Abstract
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 language | English |
|---|---|
| Pages (from-to) | 421-427 |
| Number of pages | 7 |
| Journal | Conservation Genetics Resources |
| Volume | 14 |
| Issue number | 4 |
| DOIs | |
| State | Published - Dec 2022 |
Funding
We dedicate this paper to Robb Leary who was a mentor to so many and whose intellect, humor, and candor were always on display as he brought to life the conservation and management implications of genetic data to generations of fisheries professionals. We thank Hugh Anthony, Jeff Chan, Michael Hogansen, Ron Pierce, Ray Pillipow, Maureen Small, & Nik Zymonas for supplying known-sex samples, and AVISTA, Montana Fish Wildlife and Parks, NorthWestern Energy (formally Pennsylvania Power and Lights) and the Kalispel Indian Community for funding development of the sex ID marker. Yann Guiguen at the French National Institute for Agricultural Research, Department of Animal Physiology and Livestock Systems, Lyon, France kindly provided the sequence data necessary to design the sex-identification assay. We also thank Yves Hoareau for extracting DNA from fin clips and coordinating sample prep with the Miller lab, and Ryan Kovach for providing FIS data from MT FWP populations, and Diane Whited for generating the maps. This article has been peer reviewed and approved for publication consistent with USGS Fundamental Science Practices (https://pubs.usgs.gov/circ/1367/). Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. The findings and conclusions in this article are those of the authors and do not necessarily represent the views of the U.S. Fish and Wildlife Service. GL and SJA were partially supported by a Bonneville Power Administration Grant No. 199101903 to Montana Fish, Wildlife and Parks and the U.S. National Science Foundation Grants DEB-1067613 and DEB-1258203. We dedicate this paper to Robb Leary who was a mentor to so many and whose intellect, humor, and candor were always on display as he brought to life the conservation and management implications of genetic data to generations of fisheries professionals. We thank Hugh Anthony, Jeff Chan, Michael Hogansen, Ron Pierce, Ray Pillipow, Maureen Small, & Nik Zymonas for supplying known-sex samples, and AVISTA, Montana Fish Wildlife and Parks, NorthWestern Energy (formally Pennsylvania Power and Lights) and the Kalispel Indian Community for funding development of the sex ID marker. Yann Guiguen at the French National Institute for Agricultural Research, Department of Animal Physiology and Livestock Systems, Lyon, France kindly provided the sequence data necessary to design the sex-identification assay. We also thank Yves Hoareau for extracting DNA from fin clips and coordinating sample prep with the Miller lab, and Ryan Kovach for providing F data from MT FWP populations, and Diane Whited for generating the maps. This article has been peer reviewed and approved for publication consistent with USGS Fundamental Science Practices ( https://pubs.usgs.gov/circ/1367/ ). Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. The findings and conclusions in this article are those of the authors and do not necessarily represent the views of the U.S. Fish and Wildlife Service. IS
| Funders | Funder number |
|---|---|
| Avista | |
| Montana Fish Wildlife and Parks | |
| Northwestern Energy | |
| DEB-1258203, DEB-1067613 | |
| 199101903 | |
| Institut National de la Recherche Agronomique (INRA), UMR 1388 Genetique, Physiologie et Systemes d'Elevage |
Keywords
- Bull trout
- Conservation genomics
- Genetic monitoring
- Hybridization
- RAD-seq
- Sex identification
- Single nucleotide polymorphism
- Species diagnostic loci
- Threatened species