Forskarskolan är en del av UPSC Berzelii center för skogsbioteknik och är placerad vid Umeå Plant Science Centre (UPSC), ett samarbete mellan Sveriges Lantbruksuniversitet och Umeå Universitet. UPSC är en av Europas ledande forskningsmiljöer inom experimentell växtbiologi, och världsledande inom skogsbioteknik och genomik.
Din bakgrund kan vara inom biologi, skogsvetenskap, kemi, fysik, bioteknik, matematik eller statistik. Forskarskolan erbjuder handledning, kurser och teknikplattformar i absolut världsklass och kommer att starta under hösten 2012.

Du anställs som doktorand vid ett värdföretag under 5 år (mot normala 4 år) eftersom 20% av arbetstiden kan ägnas åt arbete inom värdföretaget. Du kommer redan från början att vara en viktig del av värdföretagets organisation och skall fungera som en brygga till den akademiska forskningen. Detta ger dig en helt unik möjlighet att få en fast förankring i ett företag och viktig industriell erfarenhet.
Värdföretagen är: Bergvik Skog, Holmen Skog, Skogforsk, Stora Enso och Sveaskog/Svenska skogsplantor.
En komplett ansökan för varje doktorandtjänst markerad med respektive referensnummer skall skickas in till Registrator, SLU, Box 7070, 75007 Uppsala senast 15:e Augusti 2012.
Information om tjänsterna kan fås av respektive handledare eller av Professor Ove Nilsson ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ).

1. De genetiska mekanismerna som ger upphov till heteros (Ref: 2092/2012)

Handledare. Prof. Per Ingvarsson ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it )
Värdföretag: Stora Enso AB

Heteros benämningen på den ökningen i tillväxt och/eller produktivitet man ofta observerar i hybrider i förhållande till föräldrarnalinjerna eller föräldraarterna. Heteros har länge spelat en viktig vid förädlandet av många grödor, som till exempel majs, ris och många spannmålsvarianter. Heterosis har nyligen också blivit ett viktigt verktyg för att öka produktiviteten hos många arter av skogsträd och i synnerhet i mer snabbväxande arter såsom popplar och Eucalypts. Trots att heteros historiskt sett har varit mycket viktigt inom jordbruket, är den genetiska grunden för heteros fortfarande ganska dåligt undersökt. De viktigaste konkurrerande hypoteser omfattar dominans, överdominans och epistasi och dessa teorier ger olika förutsägelser både om den molekylära grunden för heteros och samt även hur stabil heteros kommer att vara i kommande generationer. Syftet med doktorandprojektet är att använda nyutvecklade metoderför hel-genomskartläggning (GWA) och genomisk selektion (GS) för att studera den genetiska grunden för heteros. Projektet kommer innefatta båda teoretisk undersökning av genomisk selektion i hybrider och praktiskt arbete med implementering i kommersiellt tillgängliga korsningar av olika arter av Eucalyptus.

Tjänsten innefattar 5 års finansiering som inkluderar ett års praktisk arbete vid värdföretaget, StoraEnzo. Ansökan är öppen fram till denn en lämplig kandidat idetifierats. Lämpligt startdatum för tjänsten är någon gång under andra halvåret 2012. Doktoranden kommer att handledas av Pär K. Ingvarsson och Harry Wu.

2. Genetiska verktyg för att modifiera vedegenskaper hos träd (Ref: 2093/2012)

Handledare. Prof. Urs Fischer ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it )
Värdföretag: Stora Enso AB

This project aims to produce tools to practically implement biotechnology for major wood modifications in forest plantations and to generate knowledge for modifying cellulose in wood. Application of biotechnology in forest plantations may focus on modifying wood to decrease energy required for wood chipping, decrease wood recalcitrance, avoid inhomogeneous wood by removing G-layers in tension wood, and drastically alter wood polymer composition for specific uses. An unsolved practical problem with this approach is that large modifications often have adverse effects on tree growth and survival. This project aims to identify and test promoters and transcription factors that can be used for major modifications of wood while still maintaining a healthy tree.

We want to shed more light on the machinery of cellulose biosynthesis, with the idea to produce highly modified wood. This will require the application of tissue specific promoters since ubiquitous expression of key regulators of cellulose deposition is lethal. Novel promoters will be identified from spatially highly resolved transcriptomics across developing wood of aspen. These promoters will be used to drive the expression of reporter genes or transcription factors, which have the potential to direct expression of large subsets of genes involved in cellulose biosynthesis. Since known transcriptional regulators of cellulose biosynthesis also regulate genes involved in the synthesis of other wall polymers or unrelated processes, novel transcription factors shall be identified in order to target cellulose synthesis more specifically. Alternatively, artificial transcription factors will be engineered, which can bind to promoters of cellulose synthesis genes but not to other gene regulating sequences. Chemistry, fiber mechanics and wood processing properties will be assessed in modified trees. This approach could strongly affect recalcitrance and mechanical properties of the woody raw material.

Applicants hold a MSc in Plant Biology, Biotechnology or a similar degree. Profound theoretical and practical knowledge in molecular biology and bioinformatics are required and exposure to handling of large datasets, R-language and chemical analyses are advantageous.

3. Reglering av rotbildning hos somatiska embryon i gran (Ref: 2094/2012)

Handledare. Prof. Ulrika Egertsdotter ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it )
Värdföretag: Sveaskogs Förvaltning AB

Successful regeneration of plants from somatic embryos of Norway spruce (Picea abies) was shown already in the 1980s. However, owing to the labor intensive steps of the somatic embryogenesis (SE) process for regenerating plants, it is only recently by the invention of an automated system (SweTree Technologies AB) that SE plant production can become a reality for large scale plant production in the forestry sector.
In order to implement an efficient and cost-effective process for mass propagation of SE plants from an unlimited number of genotypes, the basic protocols for somatic embryogenesis (SE) need to be further improved. One of the major bottlenecks of the process relates to inefficient germination and subsequent root development from the somatic embryos of certain genotypes, limiting the selection of genotypes that are mass propagated and thus reducing the gain from the breeding program.
During the SE process, mature somatic embryos germinate to form a root supported by a carbohydrate source under in vitro conditions. Further growth and development of the SE plant can occur in a nursery greenhouse germination environment. Recent data suggest that one way of improving the frequency of well germinating embryos, with a high probability to form robust plants, is to supply an organic nitrogen source, such as arginine.

In this project the role of nitrogen inthe regulation of root formation during germination and continued root development during plant development will be studied. Furthermore, other important factors that determine the germination success and further development of the root will be studied, such as other nutrient factors and the substrate composition.

The project work will be performed during a period of five years in close collaboration with the Svenska Skogsplantors forest tree nurseries and SweTree Technologies AB. One year of the project will be on the field site with the industry partner. The project includes both in vitro laboratory work with SE cultures and field work in nursery greenhouses with SE plants.

The student is expected to have an MSc degree, or equivalent, in a subject relevant for the project position. Previous experience with tissue culture techniques and work in a sterile environment is desirable. Excellent communication skills orally and in writing are required, both in English and Swedish.

4. Granens anpassning till varierande klimatförhållanden (Ref: 2095/2012)

Handledare. Prof. Bengt Andersson ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it )
Värdföretag: Bergvik Skog AB

Climate change will require forest regeneration material adapted to a different range of conditions than those existing today, including novel combinations of photoperiod and temperature conditions. The aim of this project is to develop norms of reaction models to describe the amount and pattern of genotype by environment interaction for Norway spruce in a climate change context. Models will describe the phenotypic response to varying environmental signals, climatic indices included, and genotypes. Responses in characters important for adaptation will be investigated, such as growth, growth rhythm, bud flush, growth termination, hardiness, survival, etc. The models will be used for selection of individuals in tree breeding or for mass propagation showing a high and stable performance in a broad range of environments with different climatic conditions. At population level, we will develop the best use of improved seedlings by deployment functions and delineating seed utilization zones over general climate gradients. It is also important to reveal G x E interaction on individual tree or family level for site specific effects like frost prone and not frost prone sites. Part of the project will involve artificial climate experiments using greenhouses and climate chambers to study the annual growth cycle in response to climate variables. Part of the project will involve mega-data analyses of population with environment interaction for Norway spruce using variables describing the climate based on meteorological data used in climate scenario research and variables that describe the site.

5. Skogsträdens populationsgenomik (Ref: 2096/2012)

Handledare. Dr. Stacey Thompson ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it )
Värdföretag: Bergvik Skog AB

Umeå Plant Science Centre is looking to fill a PhD student position in the population genomics of forest trees. The project involves the assessment of diversity and connectivity of spruce stands, pristine and managed, exotic and native, through Genotyping By Sequencing (GBS) and other high-throughput approaches. The chosen candidate will by co-advised by Stacey Lee Thompson and Nathaniel Street, and will collaborate broadly with numerous research groups at UPSC (e.g. Pär Ingvarsson, Stefan Jansson, Rosario García-Gil), Skogforsk and our industrial partner Bergvik Skog. This project utilizes the resources generated by The Spruce Genome Project, ongoing here in Umeå (http://www.congenie.org/).
How do different reforestation methods impact genomic variation within spruce stands? Clear¬cut and continuous cover forestry are contrasting natural resource management practices that have been broadly employed through Sweden for hundreds of years. Although each practice has different theoretical expectations for resulting diversity (e.g. allelic richness, relatedness, age structure, spatial dynamics), little is known about realized patterns within the reforested spruce stands of Sweden. This project will fill this knowledge-gap by using high-throughput genotyping and next generation sequencing to profile genomic diversity within forest stands under contrasting management and silvicultural practices, including the use of exotic provenances. Comparisons will be made with pristine forest sites, as well as with island populations of different ages and sizes that have recently uplifted from the Baltic and been colonized by spruce.
Site selection will be done in collaboration with our industrial partner, Bergvik Skog, with additional contributions from Skogforsk.

The chosen candidate will perform top-tier research and be exceptionally mentored as a member of the Industrial Research School in Forest Genetics, Biotechnology and Breeding. UPSC is a centre of Excellence for Plant and Forest Biology and Biotechnology, located in northern Sweden. Our ca. 200 employees (including about 40 faculty members) perform world-leading research and have access to outstanding infrastructure with many shared resources and platforms, including advanced facilities for growing, transforming and manipulating our main model systems. UPSC has been ranked as one of the top places in the world for doctoral studies. About half of our staff are non-Swedes, and the composition of employed staff and students at UPSC is highly dynamic, representing on average 36 nationalities.

The successful applicant should possess creativity, autonomy and a dedicated team spirit. The working language of UPSC is English and thus high competencies are required.
A full application consists of cover letter, your CV, certificates from higher education, copies of Bachelors/Masters thesis, a written description of your research interests, a written statement about why you are interested in the project, and contact information for three referees.
For more information about the position, contact Stacey Lee Thompson This e-mail address is being protected from spambots. You need JavaScript enabled to view it or Nathaniel Street This e-mail address is being protected from spambots. You need JavaScript enabled to view it

6. Utveckling av förädlingsmål för skogsträd (Ref: 2097/2012)

Handledare. Prof. Harry Wu ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it )
Värdföretag: Skogforsk

One of the most important tasks in designing a forest tree breeding program is to develop a breeding objective if improvement of multiple traits are considered. Through development of an economic breeding objective, the economic importance and economic weights of each breeding objective trait can be estimated and applied to a selection index for breeding selection. Economic breeding objectives have mainly been developed in animal breeding and have only recently been applied to forest tree breeding.

Scots pine and Norway spruce are the two most important species. Both species have long rotations, ranging from 50 years up to over a century, with one or several intermediate thinnings. The traditional aim of the Swedish Scots pine and Norway spruce breeding program is to breed for general purpose objectives, with a conservation objective for future climatic change. The general purpose objective is to improve vitality, growth and wood quality for optimal production efficiency across the entire Swedish forest sector. However, the general purpose objective has so far, not been based on economic breeding objectives with economic weights of breeding objective traits calculated by formal economic analyses of gains.

In this project, the PhD candidate will develop breeding objectives for one of the two main species in the Swedish tree breeding program. Economic weights for two main production systems (solid wood production, and pulp-paper production) in Sweden will be investigated in this project. Through the development of breeding objective for these products, bio-economic models or profit functions will be developed to estimate economic weights for two production systems. Genetic variance and covariance from early selection to harvest traits including wood quality traits are estimated from suitable progeny trials available for pine or spruce. The PhD candidate will implement the project for the following 6 components: 1) identifying sources of income and expenditure for production of solid-wood and pulp-paper products for either Scots pine or Norway spruce; (2) determining tree biological traits influencing costs and revenues for solid-wood and pulp-paper production; (3) defining corresponding profit equations or bio-economic models for different solid-wood and pulp-paper production systems; (4) developing economic weights of breeding objective traits for solid-wood production and pulp-paper productions; (5) estimating genetic parameters from early age to mature age for key breeding objective and selection criteria traits; (6) developing selection indices for production systems including solid-wood and pulp-paper.

The project will be developed based on Skogforsk's previous breeding objective works and will be closely aligned with current and future Skogforsk's sawing studies and genetic evaluation system of TREEPLAN. Dr Jansson will play a leading role in guiding the PhD project.

The scholarship funding is for 5 years with one year of practical experience working with Skogforsk's scientists. Application is open until a suitable applicant is recruited. It is preferable that the successful candidate should be able to start in the second half of 2012. The PhD candidate will be surpervised by Harry Wu (SLU), Gunnar Jansson (Skogforsk), and Bo Karlsson (Skogforsk).

7. Associationskartering och genomisk selektion hos skogsträd (Ref: 2098/2012)

Handledare. Prof. Harry Wu ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it )
Värdföretag: Skogforsk

Dissection of the molecular basis of trait variation in forest trees began in the 1990s with the introduction of quantitative trait locus (QTL) mapping in controlled-cross pedigrees using linkage analysis. Marker loci controlling variation in growth, tree form traits and wood properties have been founded for numerous tree species. However, QTL analysis using limited family pedigree did not result in the identification of useful markers for breeding due to very large confidence intervals on the chromosome. The recent candidate gene approach exploiting historical population-wide LD aimed to find alleles which may directly affect the phenotype and assume that linkage to the trait remained across populations and over many generations. However, two major issues with population based QTL detection are: (1) the estimated effects of SNPs only capture a small proportion of the total genetic variation in most economically important traits (usually less than 5% per SNP) , and 2) the separate steps QTL discovery, verification and estimation of allele effects in breeding populations erode the efficiency of the detection and application. The solution to this quandary does not lie in seeking the individual markers which show the largest effects on the trait but rather capitalizing on the developing capacity for scoring many markers at low cost and novel statistical methods that enable the simultaneous estimation of all marker effects. The practical implication of these results is that broad genome-wide searches will be needed to account for all the genes that control complex traits and for all the segregating variation in populations.

Genome wide selection or genomic selection (GWS or GS) was a new landmark approach, first proposed in 2001 in animal breeding. GS has now become a reality thanks to the rapid technological advances and lowered costs of high-throughput genotyping and is rapidly being adapted to crop and tree breeding.

GS uses a single step to estimate all marker effects simultaneously, retaining all of the markers as predictors of performance, thus precluding the prior search for significant marker-trait associations and by fitting allelic effects as random, rather than fixed effects. GS with enough dense markers on chromosome ensure that each QTL effect is at least covered by one or more markers through LD to recover the missing heritability typically associated with pedigree-based and population-based candidate gene approach. Simulation studies indicate that the effective population size (N_e) and marker density had the largest impact on accuracy of GS.

This PhD project will be a part of our overall larger project on genome-wide association and genomic selection in forest trees at UPSC. The overall aims of the project are to answer following questions: (1) how effective is GS relative to using conventional pedigree-based phenotypic selection in Norway spruce and Scots pine, particularly for very early selection, (2) what is the efficiency of GS applied in the same breeding population relative to applied to unrelated (cross-breeding) populations, (3) how much missing heritability can be recovered from GS for different types of traits such as growth, phenology and wood property, and (4) how do the number of markers (density), effective population size (N_e), and other genetic parameters (number of QTLs, heritability, pleiotropic and dominance effect) affect the efficiency of GS in tree breeding. The PhD project will use Norway Spruce as an example to investigate the genome-wide association and efficiency of genomic selection for Skogforsk breeding program.
The scholarship funding is for 5 years with one year of practical experience working with Skogforsk scientists. Application is open until suitable applicants are recruited. It is preferable that the successful candidates should be able to start in the second half of 2012. The PhD candidate will be supervised by Harry Wu, Pär K. Ingvarsson, and M Rosario García Gil.

8. Optimering av planttillväxt i en modern plantskola (Ref: 2099/2012)

Handledare. Prof. Torgny Näsholm ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it )
Värdföretag: Holmen Skog AB

Efficient production of conifer seedlings is based on rapid growth, driven by high rates of fertilizer application. However, following planting in the field seedlings must cope with various forms of biotic and abiotic stresses and the cultivation practises may not be optimal for seedlings to meet these stresses. The major stresses experienced by recently planted conifer seedlings include drought and herbivory, and the morphology and biochemical composition of the seedlings are important determinants for how they cope with these events. We suggest that the relative rates of acquisition of carbon and nitrogen will determine the internal balance of C and N in seedlings, which in turn will shape seedling morphology and biochemistry. This project will thus focus on the fundamental processes of C and N acquisition in conifer seedlings, with the goal of establishing new cultivation practises for large-scale seedling production