A validated amplicon panel for parentage reconstruction and selection monitoring in whitefish (Coregonus spp.)

Fish populations are notoriously difficult to monitor because their aquatic habitats limit observation. While physical or chemical tagging (e.g., adipose fin removal or Alizarin Red S staining of bones) can reduce growth or survival or requires sacrifice, genetic tools offer a less invasive and more informative alternative, allowing managers to assess stock composition and census size while enabling researchers to study ecological and evolutionary processes. Here, we introduce a novel whitefish (Coregonus spp.) amplicon panel with 2,282 SNP loci identified using whole-genome resequencing, targeting loci spread across the whitefish genome, including candidate regions relevant to growth and immunity. We successfully applied the panel in seven whitefish species (C. cf. suidteri, C. confusus, C. albellus, C. muelleri, C. fatioi, C. palaea, and one C. sp.) from seven Swiss lakes. To evaluate performance, we used offspring of known parentage from an in vitro breeding experiment with wild-caught C. confusus. Parentage assignment on 381 families yielded a 0% error rate, even when parental genotypes were missing. This panel provides a robust tool for a wide range of applications in broad taxonomic and geographic contexts for monitoring whitefish populations, a group that has historically been difficult to study within the salmonid family.

The online version contains supplementary material available at https://doi.org/10.1007/s12686-026-01449-2.