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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 (\n                    <jats:italic>Coregonus<\/jats:italic>\n                    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 (\n                    <jats:italic>C<\/jats:italic>\n                    . cf.\n                    <jats:italic>suidteri<\/jats:italic>\n                    ,\n                    <jats:italic>C. confusus<\/jats:italic>\n                    ,\n                    <jats:italic>C. albellus<\/jats:italic>\n                    ,\n                    <jats:italic>C. muelleri<\/jats:italic>\n                    ,\n                    <jats:italic>C. fatioi<\/jats:italic>\n                    ,\n                    <jats:italic>C. palaea<\/jats:italic>\n                    , and one\n                    <jats:italic>C. sp.<\/jats:italic>\n                    ) from seven Swiss lakes. To evaluate performance, we used offspring of known parentage from an in vitro breeding experiment with wild-caught\n                    <jats:italic>C. confusus<\/jats:italic>\n                    . 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.\n                  <\/jats:p>","DOI":"10.1007\/s12686-026-01449-2","type":"journal-article","created":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T09:32:49Z","timestamp":1792143169000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A validated amplicon panel for parentage reconstruction and selection monitoring in whitefish (Coregonus spp.)"],"prefix":"10.1007","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-3060-6774","authenticated-orcid":false,"given":"Caleb","family":"Beck","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1800-0821","authenticated-orcid":false,"given":"Marion","family":"Leleu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5007-5789","authenticated-orcid":false,"given":"Marina","family":"Bras\u00f3\u2010Vives","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"St\u00e9phane","family":"Daly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandesh","family":"Shrestha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gr\u00e9gory","family":"Brazzola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6143-4716","authenticated-orcid":false,"given":"Claus","family":"Wedekind","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,16]]},"reference":[{"key":"1449_CR1","doi-asserted-by":"publisher","first-page":"4733","DOI":"10.1111\/mec.12426","volume":"22","author":"A Abad\u00eda-Cardoso","year":"2013","unstructured":"Abad\u00eda-Cardoso A, Anderson EC, Pearse DE, Garza JC (2013) Large-scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead (Oncorhynchus mykiss). 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