Development of a high-density salmon SNP chip: a key tool for improving the competitiveness and sustainability of the UK salmon farming industry

鲑鱼养殖是英国经济的主要贡献者（每年5亿英镑），提供健康、高质量的食物。这一农村产业的竞争力和可持续性取决于选择性育种。虽然尖端的基因组学工具，如高密度（HD） SNP芯片现在通常用于牲畜育种决策，但鲑鱼养殖业无法获得此类工具。该项目通过开发用于选择性育种的HD鲑鱼SNP芯片来解决这一技术差距。该项目将；1)利用高通量测序检测全基因组SNP变异；2)开发HD SNP芯片；3)利用芯片对影响海虱抗性的基因座进行关联映射；4)在商业环境中验证性状相关的snp；5)实施在育种计划中使用SNP的策略，以提高对海虱的抗性，这是其他关键经济性状的典范。海虱侵扰是影响全球鲑鱼养殖的最严重疾病。在北半球，鲑鱼虱（Lepeophtheirus salmonis）尤其成问题。沙门氏菌感染鲑鱼可引起表面病变，渗透失衡，以及对其他病原体的易感性，因为宿主免疫调节和病变。几乎所有的鲑鱼养殖场都需要控制海虱的策略，通常包括频繁的化疗。每公斤鱼的海虱治疗费用从0.10欧元到0.25欧元不等，英国每年损失3400万欧元，全球每年损失3.05亿欧元。然而，如果没有这种处理，现有的鲑鱼养殖业将无法生存。通过与格拉斯哥大学和斯特林大学水产养殖研究所合作的海虱感染试点试验，LNS已经证明，在他们的亲鱼中，对海虱的抗性存在广泛的遗传变异，LNS家族对海虱的抗性遗传率为c30%。然而，海虱挑战试验是一种昂贵和费力的方法，以确定每一代的最佳选择候选鱼。基于基因组信息的直接选择方法已在若干农业部门得到应用，已被证明是一种更具成本效益和更准确的选择手段，特别是对难以/昂贵的性状进行测量。遗传标记与抗病性的关联需要鉴定全种群连锁不平衡中的标记。尽管目前可以通过CIGENE（挪威）获得专有的鲑鱼SNP芯片，但其标记密度（3K）不足以进行基因组关联定位。该项目旨在通过开发高通量基因分型工具来克服这一限制，以鉴定与养殖鲑鱼抗海虱和其他经济上重要性状相关的遗传标记。关键步骤是首先利用大规模平行测序平台（Illumina GAIIx和HiSeq2000）和减少代表性（RR）和限制性位点相关DNA （RAD）文库的生物信息学分析，确定LNS育种种群的全基因组SNP变异。其次，利用Affymetrix高通量阵列技术，设计并制作了一套定制的HD (~200K) SNP基因分型工具。第三，利用该工具通过HD SNP芯片基因分型和控制条件下感染LNS家族的准确表型关联图谱，鉴定与海虱抗性相关的SNP变异。随后，鉴定出的信息性标记和性状相关标记子集将被纳入成本较低的基因分型平台，该平台将用于验证暴露于水产养殖条件下的鱼类中与减少虱子感染水平相关的snp。将制定育种策略，将这些单核苷酸多态性应用于海虱抗性的选择，这将允许在不需要进一步疾病挑战的情况下进行遗传改良。此外，通过使用高密度芯片识别与其他重要经济性状连锁不平衡的标记，这些策略将扩展到引入其他性状的基因型选择，显著加快通过LNS育种计划实现的遗传进展。

Salmon farming is a key economic contributor to the UK (£0.5bn p.a.) and provides healthy, high quality food. The competitiveness and sustainability of this rural industry depend upon selective breeding. While cutting-edge genomics tools such as high density (HD) SNP chips are now routinely employed for livestock breeding decisions, salmon aquaculture has no access to such tools. This project addresses this technology gap by developing an HD salmon SNP chip for selective breeding. The project will; 1) use high-throughput sequencing to detect genome-wide SNP variation; 2) develop an HD SNP chip; 3) use the chip to perform association mapping of loci affecting resistance to sea lice; 4) verify trait-associated SNPs in a commercial context; 5) implement strategies for SNP use in breeding programmes to improve resistance to sea lice, a paradigm for other key economic traits.Sea louse infestation is the most serious disease affecting salmon farming worldwide. In the northern hemisphere, the salmon louse Lepeophtheirus salmonis is particularly problematic. L. salmonis infection of salmon can cause surface lesions, osmotic imbalance, and susceptibility to other pathogens because of host immunomodulation and lesions.Almost all salmon farms require sea lice control strategies, usually involving frequent chemotherapeutant treatment. Sea lice treatment costs vary from 0.10 Euros to 0.25 Euro per kg of fish, amounting to losses of 34M Euros per annum in the UK and 305M Euros per annum worldwide. However, without such treatment the existing salmon aquaculture industry would not be viable.Through a pilot sea louse infection trial in collaboration with the University of Glasgow and the Institute of Aquaculture at the University of Stirling, LNS have demonstrated there is widespread genetic variation for resistance to sea lice across their broodstock and that heritability for resistance to sea lice in LNS families is c30 percent.However sea lice challenge trials are an expensive and laborious means of identifying the best selection candidate fish in each generation. The approach of direct selection based on genomic information that has been applied in several agricultural sectors has been shown to be a more cost-effective and accurate means of selection, particularly for difficult/expensive to measure traits.Association of genetic markers with disease resistance requires identification of markers in population-wide linkage disequilibrium. Although a proprietary salmon SNP chip is currently available through CIGENE (Norway), its marker density (3K) is insufficient for genomic association mapping.This project aims to overcome this limitation through development of high-throughput genotyping tools for the identification of genetic markers associated with sea lice resistance and other economically important traits in farmed salmon.Key steps are firstly identifying genome-wide SNP variation across the LNS breeding stock by utilising massively parallel sequencing platforms (Illumina GAIIx and HiSeq2000) and bioinformatic analyses of reduced representation (RR) and restriction site-associated DNA (RAD) libraries.Secondly the design and manufacture of a custom HD (~200K) SNP genotyping tool for LNS fish using Affymetrix high-throughput array technology.Thirdly use of this tool for identification of SNP variants associated with resistance to sea lice by HD SNP chip genotyping and association mapping of accurate phenotypes in LNS families infected under controlled conditions.Subsequently the identified subset of informative and trait-associated markers markers will be incorporated into a lower cost genotyping platform which will be used for verification of SNPs associated with reduced levels of lice infestation in fish exposed to aquaculture conditions.Breeding strategies will be developed to apply these SNPs in selection for sea lice resistance, which will permit genetic improvement without the need for further disease challenge.Further, through use of the High Density chip for identification of markers in linkage disequilibrium with other economically important traits, these strategies will be extended to introduce genotypic selection for other traits, significantly accelerating genetic progress achieved via the LNS breeding programme.