PhD position on single-step genomic evaluations considering data spanning multiple generations adequately

Are you looking for a PhD and interested in quantitative genomics? Do you want to develop innovative solutions for accurate and unbiased genomic evaluations? Then, this PhD vacancy may be of interest to you.

The Animal Breeding and Genomics group at Wageningen University is looking for a PhD to take part in the MiXBLUP project, a collaboration with LUKE (Finland).

Genomic evaluations have become an integral part of modern animal breeding, widely adopted by breeding companies to enhance the accuracy and efficiency of genomic selection. This has accelerated genetic progress and has improved overall productivity and sustainability in livestock populations. In this PhD project, you will contribute to developing accurate and unbiased genomic models for large-scale within-population genomic evaluations, incorporating data from multiple generations.

Recent validation studies on single-step genomic evaluations in dairy cattle have reported inflated genomic estimated breeding values (GEBVs). It has been hypothesized that this inflation is caused by the breakdown and re-establishment of long-distance associations between Single Nucleotide Polymorphisms (SNPs) and Quantitative Trait Loci (QTLs) in each generation. As a result, SNP allele substitution effects estimated from a reference population may not be suitable for future generations, leading to the observed inflation. Furthermore, the level of inflation has been observed to vary across traits and breeds.

As a PhD student, you will work on addressing this challenge by:

• developing and validating a model that can accounts for the breakdown and re-establishment of long-distance associations between SNPs and QTLs at each generation;
• quantifying the advantages and limits of the developed model using real datasets provided by different breeding organisations;
• disseminating your results to the involved industry partners and relevant stakeholders.

Your other duties and responsibilities include:

• preparing and analysing datasets;
• communicating and disseminating results through presentations at scientific conferences and by writing scientific articles and a PhD thesis;
• attending PhD courses as part of the graduation program.

You will work here
The research is embedded within the chair Animal Breeding and Genomics, and member of the Wageningen Livestock Research team led by Prof. Roel Veerkamp. You will be co-supervised by Prof. Roel Veerkamp (WUR-ABG), Dr Jan ten Napel (WUR-ABG), Dr Jeremie Vandenplas (WUR-ABG) and Prof. Ismo Stranden (LUKE, Finland).

You are/have:

• a highly motivated person with a strong interest in using animal breeding to contribute to sustainable food production;
• an interest in genomic prediction and statistical and quantitative genetics;
• a desire to further develop your research skills and apply them into practice by developing solutions for real-life applications;
• high level of communication, writing, and presentation skills;
• fluency in spoken and written English;
• the ability to work in close contact with involved industry partners;
• the ability to work effectively as part of a large international team of students and researchers;
• the ability to work independently.

You also possess:

• a successfully completed MSc degree in Animal Breeding and Genomics;
• experience in at least one language: R, Julia (or similar), Fortran;
• additional experience in one or more of the following areas is highly desirable:
  
  • estimation of genetic parameters;
  • validation of genomic predictions;
  • working with Linux and HPC systems;
  • usage of software for large-scale genomic predictions (e.g., MiXBLUP, MiX99, ASREML, or similar).

For this position, your command of the English language is expected to be at C1 level. Sometimes it is necessary to submit an internationally recognised Certificate of Proficiency in the English Language. More information can be found here.

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

• Partially paid parental leave;
• flexible working hours that can be discussed and arranged so that they allow for the best possible work-life balance;
• a strong focus on vitality, with access to campus sports facilities for a small fee;
• a fixed year-end bonus of 8.3%;
• an 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 € 2.901,- per month rising to € 3.707,- in the fourth year in 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. We offer a temporary contract for 18 months which will be extended for the duration of the project if you perform well.

Wageningen University & Research offers plenty of opportunities for growth and development, supported by a strong internal recruitment policy and excellent training programmes.

You will work on the greenest and most innovative campus in the Netherlands, in an international and open working environment. For 20 consecutive years, we have been voted the "best university" in the Netherlands! A place to be proud of.

Coming from abroad
Wageningen University & Research is a leading university and research centre for life sciences. The themes we deal with are relevant to everyone around the world. Consequently, Wageningen has a large international community and a lot to offer to international employees.

Because we expect you to work and live in the Netherlands, 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. We can assist you with additional advice and information on various topics, such as helping your partner to find a job, securing housing, or arranging schooling. Finally, certain categories of international staff may be eligible for a tax exemption on a part of their salary during the first five years in the Netherlands.

The mission of Wageningen University & 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, 7,600 employees (6,700 fte) and 13,100 students and over 150,000 participants to WUR’s Life Long Learning, Wageningen University & Research is one of the leading organisations in its domain. The unique Wageningen approach lies in its integrated approach to issues and the collaboration between different disciplines.

Read the 5 reasons why your future colleagues enjoy working at WUR and watch the video below to get an idea of our green campus!

We will recruit for the vacancy ourselves, so no employment agencies please. However, sharing in your network is appreciated.