Identification of SNPs Associated With Salmon Lice (Lepeophtheirus salmonis) Resistance in North American Atlantic Salmon Using Transcriptome-Wide Association Study

Yuxuan Zhang; Amber F. Garber; Runsheng Li; Wenlong Cai; Mark D. Fast

doi:10.1155/are/6046684

Identification of SNPs Associated With Salmon Lice (Lepeophtheirus salmonis) Resistance in North American Atlantic Salmon Using Transcriptome-Wide Association Study

Yuxuan Zhang
, Amber F. Garber
, Runsheng Li
, Wenlong Cai^*
, Mark D. Fast^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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Abstract

Atlantic salmon (Salmo salar) is an anadromous fish species of high economic value. However, the sustainability of its aquaculture industry is seriously challenged by salmon lice (Lepeophtheirus salmonis) infestation. Developing genetic tools to improve host resistance could therefore support selective breeding efforts. In this study, we performed a family-based genome-wide association study (GWAS) in North American Atlantic salmon to identify single-nucleotide polymorphisms (SNPs) associated with salmon lice resistance. A total of 960 fish from 20 families were measured for salmon lice resistance. RNA sequencing was conducted in five families representing the largest phenotypic differences in the population, and the resulting transcriptomic data were used to identify SNPs in expressed genomic regions in a cost-effective manner. After quality control, 80,140 SNPs were retained. Using a generalized linear model, we identified 12 SNPs based on the suggestive threshold (p-value = 5 × 10⁻⁵), located on chromosomes 8, 14, and 22. Accordingly, seven lice resistance candidate genes were further identified, which were associated with cell tight adhesion dynamics, cell migration, stress modulation, and immune and inflammatory regulations. Overall, this study provides insights into the genetic architecture of salmon lice resistance and contributes to SNP marker-based selective breeding of North American Atlantic salmon.

© 2026 Yuxuan Zhang et al.

Original language	English
Number of pages	11
Journal	Aquaculture Research
Volume	2026
Issue number	1
Online published	12 Aug 2026
DOIs	https://doi.org/10.1155/are/6046684
Publication status	Published - 2026

Funding

This study was funded by the Mitigating the Impact of Climate-Related Challenges on Salmon Aquaculture (MICCSA) Project. The MICCSA project included funding from the Atlantic Canada Opportunities Agency Atlantic Innovation Fund and Innovate Newfoundland. This study was also supported by the APRC-CityU New Research Initiatives/Infrastructure Support from Central fund (Grant 9610574).

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 14 Life Below Water

Research Keywords

genome-wide association study
Lepeophtheirus salmonis resistance
North American Atlantic salmon
single nucleotide polymorphism

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This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/

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title = "Identification of SNPs Associated With Salmon Lice (Lepeophtheirus salmonis) Resistance in North American Atlantic Salmon Using Transcriptome-Wide Association Study",

abstract = "Atlantic salmon (Salmo salar) is an anadromous fish species of high economic value. However, the sustainability of its aquaculture industry is seriously challenged by salmon lice (Lepeophtheirus salmonis) infestation. Developing genetic tools to improve host resistance could therefore support selective breeding efforts. In this study, we performed a family-based genome-wide association study (GWAS) in North American Atlantic salmon to identify single-nucleotide polymorphisms (SNPs) associated with salmon lice resistance. A total of 960 fish from 20 families were measured for salmon lice resistance. RNA sequencing was conducted in five families representing the largest phenotypic differences in the population, and the resulting transcriptomic data were used to identify SNPs in expressed genomic regions in a cost-effective manner. After quality control, 80,140 SNPs were retained. Using a generalized linear model, we identified 12 SNPs based on the suggestive threshold (p-value = 5 × 10−5), located on chromosomes 8, 14, and 22. Accordingly, seven lice resistance candidate genes were further identified, which were associated with cell tight adhesion dynamics, cell migration, stress modulation, and immune and inflammatory regulations. Overall, this study provides insights into the genetic architecture of salmon lice resistance and contributes to SNP marker-based selective breeding of North American Atlantic salmon. {\textcopyright} 2026 Yuxuan Zhang et al.",

keywords = "genome-wide association study, Lepeophtheirus salmonis resistance, North American Atlantic salmon, single nucleotide polymorphism",

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journal = "Aquaculture Research",

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Identification of SNPs Associated With Salmon Lice (Lepeophtheirus salmonis) Resistance in North American Atlantic Salmon Using Transcriptome-Wide Association Study. / Zhang, Yuxuan; Garber, Amber F.; Li, Runsheng et al.
In: Aquaculture Research, Vol. 2026, No. 1, 2026.

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

TY - JOUR

T1 - Identification of SNPs Associated With Salmon Lice (Lepeophtheirus salmonis) Resistance in North American Atlantic Salmon Using Transcriptome-Wide Association Study

AU - Zhang, Yuxuan

AU - Garber, Amber F.

AU - Li, Runsheng

AU - Cai, Wenlong

AU - Fast, Mark D.

PY - 2026

Y1 - 2026

N2 - Atlantic salmon (Salmo salar) is an anadromous fish species of high economic value. However, the sustainability of its aquaculture industry is seriously challenged by salmon lice (Lepeophtheirus salmonis) infestation. Developing genetic tools to improve host resistance could therefore support selective breeding efforts. In this study, we performed a family-based genome-wide association study (GWAS) in North American Atlantic salmon to identify single-nucleotide polymorphisms (SNPs) associated with salmon lice resistance. A total of 960 fish from 20 families were measured for salmon lice resistance. RNA sequencing was conducted in five families representing the largest phenotypic differences in the population, and the resulting transcriptomic data were used to identify SNPs in expressed genomic regions in a cost-effective manner. After quality control, 80,140 SNPs were retained. Using a generalized linear model, we identified 12 SNPs based on the suggestive threshold (p-value = 5 × 10−5), located on chromosomes 8, 14, and 22. Accordingly, seven lice resistance candidate genes were further identified, which were associated with cell tight adhesion dynamics, cell migration, stress modulation, and immune and inflammatory regulations. Overall, this study provides insights into the genetic architecture of salmon lice resistance and contributes to SNP marker-based selective breeding of North American Atlantic salmon. © 2026 Yuxuan Zhang et al.

AB - Atlantic salmon (Salmo salar) is an anadromous fish species of high economic value. However, the sustainability of its aquaculture industry is seriously challenged by salmon lice (Lepeophtheirus salmonis) infestation. Developing genetic tools to improve host resistance could therefore support selective breeding efforts. In this study, we performed a family-based genome-wide association study (GWAS) in North American Atlantic salmon to identify single-nucleotide polymorphisms (SNPs) associated with salmon lice resistance. A total of 960 fish from 20 families were measured for salmon lice resistance. RNA sequencing was conducted in five families representing the largest phenotypic differences in the population, and the resulting transcriptomic data were used to identify SNPs in expressed genomic regions in a cost-effective manner. After quality control, 80,140 SNPs were retained. Using a generalized linear model, we identified 12 SNPs based on the suggestive threshold (p-value = 5 × 10−5), located on chromosomes 8, 14, and 22. Accordingly, seven lice resistance candidate genes were further identified, which were associated with cell tight adhesion dynamics, cell migration, stress modulation, and immune and inflammatory regulations. Overall, this study provides insights into the genetic architecture of salmon lice resistance and contributes to SNP marker-based selective breeding of North American Atlantic salmon. © 2026 Yuxuan Zhang et al.

KW - genome-wide association study

KW - Lepeophtheirus salmonis resistance

KW - North American Atlantic salmon

KW - single nucleotide polymorphism

UR - https://www.webofscience.com/wos/woscc/full-record/WOS:001847197900001

U2 - 10.1155/are/6046684

DO - 10.1155/are/6046684

M3 - RGC 21 - Publication in refereed journal

SN - 1355-557X

VL - 2026

JO - Aquaculture Research

JF - Aquaculture Research

IS - 1

ER -

Identification of SNPs Associated With Salmon Lice (Lepeophtheirus salmonis) Resistance in North American Atlantic Salmon Using Transcriptome-Wide Association Study

Abstract

Funding

UN SDGs

Research Keywords

Publisher's Copyright Statement

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