Uncovering the important genetic defenses against sea lice in coho salmon via CRISPR-mediated gene editing

Enhanced resistance to sea lice infestation remains one of the most important goals to
ensure sustainable Atlantic salmon farming in the marine environment. Some Pacific
salmon, notably Coho salmon, exhibit natural resistance to both Caligus rogercresseyi
(Chile) and Lepeophtheirus salmonis (Northern Hemisphere). Previous RNA-seq data
identified several Coho salmon genes that could be responsible for this difference.
To determine whether certain genes played a functional role in sea lice resistance,
CRISPR-Cas9 was used to knockout three different regions (R1 – R3) in each one of four
selected immune genes (GE1 – GE4) alongside a phenotypic marker gene (slc45a) that
produces an albino phenotype in successful knockouts. Coho salmon embryos (n=5633)
were injected with one of the four CRISPR constructs alongside slc45a, resulting in 9.3-
13.8% of alevins presenting an albino/mosaic phenotype. For wildtype (WT) controls, a
subset of embryos did not receive injections. Following development into smolts (~15
g), fish received a lice infestation challenge (100 copepodids/fish) to assess the impact
of each gene disruption on parasite susceptibility. Significantly higher lice infestations
were observed in fish with GE2 and GE4 knockouts compared to WT controls, suggesting
these genes contribute to resistance. Fin tissue from challenged fish was sequenced
(Illumina NextSeq), confirming high editing efficiency in the GE4 target, particularly at R2.
R3 edits were strongly associated with the pigment marker. Ongoing RNA-seq analysis will
evaluate how these gene disruptions affect broader expression patterns. Uncovering the
genetic basis of sea lice resistance could help develop sustainable strategies to improve
Atlantic salmon aquaculture.