Supporting material for: Investigating the genetic basis of susceptibility to amoebic gill disease and gill lesions in Atlantic salmon populations using field data

Additional file 1 of manuscript titled \"Investigating the genetic basis of susceptibility to amoebic gill disease and gill lesions in Atlantic salmon populations using field data\", which is currently under review.
Background: Gill-related morbidity and mortality are becoming a major concern to the Atlantic salmon industry worldwide. Understanding the genetic mechanism underlying susceptibility to gill diseases or lesions can help to 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 gill lesions), respectively. Results: While one novel quantitative trait locus (QTL) region on chromosome 2 was associated with susceptibility to AGD, two QTL regions on chromosomes 2 and 12 were associated with gill lesions. There was no overlap among QTL in these regions, and the lead variants explained between 3 to 10% of the genetic variance. 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 with re-sequence data, revealed a lead intergenic variant explaining 9% of the genetic variance. Conclusions: Our results provide valuable insight into the genetic architecture of susceptibility to AGD and gill lesions and can help guide mitigation efforts.