DNA-based identification of commercially important salmon and trout species (genera Oncorhynchus and Salmo) in North America Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/k3569857g

Descriptions

Attribute NameValues
Creator
Abstract or Summary
  • There are seven commercially important species of salmon and trout (genera Oncorhynchus and Salmo) in North America, many of which are closely related but command markedly different prices. The purpose of this research was to provide improved and novel methods for the detection of salmon species substitution on the commercial market. This work took place in three parts: first an existing method was optimized and improved upon, then a comprehensive collection of reference salmon sequences was built for use in species identification with DNA barcoding, and finally, based on these sequences, a novel species-specific multiplex polymerase chain reaction (PCR) assay was developed. In the first study, a PCR-restriction fragment length polymorphism (RFLP) method for salmon species identification was optimized for use with U.S. commercial products. The restriction digest was shortened to 1 h rather than overnight and the method was successful with lightly processed products. However, heavily processed samples could not be identified. Next, DNA barcoding was examined as a method for salmon species identification. Sequence information was collected for 924 reference samples from a wide geographic range. Sequences showed low intraspecies divergences (mean 0.26%), and the mean congeneric divergence was 32-fold greater, at 8.22%. The minimum interspecies divergence was always greater than the maximum intraspecies divergence, indicating that these species can be differentiated using DNA barcodes. In the next study, species-specific primers and probes were developed based on DNA barcode sequence information to diagnose salmon species in both real-time and conventional PCR systems. The primers and probes were combined into multiplex assays and tested for specificity against 94-112 reference samples representing 19-25 species. Strong signals were detected for the target species in both systems, and nonspecific amplification was minimal. Both assays showed high sensitivity, with detection levels of 0.05 to 5.0 ng (0.1 to 10% in DNA admixtures). Overall, this study presents a rapid, specific and sensitive method for salmon species identification that can be applied to mixed-species and heavily processed samples in either a conventional or real-time format.
Resource Type
Date Available
Date Copyright
Date Issued
Degree Level
Degree Name
Degree Field
Degree Grantor
Commencement Year
Advisor
Committee Member
Academic Affiliation
Non-Academic Affiliation
Keyword
Subject
Rights Statement
Language
Replaces
Additional Information
  • description.provenance : Approved for entry into archive by Julie Kurtz(julie.kurtz@oregonstate.edu) on 2009-12-30T17:14:50Z (GMT) No. of bitstreams: 1 RasmussenRosaleeS2010.pdf: 25981851 bytes, checksum: 8f7a34410563a8bf8a6815383be3665e (MD5)
  • description.provenance : Submitted by Rosalee Rasmussen (rasmusro@onid.orst.edu) on 2009-12-29T21:38:19Z No. of bitstreams: 1 RasmussenRosaleeS2010.pdf: 25981851 bytes, checksum: 8f7a34410563a8bf8a6815383be3665e (MD5)
  • description.provenance : Made available in DSpace on 2010-01-04T21:45:50Z (GMT). No. of bitstreams: 1 RasmussenRosaleeS2010.pdf: 25981851 bytes, checksum: 8f7a34410563a8bf8a6815383be3665e (MD5)
  • description.provenance : Approved for entry into archive by Linda Kathman(linda.kathman@oregonstate.edu) on 2010-01-04T21:45:50Z (GMT) No. of bitstreams: 1 RasmussenRosaleeS2010.pdf: 25981851 bytes, checksum: 8f7a34410563a8bf8a6815383be3665e (MD5)

Relationships

In Administrative Set:
Last modified: 10/20/2017

Downloadable Content

Download PDF
Citations:

EndNote | Zotero | Mendeley

Items