WP3 - Genomic basis of immune phenotypes (WUR)
The overarching aim of WP3 is to enhance our fundamental understanding of the genomic basis for innate immune function in farmed fishes by generating standardized ImmunoMaps in the six selected AQUA-FAANG species. Immune functions are most evident during infection, but the large diversity in fish pathogens makes it impossible to study commonalities to pathogen challenges between species, as few if any pathogens can be used to generate common responses. Therefore, a challenge model is proposed that utilizes immune stimulation with established mimics of bacterial and viral infection, which can be standardized across species. Subsequently, functional annotation will be done to generate ImmunoMaps, defining which regions of the genome are activated by stimulation of innate immune mechanisms. Subsequent biological interpretations will achieve a first in-depth comparative examination of the genomic basis for immune function in fishes, including a dissection of both conserved and lineage-specific immune mechanisms. 
  • Objective 3.1.
  • Objective 3.2.
  • Objective 3.3.
  • Objective 3.4.
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Establish optimal protocols for generating standardized ImmunoMaps.
Train partners in standardized and optimized immune protocols.
Deliver sequencing library preparations to generate ImmunoMaps.
 Create an improved understanding of the genomic basis for fish innate immune function.
Links with other WPs
WP3 will generate sequencing libraries for functional annotation based on WP1 standardized protocols. Bioinformatic analyses of ImmunoMaps will be performed using WP2 pipelines. Extensive cross-talk between WP3, WP4 and WP6 will occur to enhance understanding of immune cell heterogeneity in fishes and its variation across phylogeny. WP3 datasets will strongly inform WP5 in terms of prioritizing genetic variants according to the probability that they impact disease resistance in candidate QTL/GWAS regions.