Postdoctoral scholarship, 2 years, in plant developmental biology

We are looking for a highly motivated postdoctoral fellow for the Kempe Foundations funded project "Analysis of miRNA function during embryo development in Norway spruce". The postdoctoral fellowship will be placed at the Department of Forest Genetics and Plant Physiology (Swedish University of Agricultural Sciences ), which is part of Umeå Plant Science Centre . The fellowship is at full-time for two (2) years, starting 1 September 2023.

Project summary

The project aims at understanding the function of miRNAs during embryo development in the model gymnosperm species Norway spruce (Picea abies). Gene expression RNA-Seq data and expression data for miRNA from the corresponding samples from a developmental series of zygotic embryos, the associated gametophytic tissue and somatic embryos are available from a previous project. Preliminary processing of the data suggests that miRNA may be involved in the regulation of key developmental steps during embryogenesis.

Specifically, the expression data will be further analyzed to identify candidate genes and potentially associated miRNA and functional studies performed to test the hypothesis. An increased understanding of the regulation of embryo development in Norway spruce will generally support improvements of protocols for somatic embryogenesis-based propagation of commercially important conifers.

Work tasks

The suitable candidate will primarily work with bioinformatic analyses to select candidate miRNA and associated targets.

Qualifications

A strong documented background in plant developmental biology is required. Specific knowledge in regulation of embryo development is desirable. Fluent in written and spoken English. Bioinformatics expertise is essential. This includes familiarity with processing, aligning, and analyzing Illumina RNA-Seq and shortRNA-Seq data, expression normalization and quantification, differential expression analysis (preferably using DESeq2) and visualization of results. Familiarity with miRNA analysis, including identification of known and prediction of novel miRNAs, is highly desirable. Familiarity with Linux, command line / shell scripting and relevant tools is essential. Experience in use of job scheduling and HPC infrastructure is highly desirable. Experience in use of tools for reproducibility, for example, containers and git, are beneficial. The position will involve extensive work in R and/or Python in addition to running command line tools and constructing analysis pipelines. As such, experience with tools such as Snakemake or Nextflow would be beneficial. Knowledge of biostatistics is required.

Required degree: PhD in a relevant area.

Application
The application should contain:

Please send the complete application to Dr. Ulrika Egertsdotter (Ulrika.Egertsdotter@slu.se ).

Applications are accepted until the position is filled.

Position specifications

The position is located at Umeå Plant Science Center in the laboratory of Dr. Egertsdotter. The postdoc position is supported by a stipend for a 24-month period starting September 1st, 2023.

Contact

For questions, please contact Ulrika.Egertsdotter@slu.se .

About the Research Environment

The Department of Forest Genetics and Plant Physiology is part of Umeå Plant Science Centre (UPSC) which is a centre of excellence for experimental plant research and forest biotechnology in Northern Sweden. Our mission is to perform excellent and innovative basic research and generate knowledge that benefits forestry, agriculture, environment and society. We work across a wide range of disciplines in plant science reaching from cell biology to ecophysiology and from basic research to industrial applications. Our common goal is to understand the plants’ ability to grow, adapt and acclimate to a changing world and how we can breed better plants.

UPSC belongs to two universities, Swedish University of Agricultural Sciences (SLU) and Umeå University . About 200 people from more than 40 different nationalities work here. We host some 30 principal investigators, and our researchers have access to state-of-the-art analytical platforms, unique tree germplasm resources and plant growth facilities. We strive for a collaborative work environment and support our scientists throughout all career stages by providing professional training opportunities and individual career mentoring.

Umeå has a strong postdoc community organised in the Umeå Postdoc Society (UPS). UPS fosters networking amongst postdocs, organises social and career development events and works towards improving the postdoc experience in Umeå. Check out their website: https://umeapostdocsociety.se/ and do not hesitate to get in contact with them!

About SLU

SLU is a world-class international university with research, education and environmental assessment within the sciences for sustainable life. Its principal sites are in Alnarp, Umeå and Uppsala, but activities are also conducted at research stations, experimental parks and educational establishments throughout Sweden. We bring together people who have different perspectives, but they all have one and the same goal: to create the best conditions for a sustainable, thriving and better world.
SLU has just over 3,000 employees, 5,000 students and a turnover of SEK 3 billion. The university has invested heavily in a modern, attractive environment on its campuses. Read more about our benefits and what it is like to work at SLU at https://www.slu.se/en/about-slu/work-at-slu/ .