involves identifying the key molecular regulators and mechanisms of Norway Spruce frost acclimation using gene editing tools. Using this information, also the breeding opportunities of Norway Spruce cold acclimation are determined with special emphasis on warming climate.

Main supervisor: Vaugh Harry
Co-supervisor/industry partner: Björn Sundberg (Stora Enso)

Sustainable forest regeneration in a changing climate

Student: Johannes Larson

In sustainable forestry, successful forest regeneration is key for the continued desirable stand development. The current climate change creates new challenges for forest regeneration with potential large variation in weather during the seedling establishment phase. New forest regeneration systems need to be developed, and an exciting development is currently under way, transferring new basic knowledge into efficient regeneration systems. The methods include modification of seedlings’ growth conditions to meet the variable growth environment. The knowledge we in this project intend to transform into practical methods involves, for example, how forest plants interact with the surrounding soil environment and its microorganisms, how different environmental factors control the establishment of tree seedlings and how climate change can affect the conditions for forest regeneration in different parts of Sweden.

Supervisor: Annika Nordin (SLU, Umeå)
Co-supervisor: Torgny Näsholm (SLU, Umeå), Jonas Öhlund (Swetree)
Industry partner: Sveaskog

Evolution and regulation of disease resistance in conifers

Student: Hernán Dario Capador-Barreto

Conifers are by far the most important trees in Swedish forestry. However, fungal pathogens represent a significant threat to production and wood quality. Since the 1940s a breeding program to improve wood production has taken place, but breeding for resistance to pathogens has not been implemented as such. This PhD aims to study different evolutionary aspects of disease resistance in conifers to broaden the knowledge on its genetic component and contribute to the breeding program of Norway spruce in Sweden.

Supervisor: Malin Elfstrand (SLU, Uppsala)
Co-supervisor: Jan Stenlid (SLU, Uppsala)
Industry partner: 

Defining sustainable and economic forestry practices with minimal impact on soil biodiversity and maximum benefits for tree growth

Student: Lill Eilertsen

The majority of temperate and boreal forest trees live in symbioses with ectomycorrhizal fungi (EMF). Considering all benefits of EMF for forest soils and tree growth and health, their conservation is economically and ecologically highly important. Clear-cutting is a common forestry practice in Sweden that disturbs the fungal community in soils. This PhD project aims in its first part at identifying the effect of alternative harvesting practices such as gap-harvesting with various gap sizes at an experimental site installed by Bergvik Skog in Jämtland, Sweden on fungal biodiversity in soil samples using DNA-amplicon sequencing. DNA-amplicon sequencing is a tedious and laborious but today the most accurate method to identify EMF communities in soils. To make it possible for forestry companies to assess EMF biodiversity and take it into account for favoring tree growth, we are developing a rapid and cost-efficient method for EMF identification using hand-held spectroscopic devices. To validate this method, results on sensitivity and specificity of fungal identification in soil samples will be compared to data from DNA-amplicon sequencing. In a third part of this PhD project we aim at developing inoculation techniques with EMF beneficial for pine seedling growth and survival. This development involves improvement of procedures but also defining beneficial EMF combinations and is intended for future use in nurseries. Inoculating seedlings already in nurseries with EMF identified at forest sites for out-planting, has the potential to shorten the seedling’s adaptation phase after out-planting and to enhance seedling survival and growth. The long-term aim of this project is to give forest companies research-based guidelines for more sustainable forestry practices with least detrimental impact on EMF biodiversity and to provide new tools that make EMF assessment more widely accessible and EMF use a practical routine in forest management.

Supervisor: Judith Felten (SLU, Umeå)
Co-supervisor: Vaugh Harry (SLU, Umeå), Nathaniel Street (SLU, Umeå), Torny Näsholm (SLU, Umeå), Anders Dahlberg (SLU, Uppsala)
Industry partner: Bervik

Seed orchard genetics and impact on forest plantations in boreal regions

Student: Alisa Kravtsova

The future supply of biomass for the Swedish forest industry will come mostly from plantations, and seed orchards supply almost all the regeneration material used in plantation. Because of this fundamental role, all orchards should function well, producing high seed yield and breeding gain while also securing broad genetic base to support a greater forest production and resilience in future conditions. Among other issues, background pollination (also called pollen contamination) in seed orchards is a major concern for the deployment of orchard crops because contaminating pollen decrease breeding gain. How severe is the issue is not yet clear because the a few available studies on seed orchard mating systems revealed controversial results. On a different note, mating between differently adapted populations could result in increased phenotypic and genetic variance that might facilitate novel adaptation under increased climatic fluctuations. Consequently, the seed orchard practices in Sweden (e.g. transfer seed orchard southward for better seed crop yield) may positively affect species´ long-term adaptation and productivity in their northern range. This potential positive effect, however, has never been examined.

Our research activities on seed orchards aim at obtaining an overview on how orchard design, location and management practices could have affected the genetic function of each orchard and, thus, the crops´ potential for production gain and climate adaptation. We are particularly interested in assessing the following issues:

  • The regional and temporal variation in background pollen contamination in pine and spruce orchards.
  • The impact of orchard design and management practice on pedigree structure and genetic diversity of the orchard crops.
  • The differences in adaptive trait distribution and allele frequency distribution between subpopulations of orchard progenies with internal pollination and mating with external pollen, respectively.
  • The effect of assisted gene flow mediated by orchard crops on survival, growth and genetic composition in boreal forest.

Supervisor: Xiao-Ru Wang (UMU)
Co-supervisor David Hall (UMU)
Industry partner: Skogforsk (Ulfstand Wennström)

Develop breeding objective for Scots pine

Hur värderar vi bäst olika egenskaper ekonomiskt när de vägs samman vid förädling?

Student: Irena Fundova

A selection index approach of multiple traits is used for current breeding selection for Scots pine. To be able to compare different traits they have to be transformed to a common monitory unite like SEK by using economic weights. However, economic weights for improving the multiple traits at rotation age have not been properly defined using the existing production systems (solid wood, pulp and paper, and energy production systems) of the two species. For Lodgepole pine, improvement of wood stiffness and other wood quality traits along with growth and vitality is also important. Through the development of breeding objective for these products, bio-economic model or profit function will be developed to estimate economic weights for different production systems and genetic variance and covariance from early selection to harvest traits including wood quality traits are estimated. There are now suitable progeny trials available for Scots pine with tree sizes suitable for construction wood studies. These can be used for a great number of investigations of which some has started.
Main supervisor: Harry Wu
Co-supervisor: Gunnar Jansson
Industry superviros: Bengt Andersson Gull (Skogforsk)

Genomic selection in tree breeding program

Hur kan vi utveckla nya förädlingsverktyg för att integrera alla de datamängder som kommer från de nya gran och tall-genomprojekten med existerande förädlingsprogram.

Candidate gene and genome-wide association of DNA markers with phenotypic traits has made the dissection of phenotypic variation into genotypic variation possible in trees. Current development of SNP chip in whole genome sequencing and re-sequencing projects is a first step towards developing efficient DNA marker system in pine and spruce for large scale association analyses. It is envisioned that genome-wide association could cover a large portion of genetic variation for quantitative traits. Genomic selection method has advanced greatly in animal breeding program recently. With the completion of whole genome sequencing and re-sequencing of spruce and pines, genomic selection could be a reality in tree with increased efficiency of early selection. However, specific method dealing with low linkage disequilibrium and large effective population number in the tree breeding population need to be developed for effective genome-wide selection including efficient design of experiment for tree species to accurately estimate allelic effects. We will examine how the size and structure of population, experiment design, mating structure and density of markers in tree species affected the accuracy of candidate and genome-wide association studies. Adequate tools will be developed for integration of genomics with practical breeding program. This could involve development of integration strategy, estimation of genomic breeding values, and use of genomic information in designing breeding strategy.

Host Company: Skogforsk

PhD student: Ainhoa Calleja-Rodriguez
Supervisors: Harry Wu (Main supervisor),
Pär Ingvarsson, Rosario Garcia Gil, Fikret Isik, Sara Abrahamsson (Industry supervisor)

Presentation from the 2nd general meeting