Rapid SNP genotyping, sex identification, and hybrid-detection in threatened bull trout

Stephen J. Amish, Shana Bernall, Patrick DeHaan, Michael Miller, Sean O’Rourke, Matthew C. Boyer, Clint Muhlfeld, Angela Lodmell, Robb F. Leary, Gordon Luikart

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


We developed new bull trout genetic markers using Restriction-site Associated DNA sequencing (RAD-seq) to improve our ability to address questions important for their conservation and management. Samples from across the species range were sequenced and 5020 high quality single nucleotide polymorphism (SNP) loci were discovered, including hundreds with high heterozygosity (H > 0.30). We developed 63 high-heterozygosity bull trout polymorphic SNPs and one sex-identification SNP and tested them on range-wide samples. In addition, we tested previously published SNP assays including 11 species-diagnostic SNPs differentiating bull trout from brook trout and 3 brook trout variable SNPs on a broad set of range-wide samples. Genotypes from the sex-identification SNP showed 95% agreement with the field sex identification across 113 samples. The eleven species-diagnostic loci reliably discriminated between known brook trout, bull trout, and F1 hybrid control samples. These SNP assays will facilitate genotyping of partially degraded museum fin clips, and tissues with low DNA content such as scales and otoliths. Finally, these loci will allow rapid genotyping for improved resolution of bull trout population structure, sex ratios, movement patterns, and introgressive hybridization with non-native brook trout for a wide range of management questions.

Original languageEnglish
Pages (from-to)421-427
Number of pages7
JournalConservation Genetics Resources
Issue number4
StatePublished - Dec 2022


  • Bull trout
  • Conservation genomics
  • Genetic monitoring
  • Hybridization
  • RAD-seq
  • Sex identification
  • Single nucleotide polymorphism
  • Species diagnostic loci
  • Threatened species


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