Domniki Manousi from CIGENE successfully defended her PhD thesis on Thursday 11th September 2025. Domniki’s PhD was titled “Genomic Basis of Pathogen Response and Immune Gene Evolution in Atlantic Salmon” and was supervised by CIGENE’s Marie Saitou alongside Co-supervisors Sigbjørn Lien and Simen Sandve (also CIGENE).
The PhD project involved using recent advances in salmonid genomics, including new sequencing technologies and information about gene activity and regulation (functional annotation: see the AQUA-FAANG project page of our website), to investigate how the complex genome of Atlantic salmon influences key aquaculture traits such as immune responses to disease.
Domniki’s work identified complex genetic variation in Atlantic Salmon with likely impact on the expression of three gig1-like genes associated with resistance to pancreas disease (PD), which is a major economically damaging problem salmon farming, caused by the Salmonid alphavirus. A central focus was the gig1 and gig2 antiviral gene families, which play a significant role in fish health.
Analysis of gig genes across multiple fish species showed that they have expanded and diversified through genome duplication and subsequent rearrangements. In Atlantic salmon, gig genes were found to respond broadly to immune signals but also displayed differences in expression and regulation, suggesting that diversification of gene copies can influence antiviral defenses.
Finally, by studying geographically distinct populations of wild and farmed Atlantic salmon, Domniki examined how domestication and farming pressures shape immunity. This analysis revealed selection signatures in immune-related regions, including duplicated genomic regions overlapping the major histocompatibility complex (MHC). Variation in which duplicate region was selected across each distinct aquaculture group suggests that genome duplication not only increased the genetic complexity of salmon but might have also created opportunities for greater immune diversity, potentially enhancing disease resilience in farmed populations
Before defending her PhD thesis, Domniki gave a trial lecture titled “Breeding for Disease Resistance in Aquaculture: Current Approaches and Future Applications of Emerging Technologies”. This provided a broad overview of changing breeding practices in aquaculture in recent decades and the problems with disease outbreaks, and how future technological advances can improve the sustainability of fish breeding.
Domniki’s examiners were Professor Andrea Doeschl-Wilson (The Roslin Institute, University of Edinburgh),
Victoria Pritchard (Rivers and Lochs Institute, Inverness College, University of the Highlands and Islands), and Gareth Difford (NMBU).
The doctoral thesis is available for public review. For those who would like to have access to the thesis please send an e-mail to: phd-biovit@nmbu.no
CIGENE wishes to congratulate Domniki on her successful PhD project and great performance in the defence.