Development of a High-Density Genomic Platform for Coho Salmon

Coho salmon is one of the most important species for the Chilean aquaculture. However, there has been little development of genomic resources for the species. We used RNA-seq data from 20 individuals obtained from an extensive P. salmonis challenge experiment (more than 150 families tested), as well as 20 individuals that were fully sequenced obtained from two breeding populations (9x genome coverage). The animals belong to the AquaGen breeding program that incorporates the most relevant commercial populations available in Chile. The SNP discovery was carried out using a reference (rainbow trout) and a reference-free approach based on the Brujin graph, and a reference mapping approach using a genome assembly obtained using different sequencing platforms and library preparations. SNPs were validated in silico through assessments of the overlap between SNP sets, as well as the levels of linkage disequilibrium between linked SNPs, and sytney between species. SNPs discovered in coding regions represent 15% of all the variants discovered. Overall, we select more than 200k SNPs after using stringent quality control criteria. The mean inbreeding appeared to be small in spite of the several generations that the stocks have been maintained under captivity. Overall the levels of LD obtained appeared to be sufficient in order to apply these SNPs in genomic selection and association analysis, using the array developed, which is currently been developed and validated. CORFO: 14ITE2-36675. FONDEF: ID14I10090.