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

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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.