Dirk-Jan de Koning

I am interested in dissecting the genetic basis of variation in complex traits and applying this knowledge in breeding programs. My research spans traditional livestock species, with additional work involving fish, mice, and even plants.

Alongside my research career, I have extensive experience in academic leadership at various levels. In my most recent roles as Vice-Dean (responsible for research and PhD education) and Deputy Dean (with overall leadership focused on research), I have worked on strategic initiatives such as research strategy development, long-term recruitment planning, and senior academic appointments. During 2022 and 2023, we planned and carried out a major reorganization of our faculty. The new structure was implemented at the beginning of 2024, and the newly formed departments are now evolving—developing new ways of working, collaborating, and governing. I strive for inclusive leadership with clear responsibilities and decision-making at the appropriate level. Understanding complexity is one of my key strengths.

As of March 1, 2025, I serve as Pro Vice-Chancellor with responsibility for research infrastructure.

 
Academic Leadership Roles

Deputy Head of Department, 2013–2018 (final two years as joint Head of Department)
Vice-Dean for Research and PhD Education, April 2019 – March 2022
Deputy Dean, January 2022 – December 2024
Pro Vice-Chancellor (Infrastructure), March 2025 – present

My research focuses on linking DNA variation to functional variation in livestock and beyond. I am particularly interested in experimental design, data analysis, and bioinformatics.

A core area of my research is bone weakness in laying hens—a major animal welfare concern across all egg production systems. Genetic approaches can make a significant contribution to addressing this issue.

In dairy cattle, I have worked on several projects related to the genomics of fertility, modeling susceptibility and recovery from mastitis, colostrum quality, and variation in milk coagulation properties.

In the DEFEND project, we explored new strategies to mitigate African Swine Fever (in pigs) and Lumpy Skin Disease (in cattle). In the REDIVERSE project, we aimed to strengthen the genetic improvement of red dairy breeds across Europe.

 
Gigacow

Gigacow is SLU’s flagship infrastructure for large-scale data collection from dairy farms. It is a university-wide resource that is also open to external researchers. As coordinator, my role is to capture as many measurable traits (phenotypes) as possible from cows on participating farms. These data are then combined with genetic information and farm-level metadata to better understand the interactions between animals, humans, and production systems.

My own research within Gigacow focuses on the genetic characteristics of crossbred animals and their potential to improve health, productivity, and resource efficiency. A key component of Gigacow is collaboration with external partners to support technology and method development. The platform serves as a natural testbed for new sensors and machinery. Method development is also central to genetics, where both laboratory technologies and data analysis tools are continuously evolving.

 
DEFEND2020

DEFEND2020 is an EU-funded project in which we collaborate with researchers across Europe and Africa to combat the spread of Lumpy Skin Disease and African Swine Fever. SLU leads the work on understanding virus–host interactions to improve disease control. A key goal is to ensure that the tools developed in the project are accessible and usable by researchers and veterinarians worldwide.

SUSTAINIMAL

SustAinimal is a center promoting increased knowledge in the production animals' role for competitive, sustainable and resilient agriculture and food production in Sweden.

 
Aquaculture

We have recently established new research in aquaculture. Together with Christos Palaiokostas, I am responsible for the Swedish breeding programs for rainbow trout and Arctic charr. We also collaborate with other Nordic countries through the Aquarctic project. In addition, I chair the SLU Aquaculture Platform, which aims to integrate and promote aquaculture research and education across the university.

 
Editorial Roles

In addition to my research, I am active in scientific publishing. I serve as Senior Editor for G3: Genes, Genomes, Genetics and as Associate Editor for Genetics.

I contribute to a number of undergraduate and PhD courses mainly related to genomic selection, poultry breeding and aquaculture. 

• MSC, Wageningen University 1996
• PHD, Wageningen University 2001
• 2007 - 2010 Band 4 Group Leader*, Roslin Institute
• 2003 - 2007 Career Track Appointment, Roslin Institute
• 2001 - 2003 Post- Doctoral position, Roslin Institute
• 1997 - 2001 PhD Student, Wageningen University
• 1996 – 1997 MTT Agricultural Research Centre of Finland

*1-10-2007: Merger of the Roslin Institute with University of Edinburgh

PhD students, completed:

Suzanne Rowe, Roslin Institute, University of Edinburgh, defended October 2008 (main supervisor).

Alex Lam, Roslin Institute, University of Edinburgh, defended January 2009 (main supervisor).

Claudia Cabrera, Roslin Institute, University of Edinburgh, defended June 2009 (main supervisor).

Cecile Massault, Roslin Institute, University of Edinburgh and Wageningen University, defended July 2010 (co-supervisor).

Zhang Zhe, China Agricultural University, Beijing (co-supervisor), defended 2011

Eva Strucken, Humbolt University, Berlin (Co-supervisor), defended June 2012.

Imran Zahoor, Roslin Institute, University of Edinburgh, (co-supervisor) defended December 2012.

André Hidalgo, SLU and WUR, defended December 2015 (SLU main supervisor)

Bruno Louro, Universidade do Algarve, Faro (co-supervisor), defended 2015

Sandrine Duchémin, SLU and WUR, defended May 2016 (SLU main supervisor)

Xiaowei Mao, Aarhus University and SLU Defended 21 November 2016(SLU main supervisor)

Amabel Tenghe, WUR and SLU, Defended 28 April 2017 (co-supervisor)

Berihu Welderufael, Aarhus University and SLU, Defended 20 November 2017 (main supervisor)

Jovana Marjanovic. WUR and SLU, Defended 20 April 2018 (SLU main supervisor)

Sofia Nyman, SLU, Defended PhD 18 May 2018 (co-supervisor)

Levinus Leonard, UDSM Tanzania, Defended February 2019 (co-supervisor)

Juan Cordero, SLU and WUR (main Supervisor) 28 February 2020

Esinam Amuzu, Wageningen University and SLU (SLU main supervisor) 6 March 2020

Vinicius da Silva, Wageningen University and SLU (co-supervisor) 25 January 2020

Zeratsion Abera Desta, SLU (co-supervisor), 11 November 2020

Redempta Athanas, SLU and UDSM Tanzania, (main supervisor) 4 December 2020

Christer Simon, SLU and UDSM Tanzania, (main supervisor) 24 November 2022

Moses Mbiru, UDSM Tanzania, (co-supervisor) 19 August 2022

Mohammed Sallam, SLU (main supervisor) 7 March 2025

Post-doctoral supervision

Wenhua-Wei, June 2005-May 2009, now lecturer in Statistical Genetic at Manchester University

Suzanne Rowe, October 2008-December 2010. Now Research Lead at Ag-Research New Zealand

Burak Karacaören, January 2008-June 2010, now at University of Akdeniz, Turkey

Javad Nadaf, September 2009-August 2010, now at McGill University, Canada.

Fernando Lopes-Pinto: December 2011- September 2015, now researcher at SLU

Elisabeth Jonas: March 2012-June 2016, now associate professor at SLU

Anna Maria Johansson: January 2013-June 2015, now associate professor at SLU

Sandrine Duchemin: September 2016- December 2018

Elena Mouresan: September 2016-December 2018

Martin Johnsson: March 2017-2021

Kim Jäderkvist: January 2018-April 2018

Sofia Nyman: June 2018-2020

Tomas Klingström: October 2018-2022

Martin Johnsson, Helena Wall, Fernando A Lopes Pinto, Robert H Fleming, Heather A McCormack, Cristina Benavides-Reyes, Nazaret Dominguez-Gasca, Estefania Sanchez-Rodriguez, Ian C Dunn, Alejandro B Rodriguez-Navarro, Andreas Kindmark, Dirk-Jan de Koning, Genetics of tibia bone properties of crossbred commercial laying hens in different housing systems, G3 Genes|Genomes|Genetics, Volume 13, Issue 2, February 2023, jkac302, https://doi.org/10.1093/g3journal/jkac302

Jovana Marjanovic, Han A Mulder, Lars Rönnegård, Dirk‐Jan de Koning, Piter Bijma. 2022. Capturing indirect genetic effects on phenotypic variability: Competition meets canalization. Evoltuionary Application. 15 (4): 694-705.  https://doi.org/10.1111/eva.13353

Banabazi, M.H., Freimanis, G., Goatley, L.C. et al. The transcriptomic insight into the differential susceptibility of African Swine Fever in inbred pigs. Sci Rep 14, 5944 (2024). https://doi.org/10.1038/s41598-024-56569-2

Sallam M, Göransson L, Larsen A, Alhamid W, Johnsson M, Wall H, de Koning D-J and Gunnarsson S (2024) Comparisons of longitudinal radiographic measures of keel bones, tibiotarsal bones, and pelvic bones versus post-mortem measures of keel bone damage in Bovans Brown laying hens housed in an aviary system. Front. Vet. Sci. 11:1432665. doi: 10.3389/fvets.2024.1432665

De Koning, DJ., Dominguez-Gasca, N., Fleming, R.H. et al. An eQTL in the cystathionine beta synthase gene is linked to osteoporosis in laying hens. Genet Sel Evol 52, 13 (2020). https://doi.org/10.1186/s12711-020-00532-y

Martin Johnsson, R. Chris Gaynor, Janez Jenko, Gregor Gorjanc, Dirk-Jan de Koning and John M. Hickey. 2019 Removal of alleles by genome editing (RAGE) against deleterious load. Genetics Selection Evolution 2019 51:14 https://doi.org/10.1186/s12711-019-0456-8

Nyinondi, CS, Mtolera, MSP, Mmochi, AJ, et al. Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing. Ecol Evol. 2020; 10: 10044– 10056. https://doi.org/10.1002/ece3.6664