Evaluating the Genetic Impact of Stocking on Brook Charr (Salvelinus fontinalis) by Means of SNP Population Genomics

Salmonids rank among the socio-economic most valuable fishes worldwide, but also among the most affected by genetic introgression as a consequence of a long tradition of stocking with hatchery-reared conspecifics. In this study, we developed and genotyped 280 SNP from transcribed (coding) regions by means of next-generation sequencing in order to: i) investigate the potential adaptation of brook charr (Salvelinus fontinalis) to their natural and aquacultural environments; ii) evaluate the consequences of various levels of restocking and resulting introgression rates on the genetic integrity of natural populations, and iii) test whether introgression occurred in a homogeneous way for all markers or if differential selection at specific markers might be at play. Thus, we sampled 9 natural populations that underwent different intensity of stocking over a period of 5 generations as well as a reference hatchery population. Simulations between wild and wild vs domestic populations identified 5 and 6 potential outliers. As previously reported with microsatellites, we observed a positive relationship between stocking intensity and genetic diversity, as well as a decrease in population differentiation. SNP analysis also revealed a significant increase in measure of individual admixture proportions. We also identified SNP for which the rate of introgression has been either more restricted or enhanced relative to neutral expectations. These results suggest that selection has favored or hampered the introgression of genomic blocks into the introgressed wild populations and that these are not yet fixed in the wild populations. Overall, this study highlights the usefulness of these new SNP markers to investigate the consequences of stocking practices on the integrity of potentially adaptive genetic variation in brook charr.