Investigating Genetic Structure and Phenotype-Genotype Association in Lake Trout Ecotypes by Means of GBS Population Genomics

Lake trout (Salvelinus namaycush) have radiated into different ecotypes in several lakes of North America. In Lake Superior, four ecotypes are recognized that differ in diet, habitat, lipid content and morphology. However, little is known on the fine scale genetic structure and possible adaptation underlying these ecotypes. Our goal is to quantify the genetic structure of lake trout and identifying possible adaptive genetic divergence (including genotype-phenotype association) between the different ecotypes using GBS. Understanding the underlying causes of this variation is essential in order to maintain genetic diversity and conserving possible important specific adaptations. 474 Lake trout from four different sites were sequenced on the Iron torrent platform, with an average of 3.2 M reads per individuals allowing to genotype 4800 filtered single-nucleotide polymorphisms (SNPs). Not surprisingly most of the variation occurred at the individual level, however similar partition of variation was found between the different morph at the same site and among similar morph from different sites. These findings suggest a more complex system than previously thought with various evolutionary mechanisms accounting for the observed phenotypic variation. We are currently identifying markers potentially under directional selection and/or co-varying with phenotypic traits and these results will also be presented.