Vacant job

Department of Animal Biosciences

We are looking for a researcher to prepare future projects on the genetic basis of feralization in chickens

About the position

We are seeking a motivated and engaged researcher with knowledge of the genetic consequences of feralization and how these processes can alter the phenotype of feral and wild chickens. The position involves working on and leading a project where you will analyze genomic, transcriptomic, and methylation data obtained from feral birds from Hawaii and Bermuda. The goal is to determine the genetic basis of feralization, with a particular focus on the role of critical regions in shaping phenotypic variation.

A large amount of 'single-cell' data will also be analyzed to understand how the genetic basis of feralization corresponds to the differences induced by domestication from a wild state. These identified regions and genes will then be used to produce a transgenic chicken to transform a domestic chicken into a wild type, as part of an ongoing project with Revive & Restore. Opportunities for research visits abroad may exist. The research involves bioinformatics work with large-scale genomic, transcriptomic, and methylomic data, as well as 'single-cell' analysis.

Requirements

You must hold a PhD in animal science, veterinary medicine, natural sciences, or engineering. You must also have documented good proficiency in written and spoken English. The project involves exploring the evolutionary mechanisms behind feralization and domestication in chickens, analyzing WGS and RAD-seq data (genomics), RNA-seq data (transcriptomics), MeDIP-seq data (methylomics), as well as scRNA-seq and scATAC-seq data (single-cell omics) from feral chickens from various populations.

Necessary methods and skills include:

• Quantification of gene expression (both bulk RNA-seq and scRNA-seq) and chromatin accessibility (scATAC-seq) in different tissues.
• Investigation of differential gene expression (e.g., using DESeq2 and EdgeR).
• Identification of putative selective sweeps using a combination of methods (SweepFinder2, SweeD, OmegaPlus, Rehh, Tajima’s D).
• Analysis of homozygosity (ROH) and calculation of inbreeding coefficients (F_ROH).
• Calculation of various population genetic measures (e.g., heterozygosity, LD curve).
• Performing QTL analyses (Quantitative Trait Loci) and GWAS (Genome-wide Association Study) to identify associations between genotypes and morphological and behavioral traits (using both MatrixEQTL and GEMMA), as well as expression patterns (using MatrixEQTL).

Familiarity with different versions of the chicken reference genome, data processing in high-performance computing environments (HPC) such as PDC and UPPMAX is required, as well as advanced coding skills in programming languages such as R, Bash (Linux), Python, Matlab, and Mathematica.

Since this project is ongoing, all the above skills are mandatory, and only candidates who meet all the aforementioned requirements will be considered. Emphasis will also be placed on personal qualities such as engagement, teamwork, analytical ability, independence, initiative, and organizational skills.

The position will be offered to the candidate who, after a qualitative assessment, is judged best suited to perform and develop the project tasks and contribute to a positive development of the subject area. Language: The applicant must be able to write and communicate in English.

About us

As a researcher, you will work at the Department of Genetics, Breeding, Biochemistry, and Bioinformatics.

The Department of Animal Biosciences is part of the Faculty of Veterinary Medicine and Animal Science and is responsible for education and research in several basic and applied scientific areas. These areas include anatomy, physiology, biochemistry, pathology, pharmacology, toxicology, genetics, breeding, immunology, bacteriology, virology, parasitology, epizootiology, comparative medicine, food safety, bioinformatics, and One Health. Our research covers everything from production animals to sport and companion animals, laboratory animals, and wild animals. The department's researchers work across the spectrum from molecular mechanisms and microbiology to animal structure, function, and behavior, and how these are affected by breeding, physical activity, husbandry, production, stress, environmental factors, and diseases.

More information about the department: Link to website (https://www.slu.se/om-slu/organisation/institutioner/husdjurens-biovetenskaper/)

Read more about our benefits and what it is like to work at SLU at slu.se (https://www.slu.se/om-slu/jobba-pa-slu/)

Location: Uppsala, Ultuna

Employment type: Permanent. SLU may apply a probationary period.

Scope: 100%

Start date: By agreement.

Application: Welcome to submit your application via the button below by 2026-06-12.

Union representatives: Link to union representatives (https://internt.slu.se/min-anstallning/facket/kontaktpersoner/)

Sveriges lantbruksuniversitet (SLU) plays a key role in the development of sustainable life, based on science and education. Through our focus on the interactions between humans, animals, and ecosystems, and responsible use of natural resources, we contribute to sustainable societal development and good living conditions on our planet. Main campuses are in Alnarp, Umeå, and Uppsala, but operations are also conducted at research stations, trial parks, and educational centers throughout the country. SLU has over 4,000 employees, 6,000 students and doctoral students, and a turnover of over 4.5 billion SEK. The university invests in attractive environments on its campus areas. We work for an equal and inclusive working environment where open dialogue between people with different experiences lays the foundation for scientific rigor, creativity, and development. We therefore welcome people with different backgrounds and perspectives to apply for the current position.