PhD student in Quantitative genomics

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 ecosystem studies. Learn more at www.ieg.uu.se.

We are now looking for a PhD student in Quantitative genomics to the program Plant Ecology and Evolution

Project description
This doctoral position is part of a Formas project that stems from a collaboration with Skogforsk, the Swedish Institute for Forest Research, and has both a basic research perspective and an applied perspective.

Productive forest land represents ~55% of Sweden's total land area and wood production kept increasing since the 1950’s. Being able to produce better wood-bioproducts is thus of paramount importance in order to keep up with sustainable development goals while satisfying increasing worldwide demand. Genomics-based breeding techniques represent the future of tree breeding programs as they allow us to shorten the breeding cycles while increasing the selection intensity together with a reduced phenotyping effort. Traditionally, these methods are applied using single nucleotide polymorphisms (SNPs) as genetic markers. However, studies about genomic structural variations suggest a main role of gene copy number variations (gCNVs) in the control of phenotypic traits.

The project aims at incorporating gCNVs into genomics-based breeding techniques in order to increase their accuracy and efficiency. Using Norway spruce as biological model, we aim at:

1. Rethinking the population and quantitative genetics framework to integrate information about gCNVs.
2. Further developing methods for the genome-wide dissection of quantitative traits by incorporating gCNVs.
3. Evaluating and testing the gain in model accuracy, predictive power and ultimately in productivity by incorporating gCNVs in a genome informed prediction and selection effort within the existing Norway spruce breeding program.

Duties
The selected candidate will conduct quantitative genomic studies using designed crosses and common-garden like experiments, perform wet-laboratory experiments (e.g. DNA extraction, quantitative PCR), generate and analyze -omics data. The project also includes field work to measure phenotypic traits of interest in Skogforsk’s trials.

Qualifications required
To meet the entry requirements for doctoral studies, you must

• hold a Master’s (second-cycle) degree in Evolutionary Biology or Population and Quantitative Genetics/Genomics.
• have completed at least 240 credits in higher education with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
• have acquired substantially equivalent knowledge in some other way.

We attach great importance to personal qualities such as initiative, creative thinking, the ability to collaborate and to get involved in the life of the research group and the institute. Candidates must be able to express themselves very well in English, both orally and in writing.

Qualifications desired
The applicant should master the main concepts in Evolutionary Biology, have a background in population genetics/genomics and a solid foundation in the statistical considerations for these analyses as well as a taste for bioinformatics. The following skills will be considered a merit: Molecular biology/wetlab, Programming, Mathematics / Modelling, Variant calling. Please note that a background in Plant Biology is not mandatory.

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 §7. Scope of employment: full-time. Starting date 2025-09-01 or as agreed. Placement: Uppsala.

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.

For further information about the position, please contact
Associate Professor, Pascal Milesi, pascal.milesi@scilifelab.uu.se. Researcher, Henrik Hallingbäck, henrik.hallingback@skogforsk.se.

Application instructions
The application should include 1) a letter describing yourself, your research interests, why you want to pursue a Ph.D., and why you are suitable for the position (1 page maximum), 2) your CV including a brief description of your education, 3) a copy of your master's degree and your course grades, along with a copy of your master's thesis, 4) names and contact details of at least two referees (email addresses). The application should be written in English.

You are welcome to submit your application no later than July, the 21th 2025. UFV-PA 2025/2161.

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