Dirk-Jan De Koning

I am interested to dissect the genetic basis of variation in complex traits and use of this information in breeding programs. My research covers traditional livestock species as well as excursions to fish, mice and even plants.

Beside my research career, I have extensive experience in academic leadership at the Section, Departmental, and Faculty level. In my most recent acedemic leadership roles as Vice-Dean (with responsibility for research and PhD education) and Deputy Dean (overall leadership with a focus on research), I have worked with overarching questions like research strategy development, strategic long-term recruitment plans and higher academic appointments. During 2022 and 2023 we planned and performed a re-organization of our faculty structure. The implementation of the new structure became a fact at the start of 2024 and the new departments are currently taking shape: developing new ways of working, collaborating, and managing. I aim for inclusive leadership with clear responsiblities and decision-taking at the right levels. Understanding complexity is one of my key attributes.

Assignments:

Deputy Head of Department 2013-2018 (last two years as joint HoD)

April 2019- March 2022 Vice Dean for research and research education

January 2022-December 2024 Deputy Dean

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

My research focuses on linking DNA variation to functional variation in livestock and beyond. I am interested in experimental design as well as data analysis and bioinformatics. A large recent research project has been on the development of novel tools for molecular breeding in RA2 of Mistra Biotech. 

A core area of my research is bone weakness in laying hens. This is a major welfare concern in all egg production systems but genetics can make a strong contribution.

In dairy cattle, I have been involved in projects about the genomics of fertility, modelling of susceptibility and recovery to mastitis, quality of colostrum, and variation in milk coagulation.

In the DEFEND project we have studied new ways 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 breds across Europe. 

Gigacow

Gigacow is SLU's investment in large-scale data collection from dairy farms. It is a university-wide resource that can also be used by external researchers. As coordinator, my job is to capture as many measurable characteristics (phenotypes) as possible from the cows on the farms participating in the network. We then supplement these measurements with genetic information from each animal as well as other information about the farms in order to better understand the interaction between animals, humans and production methods. My own research focus is on exploring the genetic characteristics of crosses and the potential for increasing animal health, productivity and resource efficiency on our cows. An important part of the work in Gigacow is to to collaborate with other parties in order to support work on technology and method development where our platform makes Gigacow a natural test bed for new sensors and machines. Method development is also an important part of genetics where both machines that analyze genetic material and the software that analyzes data are constantly being developed.

Defend2020

Defend2020 is an EU project in which we collaborate with researchers in Europe and Africa to stop the spread of Lumpy Skin Disease and African swine fever. In the project, SLU is responsible for the study of the interaction between viruses and host animals in order to better manage and fight the two viruses. An important part of the work is also to ensure that the tools produced by the project can be used by researchers and veterinarians all over the world. 

We have established new research in the area of aquaculture. Together with Christos Palaiokostas we are repsonsible for the Swedish breeding programs in rainbow trout and Arctic charr. We collaborate with other Nordic countries in the Aquarctic project. I also chair the SLU Aquaculture platform, which aims to integrate and promote aquaculture research and education across SLU. 

On the periphery I am Senior Editor for G3|Genes, Genomes, Genetics  and associate editor for Genetics.

• 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

PhD students, in-progress:

Christer Simon, SLU and UDSM Tanzania, (main supervisor)

Moses Mbiru, UDSM Tanzania, (co-supervisor)

Mohammed Sallam, SLU (main supervisor)

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-ongoing

Kim Jäderkvist: January 2018-April 2018

Sofia Nyman: June 2018-2020

Tomas Klingström: October 2018-ongoing

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

Biaty Raymond, Anna Maria Johansson, Heather Anne McCormack, Robert Hall Fleming, Matthias Schmutz, Ian Chisholm Dunn, Dirk Jan De Koning. 2018. Genome-wide association study for bone strength in laying hens. Journal of Animal Science 96 (7), 2525-2535

J. Willforss, J.M. Morrell, S. Resjö, T. Hallap, P. Padrik, V. Siino, D.J. de Koning, E. Andreasson, F. Levander, P. Humblot. 2021. Stable bull fertility protein markers in seminal plasma. Journal of Proteomics 236: https://doi.org/10.1016/j.jprot.2021.104135

https://www.slu.se/en/Collaborative-Centres-and-Projects/mistra-biotech/

https://defend2020.eu/

https://www.slu.se/en/subweb/sustainimal/