Genomic Approaches for Understanding Genetic Variation in Coho Salmon Populations

Due to the increased importance of the Coho salmon for the Chilean aquaculture, it is necessary to develop genomic resources aimed at implementing genomic selection for traits that are difficult to measure such as Piscirickettisa salmonis (PS) resistance. We first targeted regions of the genome for SNP discovery and paralogous assessment using different sources of information: Reduced Representation Sequencing (RRS) of haploid embryos, RRS of diploid individuals and RNAseq using information of susceptible and resistant families after being exposed to PS. We are further characterizing genomic variability using whole genome sequencing. Mapping and kmer based approaches were used for SNP discovery. A draft assembly was obtained from reduced representation data (60x). In all cases the rainbow trout and the salmon genome was used and results were compared. Without filtering around 25% of the SNPs appear to be paralogous. Overall, 200K SNPs could be predicted after stringent quality control. The ratio of Ts/Tv was 1.5. The SNPs discovered in coding regions appear to be mostly under balancing selection (Tajima D). The inbreeding of the population appeared to be small. Deseq2 analysis using survivors and moribund fish sampled at the peak of mortality showed that several genes related to metal ion binding and cellular processes appear to be differentially expressed.  The results obtained with this information will be crucial for measuring the effects of selection, mapping loci associated with disease resistance and broodstock management. FONDEF: ID14I10090.