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Using Pooled DNA of a Reference Population in Genomic Selection for a Disease Trait in Atlantic Salmon

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Kjetil Aune


PAGXXV; San Diego, CA, 2017-01-14–2017-01-18

Sonesson, Anna Kristina; Bakke, Haavard; Malacrida, Giorgio; Aslam, Muhammad Luqman; Baranski, Matthew

In aquaculture breeding, genomic selection is used for invasive traits that cannot be measured on selection candidates, e.g. fillet quality and disease resistance. The number of fish to genotype each generation is often large (e.g. 10-100 selection candidates per family and equally many sibs of the candidates as reference population from 100-600 families). Here, we will calculate accuracy of selection when SNP effects are estimated in pools of DNA from individuals with extreme phenotypes, and compare this accuracy to accuracy from individually genotyped reference individuals. Data comes from an Atlantic salmon population challenged for pancreas disease, with surviving/dead individuals. At the end of the challenge test of 5223 individuals, 856 individuals were selected to develop two pools of dead fish (173 and 204 individuals) and two pools of surviving fish (205 and 273 fish). Sequence libraries were prepared and sequenced to around 40x coverage. From the sequence information, genotypes were extracted. In addition, the same fish and sibs of these had individual genotypes from a SNP chip. 45812 SNPs overlapped between the sequence data set and SNP chip. These SNPs were used to estimate GBLUP breeding values in the pooled and individual data sets. The accuracy was 0.716 for the individually genotyped animals based on SNP effects estimated in the pooled data, and 0.737 when SNP effects were estimated in the individually genotyped data. This shows that pooling of individuals with extreme genotypes is a powerful means of saving genotyping costs in genomic selection for disease traits in Atlantic salmon.