Researcher in Animal Science

Role: Researcher in Animal Science
Organization: The Swedish University of Agricultural Sciences (SLU)
Department: Department of Animal Biosciences
Location: Uppsala, Ultuna, Sweden
Contract Type: Permanent, Full-time (100%)
Application Deadline: 12 Jun 2026 - 12:00 (UTC)

Job Overview
The Department of Animal Biosciences is looking for a motivated and committed researcher to understand the genetic consequences of feralisation and how these processes can alter the phenotype in feral and wild chickens. The position involves working and directing a project analyzing genomic, transcriptomic, and methylation data obtained from feral birds from Hawaii and Bermuda. The goal is to determine the genetic basis of feralisation, particularly the role critical regions play in shaping phenotypic variation. Additionally, single-cell data will be analyzed to understand how the genetic basis of feralization corresponds to differences elicited by domestication from a wild state. Identified regions and genes will be used to help produce a transgenic chicken to turn a domestic chicken wild, as part of an ongoing project with Revive & Restore. Opportunities for research visits abroad may be available.

Responsibilities
- Analyze large-scale genomic, transcriptomic, and methylomic data, as well as single-cell analysis data.
- Explore evolutionary mechanisms behind feralization and domestication in chickens.
- Analyze WGS data and RAD-seq data (genomics).
- Analyze RNA-seq data (transcriptomics).
- Analyze MeDIP-seq data (methylomics).
- Analyze scRNA-seq and scATAC-seq (single-cell omics) data of feral chicken from different populations.
- Quantify gene expression (both bulk RNA-seq and scRNA-seq) and chromatic accessibility (scATAC-seq) in different tissues.
- Investigate differential gene expression using tools such as DESeq2 and EdgeR.
- Find putative selective sweeps using a combination of methods including SweepFinder2, SweeD, OmegaPlus, Rehh, and Tajima’s D.
- Analyze runs of homozygosity (ROH) and calculate inbreeding coefficients (FROH).
- Calculate diverse population genetics metrics (e.g., heterozygosity, LD curve).
- Perform QTL (Quantitative Trait Loci) analyses and GWAS (Genome-wide Association Study) to identify associations of genotypes with morphological and behavioral traits using MatrixEQTL and GEMMA.
- Analyze expression patterns using MatrixEQTL.
- Contribute to the positive development of the subject area.

Requirements and Qualifications
- Education: PhD in animal science, veterinary medicine, natural sciences, or engineering.
- Language: Documented proficiency in written and spoken English.
- Technical Skills:
- Familiarity with different versions of the chicken reference genome.
- Computing in High-Performance Computing (HPC) environments such as PDC and UPPMAX.
- Advanced coding skills in programming languages: R, Bash (Linux), Python, Matlab, and Mathematica.
- Note: As this project is ongoing, all the above skills are requirements, and only candidates fully meeting all of the above will be considered.
- Personal Qualities: Commitment, ability to collaborate, analytical skills, independence, initiative, and organizational skills.

What They Offer
- Indefinite-term employment (SLU may use probationary employment).
- Start date: As agreed.
- Work environment characterized by inclusivity and gender equality.
- Opportunities for research visits abroad.
- SLU provides attractive environments on all campuses and invests in sustainable societal development.

About the Department
The Department of Animal Biosciences is part of the Faculty of Veterinary Medicine and Animal Science and is responsible for education and research in areas including anatomy, physiology, biochemistry, pathology, pharmacology, toxicology, genetics, breeding, immunology, bacteriology, virology, parasitology, epizootology, comparative medicine, food safety, bioinformatics, and One Health. Research covers production animals, sport and companion animals, laboratory animals, and wild animals, ranging from molecular mechanisms to animal structure, function, and behavior.