Data from: Mapping and validation of a major QTL affecting resistance to pancreas disease (salmonid alphavirus) in Atlantic salmon (Salmo salar)

Pancreas disease (PD), caused by a salmonid alphavirus (SAV), has a large negative economic and animal welfare impact on Atlantic salmon aquaculture. Evidence for genetic variation in host resistance to this disease has been reported, suggesting that selective breeding may potentially form an important component of disease control. The aim of this study was to explore the genetic architecture of resistance to PD, using survival data collected from two unrelated populations of Atlantic salmon; one challenged with SAV as fry in freshwater (POP 1) and one challenged with SAV as post-smolts in sea water (POP 2). Analyses of the binary survival data revealed a moderate-to-high heritability for host resistance to PD in both populations (fry POP 1 h2~0.5; post-smolt POP 2 h2~0.4). Subsets of both populations were genotyped for single nucleotide polymorphism markers, and six putative resistance quantitative trait loci (QTL) were identified. One of these QTL was mapped to the same location on chromosome 3 in both populations, reaching chromosome-wide significance in both the sire- and dam-based analyses in POP 1, and genome-wide significance in a combined analysis in POP 2. This independently verified QTL explains a significant proportion of host genetic variation in resistance to PD in both populations, suggesting a common underlying mechanism for genetic resistance across lifecycle stages. Markers associated with this QTL are being incorporated into selective breeding programs to improve PD resistance.胰腺疾病（Pancreas disease, PD）由鲑鱼甲病毒（salmonid alphavirus, SAV）引发，对大西洋鲑养殖产业造成严重的经济损失与动物福利负面影响。已有研究报道宿主对该疾病的抗性存在遗传变异，这提示选择性育种或可成为病害防控的重要组成部分。本研究旨在探究胰腺疾病抗性的遗传结构，研究使用了来自两个无亲缘关系的大西洋鲑种群的存活数据：其中一个种群为淡水环境中以稚鱼（fry）阶段攻毒的种群（POP 1），另一个为海水环境中以后稚鱼（post-smolt）阶段攻毒的种群（POP 2）。对二分类存活数据的分析显示，两个种群的宿主胰腺疾病抗性均具有中等到高等的遗传力（稚鱼种群POP 1的h²≈0.5；后稚鱼种群POP 2的h²≈0.4）。研究团队对两个种群的部分个体进行了单核苷酸多态性（single nucleotide polymorphism, SNP）标记基因分型，共鉴定出6个候选抗性数量性状位点（quantitative trait loci, QTL）。其中一个QTL在两个种群中均被定位至3号染色体的同一区域：在POP 1的父系与母系分析中均达到染色体水平显著性，在POP 2的联合分析中则达到全基因组水平显著性。这一经独立验证的QTL可在两个种群中解释宿主胰腺疾病抗性的显著遗传变异占比，提示不同生命周期阶段的抗性遗传机制具有共性。目前该QTL的关联标记已被纳入选择性育种计划，以提升大西洋鲑对胰腺疾病的抗性。