Thesis
The hybrid dilemma: creating genetic tools to help managers conserve native Pacific trout
Washington State University
Master of Science (MS), Washington State University
2010
Handle:
https://hdl.handle.net/2376/100320
Abstract
Hybridization events between native cutthroat trout subspecies and introduced non-native rainbow trout are increasing the rate of genomic extinctions in native salmonid populations in western North America (Allendorf et al., 2004). The main objective of our research was to develop a suite of linked species-specific single nucleotide polymorphism (SNP) genotyping markers and associated TaqMan SNP genotyping assays that can be used as a standardized management tool to identify hybrids between rainbow trout and various subspecies of cutthroat trout. Many of the previous studies used microsatellites as their marker of choice (reviewed in Boyer et al., 2008). These rapidly evolving and highly polymorphic markers have been very effective in differentiating intraspecific populations, however they are less effective at the interspecies level due to homoplasy, high error rates in scoring large numbers of alleles, and overlap in a wide range of microsatellite sizes at the species level (Pritchard et al., 2007; Narum et al. 2008). A suite of random PCR based markers developed by Ostberg and Rodriguez (2002) has also been widely used. Because these markers rely on subjective scoring of electrophoresis band sizes from unknown genomic fragments, standardization of these markers has been problematic across various labs (Christian Smith, pers. comm.). For these reasons, I developed a suite of 12 species and subspecies-specific linked haplotype single nucleotide polymorphisms (SNPs) which can be used to help distinguish rainbow trout ((RT) Oncorhynchus mykiss) from the four major subspecies of cutthroat trout: Westslope cutthroat trout ((WCT) Oncorhynchus clarki lewisi), Yellowstone cutthroat trout ((YCT) Oncorhynchus clarki bouvieri), coastal cutthroat trout ((CCT) Oncorhynchus clarki clarki), Lahontan cutthroat trout ((LCT) Oncorhynchus clarki henshawi), as well as their hybrids. The scoring of SNP bases is definitive, TaqMan SNP genotyping assays allow for easy standardization between labs, and new technologies make genotyping large numbers of samples increasing efficient and cost effective.
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Details
- Title
- The hybrid dilemma
- Creators
- Andrew S. Harwood
- Contributors
- Ruth B. Phillips (Degree Supervisor)John G. Bishop (Degree Supervisor)
- Awarding Institution
- Washington State University
- Academic Unit
- Environment, School of the (CAHNRS)
- Theses and Dissertations
- Master of Science (MS), Washington State University
- Publisher
- Washington State University; [Pullman, Washington] :
- Identifiers
- 99900525037301842
- Language
- English
- Resource Type
- Thesis