Aquaculture Europe 2023

September 18 - 21, 2023


Add To Calendar 21/09/2023 14:45:0021/09/2023 15:00:00Europe/ViennaAquaculture Europe 2023GENETIC ARCHITECTURE OF RESISTANCE TO SEA LICE IN ATLANTIC SALMON: CONSISTENCY ACROSS TWO SEA LICE SPECIESSchubert 5The European Aquaculture Societywebmaster@aquaeas.orgfalseDD/MM/YYYYaaVZHLXMfzTRLzDrHmAi181982


C. Fraslin1*, J.P. Lhorente2, O. Kristjánsson3, R. Bangera4, M. Rye4, R.D. Houston4, and D. Robledo1

1 The Roslin Institute, The Royal (Dick) School of Veterinary Study, The University of Edinburgh, Edinburgh, United-Kingdom

2 Benchmark Genetics, Puerto Varas, Chile

3 Benchmark Genetics, Reykjavik, Iceland

4Benchmark Genetics, Bergen, Norway




Sea lice are parasitic crustaceans that infest Atlantic salmon (Salmo salar). They attach to the skin of salmons and feed on tissue, mucus and blood, causing abrasion-like lesions, open injuries and stress that in turns lead to reduced growth rates, secondary infection due to opportunistic pathogens and increased mortality. Sea lice represent one of the most important threats to salmon aquaculture and welfare, causing millions of losses worldwide. Several species of lice can affect Atlantic salmon, with Lepeophtheirus salmonis  being predominant  in the northern hemisphere and Caligus rogercresseyi in the southern hemisphere. Better understanding of genetic resistance to both parasites is a prerequisite to include in selective breeding strategies to improve lice resistance.  Here we study resistance to both L. salmonis and C. rogercresseyi in Atlantic salmon, working with the same salmon families in the two hemispheres to assess whether resistance to both parasites has the same genetic background.

Material and methods

 During three consecutive years, 2017 to 2019, a total of 4 375, 3 730 and 5  346 Atlantic salmon  fish were produced, respectively, belonging to 160 to 200 full-sib families from Benchmark Genetics breeding programme. For each year-class (YC) , the offspring were separated into two groups at  the eyed  eggs stage and sent to two different  locations  for rearing and disease challenge. Half of the offspring  were challenged in Iceland with L. salmonis ,  while the other half  were challenged in  Chile  using C. rogercresseyi . A s imilar challenge protocol  was used across locations and year-classes. Briefly, fish were raised in separate family tanks until tagging ,  and  then mixed. For the challenge, fish were separated into 2 to 4 tanks with  a recirculating system,  and  30 (in Iceland)  or  40 (in Chile) copepodite of  lice  per fish were deposited in each tank. After 7 to 15 days, the number of lice (at sessile stage) attached to each fish were visually assessed and reported as sea lice count (SLC). The body weight (BW) of each fish was recorded before and after the challenge.

 The fish were genotyped using 57K (Chile, YC2017) or 65K SNP (all other year-classes) array s (with 33K shared SNPs). Standard quality controls on SNPs and individuals were performed using PLINK [1] in each dataset separately ,  and then all were merged into a single dataset. Genotype imputation using FImpute3 [2]  was performed to obtain a  final dataset with 61,065 SNPs .

Genetic parameters (variance, heritability and genetic correlation) were estimated using blupf90 [3] . Genome wide association studies (G WAS) were performed with a mixed- linear-model implemented in GCTA [4] to detect QTL associated with resistance. The animal model used for variance component estimation and GWAS included tank, sex  and counter (when available) as fixed effect and  body weight as covariate .


Heritability of Atlantic salmon r esistance to each lice  species was consistent across year-classes a nd estimated to be low for L. salmonis and moderate for  C.  rogercresseyi (Table 1) . A  low to  null genetic correlation was observed in YC2017 and YC2019  between resistance to the two lice species . In YC2018, a high positive genetic correlation was estimated for resistance to L. salmonis and resistance to C. rogercresseyi.

Body weight was highly heritable in both locations, with a higher heritability in Iceland than in Chile for YC17 and YC18 . High positive genetic correlations were estimated across locations for body weight measured within a year class.

The GWAS performed showed that r esistance to both sea lice species is  highly polygenic. Only one QTL above the 5% genome wide significance threshold was identified,  located  on chromosome Ssa15 for resistance to  C. rogercresseyi  in YC2017.

Discussion and conclusion

 Resistance to  L. salmonis  and resistance to  C. rogercresseyi  in Atlantic salmon  are highly polygenic.  It is unclear whether resistance to the two species share common  genetic mechanisms. The absence of genetic correlation for resistance to the two sea lice species in YC2017 and YC2019 and the high positive correlation observed in YC20 18 might be because of differences in the challenge methods and the parasite counting procedure .  Indeed, the size of the fish at challenge and the number of days of challenged  and the number of  people  involved in the counting of the lice varied according to the location and the year, reflecting normal practices in the farms.  A meta-analysis combining all three year-class will be  performed  to better understand the genetic architecture of sea lice resistance using a powerful dataset of over 10,000 fish.


[1]  Chang CC, et al.  Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 2015;4:7 .

[2] Sargolzaei M, et al. A new approach for efficient genotype imputation using information from relatives. BMC Genomics 2014;15.

[3]  Misztal I, et al. BLUPF90 and related programs (BGF90). Proc. 7th World Congr . Genet. Appl. Livest . Prod., vol. Comm. No.28, Montpellier, France.: 2002, p. 743–4.

[4] Yang J, et al. GCTA: A tool for genome-wide complex trait analysis. Am J Hum Genet 2011;88:76 –82.