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.

附加文件1，收录于题为《利用现场数据研究大西洋鲑鱼种群对阿米巴鳃病和鳃损伤易感性的遗传基础》的手稿中，该手稿目前正在审阅中。
背景：鳃部相关疾病和死亡率已成为全球大西洋鲑鱼产业的一大关注点。揭示导致鳃部疾病或损伤的遗传机制，有助于指导缓解措施的实施。通过对挪威和加拿大两个大型大西洋鲑鱼种群群体的鳃部评分进行了全基因组关联分析，这两个群体分别在大西洋鲑鱼阿米巴鳃病（AGD）爆发期间和收获时（称为鳃损伤）进行了表型鉴定。结果：虽然染色体2上发现的一个新的数量性状位点（QTL）区域与AGD易感性相关联，但染色体2和12上的两个QTL区域与鳃损伤相关。这些区域中的QTL没有重叠，且领先变异体解释了3%至10%的遗传变异。位于或接近领先变异体内部的潜在候选基因包括tfeb、ZSCAN12l和ifi44l，其中大部分基因在免疫功能方面发挥作用。利用重测序数据对与AGD相关的识别QTL区域进行精细定位，发现了一个解释了9%遗传变异的领先间基因变异体。结论：我们的研究结果为AGD和鳃损伤易感性的遗传架构提供了宝贵的见解，并有助于指导缓解措施的实施。