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 SNP markers, and six putative resistance 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.由鲑鱼阿尔法病毒（salmonid alphavirus, SAV）引发的胰腺疾病（Pancreas disease, PD），对大西洋鲑鱼养殖造成了显著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，提示选择性育种或可成为疾病防控的重要组成部分。本研究旨在解析PD抗性的遗传架构，研究使用了来自两个无亲缘关系的大西洋鲑鱼种群的存活数据：一个种群为在淡水环境中以稚鱼（fry）阶段人工感染SAV（种群1），另一个为在海水环境中以后稚鱼（post-smolts）阶段人工感染SAV（种群2）。对二元存活数据的分析显示，两个种群的宿主PD抗性均具有中至高遗传力（heritability）：稚鱼种群1的h²≈0.5；后稚鱼种群2的h²≈0.4。研究人员对两个种群的子集进行了单核苷酸多态性标记（single nucleotide polymorphism, SNP markers）基因分型，共鉴定出6个潜在的抗性相关数量性状位点（quantitative trait locus, QTL）。其中一个QTL在两个种群中均定位至3号染色体的相同区域：在种群1的父系分析（sire-based analyses）与母系分析（dam-based analyses）中均达到染色体水平显著性（chromosome-wide significance），在种群2的联合分析（combined analysis）中则达到全基因组水平显著性（genome-wide significance）。这一经过独立验证的QTL在两个种群中均解释了显著比例的宿主PD抗性遗传变异，提示不同生命周期阶段的PD遗传抗性存在共同的潜在机制。目前，与该QTL关联的标记已被纳入选择性育种计划，以提升大西洋鲑鱼对PD的抗性。