A 200K SNP chip reveals a novel Pacific salmon louse genotype linked to differential efficacy of emamectin benzoate

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dc.contributor.author Messmer, Amber M.
dc.contributor.author Leong, Jong S.
dc.contributor.author Rondeau, Eric B.
dc.contributor.author Mueller, Anita
dc.contributor.author Despins, Cody A.
dc.contributor.author Minkley, David R.
dc.contributor.author Kent, Matthew P.
dc.contributor.author Lien, Sigbjørn
dc.contributor.author Boyce, Brad
dc.contributor.author Morrison, Diane
dc.contributor.author Fast, Mark D.
dc.contributor.author Norman, Joseph D.
dc.contributor.author Danzmann, Roy G.
dc.contributor.author Koop, Ben F.
dc.date.accessioned 2018-11-02T08:00:48Z
dc.date.available 2018-11-02T08:00:48Z
dc.date.copyright 2018 en_US
dc.date.issued 2018
dc.identifier.citation Messmer, A.M., Leong, J.S., Rondeau, E.B., Mueller, A., Despins, C.A., Minkley, D.R., … Koop, B.F. (2018). A 200K SNP chip reveals a novel Pacific salmon louse genotype linked to differential efficacy of emamectin benzoate. Marine Genomics, 40, 45-57. https://doi.org/10.1016/j.margen.2018.03.005 en_US
dc.identifier.uri https://doi.org/10.1016/j.margen.2018.03.005
dc.identifier.uri http://hdl.handle.net/1828/10227
dc.description.abstract Antiparasitic drugs such as emamectin benzoate (EMB) are relied upon to reduce the parasite load, particularly of the sea louse Lepeophtheirus salmonis, on farmed salmon. The decline in EMB treatment efficacy for this purpose is an important issue for salmon producers around the world, and particularly for those in the Atlantic Ocean where widespread EMB tolerance in sea lice is recognized as a significant problem. Salmon farms in the Northeast Pacific Ocean have not historically experienced the same issues with treatment efficacy, possibly due to the relatively large population of endemic salmonid hosts that serve to both redistribute surviving lice and dilute populations potentially under selection by introducing naïve lice to farms. Frequent migration of lice among farmed and wild hosts should limit the effect of farm-specific selection pressures on changes to the overall allele frequencies of sea lice in the Pacific Ocean. A previous study using microsatellites examined L. salmonis oncorhynchi from 10 Pacific locations from wild and farmed hosts and found no population structure. Recently however, a farm population of sea lice was detected where EMB bioassay exposure tolerance was abnormally elevated. In response, we have developed a Pacific louse draft genome that complements the previously-released Atlantic louse sequence. These genomes were combined with whole-genome re-sequencing data to design a highly sensitive 201,279 marker SNP array applicable for both subspecies (90,827 validated Pacific loci; 153,569 validated Atlantic loci). Notably, kmer spectrum analysis of the re-sequenced samples indicated that Pacific lice exhibit a large within-individual heterozygosity rate (average of 1 in every 72 bases) that is markedly higher than that of Atlantic individuals (1 in every 173 bases). The SNP chip was used to produce a high-density map for Atlantic sea louse linkage group 5 that was previously shown to be associated with EMB tolerance in Atlantic lice. Additionally, 478 Pacific louse samples from farmed and wild hosts obtained between 2005 and 2014 were also genotyped on the array. Clustering analysis allowed us to detect the apparent emergence of an otherwise rare genotype at a high frequency among the lice collected from two farms in 2013 that had reported elevated EMB tolerance. This genotype was not observed in louse samples collected from the same farm in 2010, nor in any lice sampled from other locations prior to 2013. However, this genotype was detected at low frequencies in louse samples from farms in two locations reporting elevated EMB tolerance in 2014. These results suggest that a rare genotype present in Pacific lice may be locally expanded in farms after EMB treatment. Supporting this hypothesis, 437 SNPs associated with this genotype were found to be in a region of linkage group 5 that overlaps the region associated with EMB resistance in Atlantic lice. Finally, five of the top diagnostic SNPs within this region were used to screen lice that had been subjected to an EMB survival assay, revealing a significant association between these SNPs and EMB treatment outcome. To our knowledge this work is the first report to identify a genetic link to altered EMB efficacy in L. salmonis in the Pacific Ocean. en_US
dc.description.sponsorship AMM performed all extractions prior to sequencing and SNP-chip analysis. JSL, MPK and SL performed genomic alignments, SNP identifications, SNP chip design and validation, and SNP calling. DRM performed heterozygosity analyses. MDF bred families for linkage mapping while RGD performed linkage mapping and EBR performed pseudo-chromosome construction. BB and DM collected samples for SNP chip analysis and EMB assays. AMM drafted original R-script, which was further modified by EBR and AM. CAD and EBR designed primers and analysed genotyped lice from EMB assays. EBR, AMM and DRM drafted the manuscript, and BFK conceived of and coordinated the study. We would like to thank Elanco Animal Health Canada, Marine Harvest Canada, the Atlantic Canada Opportunities Agency - Atlantic Innovation Fund (199308), Compute Canada, the University of Victoria, the University of Prince Edward IslandAtlantic Veterinary College and the University of Guelph for financial or material contributions to this work. We would like to thank staff at the BC Centre for Aquatic Health sciences for performing EMB assays, and we would like to thank Ben Sutherland, Scott Pavey and Ryosuke Yazawa for collecting additional lice that contributed to this work. en_US
dc.language.iso en en_US
dc.publisher Marine Genomics en_US
dc.subject Sea lice en_US
dc.subject Lepeophtheirus salmonis en_US
dc.subject EMB en_US
dc.subject SLICE en_US
dc.subject Resistance en_US
dc.subject Salmon farm en_US
dc.title A 200K SNP chip reveals a novel Pacific salmon louse genotype linked to differential efficacy of emamectin benzoate en_US
dc.type Article en_US
dc.description.scholarlevel Faculty en_US
dc.description.reviewstatus Reviewed en_US

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