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Sofia Mikko

Sofia Mikko
Researcher and teacher at the Department of Animal Breeding and Genetics & Director of Undergraduate Studies at the Department of Anatomy. Physiology and Biochemistry. Research focus on understanding the biology behind different traits and diseases in animals.


Horses play a big role in my life. In most of my spare time I am busy with my horses - both for leisure and competition - and in my research I study genetics behind different traits and diseases. 

I have a strong interest in understanding the biology behind different traits and diseases in animals. One way to get more knowledge about biologic functions is to investigate the genome, and by functional genomics, understand the underlying biology. As a student I was early fascinated by the novel emerging techniques, and decided to specialize in molecular genetics. This has guided me into a number of different projects in several species, but the main focus has always been the molecular cell biology behind the traits.

Using the latest large-scale development of molecular genetic methods, we can significantly increase our knowledge of the genetic basis of performance and other characteristics.


I teach on various courses, mainly on the subject of disease genetics and coat color genetics in animals. 

I am currently director of studies at the Department of Anatomy, Physiology & Biochemsitry (AFB), SLU.

I am the course leader of the course Genome Analysis for Master and PhD students. 


My research specialization is to combine molecular and population genetic/genomic approach to study physiology, morphology, development, diseases and other traits primarily in the horse but also other animals. When putting the results into an evolutionary context, many fundamental traits are shared between species, and this knowledge is helpful in comparative studies between mammalian species.

Molecular genomics have a great potential in explaining biology, and in the new era of high throughput sequencing and genotyping, also multigenic, and multifactorial traits may be investigated. In particular, molecular genomic tools together with population genetics, combined with family information, and pedigree information could discover genomic regions under selection, harbouring genes of functional importance.

When performing genomic studies, it is crucial to have a broad knowledge about biological functions, to be able to judge if the significant results are relevant or not. Several of my projects involve congenital traits and diseases with neurological, and/or developmental functions.

My current research includes:

Most of the research is performed in cooperation with other researchers, and I am also involved in some genetics projects in sheep, and moose.


Executive Secretary of the International Society of Animal Genetics (ISAG)

Board of Stitchting International Foundation for Animal Genetics (IFAG)


PhD thesis 1992-1997

  • "A Comparative Analysis of Genetic Diversity at Mhc DRB Loci in Some Ruminant Species", Swedish University of Agricultural Sciences. Supervisor: Professor Leif Andersson, SLU. 

Postdoc/Researcher 1997 - 2001 at the Department of Medical Pharmacology / Department of Neuroscience, Uppsala University

  • Investigation of NPY-recpetors in chicken

Head of Section and Laboratory Director 2001 - 2016

Since 2001 researcher at the Department of Animal Breeding and Genetics, SLU


I am currently co-supervisor of two doctoral students:

  • Paulius Bartulis at the Department of Biomedical Sciences and Veterinary Public Health (main supervisor Johan Höglund)
  • Michela Ablondi at Parma University, Italy (main supervisor Alberto Sabbioni)

I have been the co-supervisor of three doctoral students that have finished their degrees:

  • Maulik Upadhyay, 2016-2019, Ph.D. degree (Other supervisors: Göran Andersson, SLU, Richard Croijmans, Wageningen University, Hendrik-Jan Megens, Wageningen University, Martien Groenen, Wageningen University, and Emma Svensson, Uppsala University). Maulik was an EGS-ABG student and got a joint degree at SLU and Wageningen University.
  • Agnese Viluma, 2013-2017, Ph.D. degree (Other supervisors: Tomas Bergström, SLU and Göran Andersson, SLU)

  • Lisa S Andersson 2008-2012, Ph.D. degree (Other supervisors: Gabriella Lindgren, SLU, and Hans Broström, SLU)

After their doctoral studies, Lisa Andersson continued as the CEO of our spin-off company Capilet Genetics that holds the two patents resulting from her doctoral student projects. Agnese Viluma currently holds a PostDoc position with Prof. Hans Ellegren at Uppsala University. Maulik Upadhyay holds a PostDoc position in Germany.

I have also supervised more than 50 undergraduate students who have completed their degree projects at the Department of Animal Breeding and Genetics.

Selected publications

Solé M, Ablondi M, Binzer-Panchal A, Velie BD, Hollfelder N, Busy N, Ducro BJ, Francois L, Janssens S, Schurink A, Viklund Å, Eriksson S, Isaksson A, Kultima H, Mikko S, Lindgren G. Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds. BMC Genomics, 2019, 20:759

Upadhyay M, Eriksson S, Mikko S, Strandberg E, Stålhammar H, Groenen MAM, Croojmans RPMA, Amdersson G, Johannson AM. Genomic relatedness and diversity of Swedish native cattle breeds. Genet Sel Evol, 2019, 51:56

Ablondi M, Viklund Å, Lindgren G, Eriksson S, Mikko S. Signatures of selection in the genome of Swedish warmblood horses selected for sport performance. BMC Genomics, 2019, 20:717

Rochus CM, Westberg Sunesson K, Jonas E, Mikko S, Johansson AM. Mutations in ASIP and MC1R: dominant black and recessive black alleles segregate in native Swedish sheep populations. Animal Genetics, 2019 

Viluma A, Mikko S, Hahn D, Skow L, Andersson G, Bergström TF. Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology. Science Reports, 2017, 7:45518

Bauer A, Hiemisch T, Jagannathan V, Neuditschko M, Bachmann I, Rieder S, Mikko S, Penedo MC, Tarasova N, Vitková M, Sirfori N, Roccabianca P, Leeb T, Welle MM. A Nonsense Variant in the ST14 Gene in Akhai-Teke Horses with Naked Foal Syndrome. G3, 20177(4):1315-1321

Rafati N, Andersson LS, Mikko S, Feng C, Raudsepp T, Pettersson J, Janecka J, Wattle O, Ameur A, Thyreen G, Eberth J, Huddleston J, Maliq M, Bailey E, Eichler EE, Dalin G, Chowary B, Andersson L, Lindgren G, Rubin CJ. Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies. G3, 2017, 6(7):2213-23

Andersson LS, Larhammar M, Memic F, Wootz H, Schwochow D, Rubin CJ, Patra K, Arnason T, Wellbring L, Hjälm G, Imsland F, Petersen JL, McCue ME, Mickelson JR, Cothran G, Ahituv N, Roepstorff L, Mikko S, Vallstedt A, Lindgren G, Andersson L, Kullander K. Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice. Nature 488 (7413): 642-6, 2012.

Wik L, Mikko S, Klingeborn M, Stéen M, Simonsson M, Linné T. Polymorphisms and variants in the prion protein sequence of European moos (Alces alces), reindeer (Rangifer tarandus), roe deer (Caproeolus capreolus) and fallow deer (Dama dama) in Scandinavia. Prion, 2012, 6(3):256-60


Researcher at the Department of Animal Breeding and Genetics; Molecular genetics, HgenLab
Telephone: +4618671979
Postal address:
HGEN, Husdjursgenetiska laboratoriet, Box 7023
Visiting address: Ulls väg 26, Uppsala

Publications list: