Sea lice (Caligus rogercresseyi) is an ectoparasite which causes major production losses in the salmon aquaculture industry worldwide. Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) are two of the most susceptible salmonid species to sea lice infestation. The objectives of this study were to: (1) identify genomic regions associated with resistance to Caligus rogercresseyi in Atlantic salmon and rainbow trout by performing single-step Genome-Wide Association studies (ssGWAS), and (2) identify candidate genes related to trait variation based on exploring orthologous genes within the associated regions across species. A total of 2626 Atlantic salmon and 2643 rainbow trout were challenged and genotyped with 50 K and 57 K SNP panels, respectively. We ran two independent ssGWAS for sea lice resistance on each species and identified 7 and 13 regions explaining more than 1% of the genetic variance for the trait, with the most important regions explaining 3% and 2.7% for Atlantic salmon and rainbow trout, respectively. We identified genes associated with immune response, cytoskeleton function, and cell migration when focusing on important genomic regions for each species. Moreover, we found 15 common orthogroups which were present in more than one associated genomic region, within- or between-species; however, only one orthogroup showed a clear potential biological relevance in the response against sea lice. For instance, dual-specificity protein phosphatase 10-like (dusp10) and dual-specificity protein phosphatase 8 (dusp8) were found in genomic regions associated with lice density in Atlantic salmon and rainbow trout, respectively. Dusp10 and dusp8 are modulators of the MAPK pathway and might be involved in the differences of the inflammation response between lice resistant and susceptible fish from both species. Our results provide further knowledge on candidate genes related to sea lice resistance and may help establish better control for sea lice in fish populations.

海虱（Caligus rogercresseyi）是一种体外寄生虫，会导致全球鲑鱼水产养殖业的重大生产损失。大西洋鲑鱼（Salmo salar）和虹鳟鱼（Oncorhynchus mykiss）是最容易受到海虱侵染的两种鲑科鱼类。本研究的目的是：(1)通过单步全基因组关联研究 (ssGWAS) 确定与大西洋鲑鱼和虹鳟鱼抗性相关的基因组区域，以及 (2) 确定与性状相关的候选基因基于探索跨物种相关区域内的直系同源基因的变异。总共 2626 条大西洋鲑鱼和 2643 条虹鳟鱼分别接受了 50 K 和 57 K SNP 组的挑战和基因分型。我们对每个物种的海虱抗性进行了两次独立的 ssGWAS，并确定了 7 个和 13 个区域解释了该性状超过 1% 的遗传变异，其中最重要的区域分别解释了大西洋鲑鱼和虹鳟鱼的 3% 和 2.7% 。当我们关注每个物种的重要基因组区域时，我们鉴定了与免疫反应、细胞骨架功能和细胞迁移相关的基因。此外，我们还发现了 15 个常见的直系群，它们存在于物种内或物种间的多个相关基因组区域中；然而，只有一种邻基在针对海虱的反应中表现出明显的潜在生物学相关性。例如，在大西洋鲑鱼和虹鳟鱼中与虱子密度相关的基因组区域中分别发现了双特异性蛋白磷酸酶 10 样( dusp10 ) 和双特异性蛋白磷酸酶 8 ( dusp8 )。Dusp10和dusp8是 MAPK 通路的调节剂，可能与两个物种的抗虱鱼和易感虱鱼之间炎症反应的差异有关。我们的结果提供了有关与海虱抗性相关的候选基因的进一步知识，并可能有助于更好地控制鱼类种群中的海虱。