PhD “Identification of unique or deleterious genetic variation across Dutch cattle breeds using whole genome sequencing data” We are looking for a PhD candidate who is interested in biodiversity, in particular the conservation of farm animal genetic diversity. Are you interested in this topic and in analysing whole genome sequencing data within and across Dutch cattle breeds? Then we might have an opportunity for you at Wageningen University & Research to start your PhD research.

Livestock breeds contain unique genetic variation, that can be neutral, adaptive to local conditions, or harmful. The genomic regions containing this variation can be under selection or moving to fixation due to inbreeding.

Whole genome sequence data can be used to locate variants of interest, but sequence data is usually aligned against the public reference genome. Novel sequencing technology, long read sequencing, has made it possible to create breed specific reference genomes, to which other sequenced individuals of the same breed can be aligned to identify within breed variation. Also, those breed specific reference genomes can be combined in a Pan-Genome to identify variation across breeds.

Long reads and pan-genome are especially powerful to detect unique structural variation like copy number variants, which has proven very difficult with short-read sequencing. Moreover investigating the presence and frequency of harmful mutations in the genome of rare breeds (=the genetic load), within and across populations, can indicate the risk of loss of fitness of populations or individuals.

The aim of the project is to better understand the genomic differences within and between Dutch cattle breeds. The results of the PhD project will be relevant for the further development of the conservation program and gene bank for livestock breeds, managed by the Centre for Genetic Resources, the Netherlands (CGN).

You will be part of the Animal Breeding and Genomics group of Wageningen University and Research, and in this research project you will collaborate closely with the Centre for Genetic Resources, the Netherlands (CGN). The project is funded by the Dutch Ministry of Agriculture, Nature and Food Quality.

We ask

  • a university degree (MSc) in a discipline relevant to the PhD project (e.g. genomics, molecular genetics, bio-informatics, quantitative genetics);
  • interest in biodiversity, in particular the conservation of farm animal genetic diversity
  • experience with the analysis of genomic data;
  • clear scientific ambition in the conduct and publication of research work;
  • good control of English (both verbally and written); for this position your command of the English language is expected to be at C1 level.
  • a social, critical and positive learning attitude towards achieving excellence; a pro-active, independent working style
  • a social team player attitude

We offer

We offer a challenging, innovative and future oriented research project, embedded in a stimulating scientific and stakeholder environment.

Wageningen University & Research offers excellent terms of employment. A few highlights from our Collective Labour Agreement include:

  • sabbatical leave, study leave, and paid parental leave;
  • working hours that can be discussed and arranged so that they allow for the best possible work-life balance;
  • the option to accrue additional holiday hours by working more, up to 40 hours per week;
  • there is a strong focus on vitality and you can make use of the sports facilities available on campus for a small fee;
  • a fixed December bonus of 8.3%;
  • excellent pension scheme.

In addition to these first-rate employee benefits, you will receive a fully funded PhD position and you will be offered a course program tailored to your needs and the research team.The gross salary for the first year is € 2.541,-per month rising to € 3.247,- in the fourth year, according to the Collective Labour Agreements for Dutch Universities (CAO-NU) (scale P). This is based on a full-time working week of 38 hours. In principle this is a 48 month PhD position. We offer a temporary contract for 18 months which will be extended with 30 months if you perform well.

There are plenty of options for personal initiative in a learning environment, and we provide excellent training opportunities. We are offering a unique position in an international environment with a pleasant and open working atmosphere.

You are going to work at the greenest and most innovative campus in Holland, and at a university that has been chosen as the “Best University” in the Netherlands for the 16th consecutive time.

Coming from abroad
Wageningen University & Research is the university and research centre for life sciences. The themes we deal with are relevant to everyone around the world and Wageningen, therefore, has a large international community and a lot to offer to international employees. Applicants from abroad moving to the Netherlands may qualify for a special tax relief, known as the 30% ruling. Our team of advisors on Dutch immigration procedures will help you with the visa application procedures for yourself and, if applicable, for your family.

Feeling welcome also has everything to do with being well informed. Wageningen University & Research’s International Community page contains practical information about what we can do to support international employees and students coming to Wageningen. Furthermore, we can assist you with any additional advice and information about helping your partner to find a job, housing, schooling, and other issues.

More information

For more information about this function and procedure, please contact Aniek Bouwman ( or Mirte Bosse ( or Sipke Joost Hiemstra ( of the Centre for Genetic Resources, the Netherlands (CGN)
For more information about the procedure, please contact

Do you want to apply?
You can apply directly using the apply button on the vacancy page on our website which will allow us to process your personal information with your approval.
This vacancy will be listed up to and including the 15th of August, 2022. Job interviews are expected to take place after 25th of August, 2022.
The preferred starting date for this position is the 15th of September, 2022.

Equal opportunities
Wageningen University & Research (WUR) employs a large number of people with very different backgrounds and qualities, who inspire and motivate each other. We want every talent to feel at home in our organisation and be offered the same career opportunities. We therefore especially welcome applications from people who are underrepresented at WUR. For more information please go to our inclusivity page. A good example of how WUR deals with inclusiveness can be read on the page working at WUR with a functional impairment.

We are

Wageningen University & Research
The mission of Wageningen University and Research is “To explore the potential of nature to improve the quality of life”. Under the banner Wageningen University & Research, Wageningen University and the specialised research institutes of the Wageningen Research Foundation have joined forces in contributing to finding solutions to important questions in the domain of healthy food and living environment.

With its roughly 30 branches, 7.200 employees and 13.200 students, Wageningen University & Research is one of the leading organisations in its domain. An integrated approach to problems and the cooperation between various disciplines are at the heart of Wageningen’s unique approach. WUR has been named Best Employer in the Education category for 2019-2020.

Wageningen University & Research Animal Breeding and Genomics (WUR-ABG)is the centre of excellence for all national and international animal breeding and genomics activities (research and education) of Wageningen University & Research.

Centre for Genetic Resources, the Netherlands (CGN)carries out Statutory Research Tasks for the Dutch Ministry of Agriculture, Nature and Food quality, and focuses on conservation and use of vegetable crops, farm animal breeds and autochthonous forest species

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