Genomic selection for improved resistance to Amoebic Gill Disease in farmed Atlantic salmon

大西洋鲑鱼是英国经济中最有价值的水产养殖品种（每年6亿英镑），并为农村和沿海社区提供了主要的就业来源。目前，阿米巴鳃病（AGD）是影响鲑鱼可持续生产的最严重威胁之一。感染可导致生长减慢，治疗和管理费用高昂，对其他病原体的易感性增加，如果不加以治疗，还会导致死亡。因此，农业发展带来了巨大的经济和福利负担。自1980年以来，AGD一直是塔斯马尼亚州的一个问题，那里的控制成本很高（每公斤鲑鱼1澳元）。然而，与不进行治疗所造成的损失相比，这些费用显得微不足道。2012年，英国生产了1.62亿公斤鲑鱼，因此类似的控制成本每年将给经济造成约9000万英镑的损失。我们之前的tsb资助的工作导致了大西洋鲑鱼的第一个高密度SNP基因分型阵列的开发，并使基因组选择策略在鲑鱼育种中的测试和应用成为可能。在这个项目中，我们的目标是应用该阵列和知识，通过基因组选择来提高养殖鲑鱼种群的AGD抗性。通过进行控制AGD挑战实验和利用在农场环境中收集的鳃损伤数据，我们旨在确定和基准准确的表型，并将这些数据与密集的基因型数据相结合，以大幅提高AGD抗性。虽然基因组选择（利用密集的遗传标记信息来预测个体选择候选者的育种值）在陆地畜牧业中是常规的，但它最近才应用于水产养殖。LNS已被国际公认为该领域的先驱，该拟议项目将进一步发展基因组选择，作为准确有效的抗病选择性育种途径。虽然最初的目标性状是抗AGD，但其他经济和环境上重要的目标性状（如鱼片质量，对其他病原体的抗性）将得到改善。该项目的产出将对英国鲑鱼养殖业产生积极的经济、动物福利和环境影响。

Atlantic salmon is the most valuable aquaculture species to the UK economy (£0.6 bn/annum) and provides a major source of employment in rural and coastal communities. Currently, Amoebic gill disease (AGD) is one of the most serious threats to the sustainable production of salmon. Infection can result in reduced growth, substantial treatment and management costs, increased susceptibility to other pathogens and, if untreated, mortality. Therefore, AGD presents a large economic and welfare burden. AGD has been a problem in Tasmania since 1980, where control costs are high ($1AUS/kg salmon). However, these costs are dwarfed by losses that would be incurred without treatment. The UK produced 162M kg of salmon in 2012, hence similar control costs here would cost ~£90M/year to the economy. Our previous TSB-funded work has led to the development of the first high-density SNP genotyping arrary for Atlantic salmon and enabled testing and application of genomic selection strategies in salmon breeding. In this project, we aim to apply this array and knowledge to improve AGD resistance in farmed salmon stocks using genomic selection. By performing a controlled AGD challenge experiment and utilising gill damage data collected in the farm environment, we aim to identify and benchmark accurate phenotypes and combine these data with dense genotype data to substantially improve AGD resistance. While genomic selection (utilising dense genetic marker information to predict breeding values for individual selection candidates) is routine in the terrestrial livestock sector, it has only recently been applied to aquaculture. LNS are already internationally recognised as pioneers in this area and this proposed project will further develop genomic selection as a route to accurate and effective selective breeding for disease resistance. While the intitial target trait is AGD resistance, other economically and environmentally important target traits (e.g. fillet quality, resistance to other pathogens) will be improved. The outputs of the project will have positive economic, animal welfare and environmental implications for the UK salmon farming industry.