High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure

Deepali Vasoya, Thomas Tzelos, Lindert Benedictus, Anna Eleonora Karagianni, Scott Pirie, Celia Marr, Charlotta Oddsdóttir, Constanze Fintl, Timothy Connelley*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


The Major Histocompatibility Complex (MHC) genes play a key role in a number of biological processes, most notably in immunological responses. The MHCI and MHCII genes incorporate a complex set of highly polymorphic and polygenic series of genes, which, due to the technical limitations of previously available technologies, have only been partially characterized in non-model but economically important species such as the horse. The advent of high-throughput sequencing platforms has provided new opportunities to develop methods to generate high-resolution sequencing data on a large scale and apply them to the analysis of complex gene sets such as the MHC. In this study, we developed and applied a MiSeq-based approach for the combined analysis of the expressed MHCI and MHCII repertoires in cohorts of Thoroughbred, Icelandic, and Norwegian Fjord Horses. The approach enabled us to generate comprehensive MHCI/II data for all of the individuals (n = 168) included in the study, identifying 152 and 117 novel MHCI and MHCII sequences, respectively. There was limited overlap in MHCI and MHCII haplotypes between the Thoroughbred and the Icelandic/Norwegian Fjord horses, showcasing the variation in MHC repertoire between genetically divergent breeds, and it can be inferred that there is much more MHC diversity in the global horse population. This study provided novel insights into the structure of the expressed equine MHC repertoire and highlighted unique features of the MHC in horses.

Original languageEnglish
Article number1422
Issue number7
Publication statusPublished - Jul 2023

Bibliographical note

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© 2023 by the authors.

Other keywords

  • breed diversity
  • equine
  • high-throughput sequencing
  • Major Histocompatibility Complex (MHC)
  • polymorphism


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