Investigating the genetic basis of susceptibility to amoebic gill disease and idiopathic gill lesions in Atlantic salmon populations using field data

Abstract Background Gill-related morbidity and mortality have become a major concern to the Atlantic salmon industry worldwide. Understanding the genetic mechanisms underlying susceptibility to gill diseases or lesions can help guide mitigation efforts. Genome-wide association analysis was conducted on gill scores from two large cohorts of Atlantic salmon populations, reared in Norway and Canada, that were phenotyped during amoebic gill disease (AGD) outbreaks and at harvest (referred to as idiopathic gill lesions (IGL)), respectively. Results Whereas one novel quantitative trait locus (QTL) region on chromosome 12 was associated with susceptibility to AGD, two QTL regions on chromosomes 2 and 12 were associated with IGL. There was an overlap between the QTL region on chromosome 12 for AGD and IGL. The lead variant(s) identified explained approximately 7% of the additive genetic variance for AGD, and 3 and 10% for IGL, for the QTL on chromosomes 2 and 12, respectively. Putative candidate genes identified within or close to the lead variants include tfeb, zscan12l, and ifi44l, with the majority of these genes playing roles relating to immune functions. Fine-mapping the identified QTL region associated with AGD using re-sequence data revealed a lead intergenic variant explaining 9% of the additive genetic variance. Conclusions Our results provide valuable insight into the genetic architecture of susceptibility to AGD and IGL, suggesting that both traits may be partly under the same genetic control. Future studies are warranted, especially on the genetic correlation between AGD and IGL.