Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus) Public Deposited

http://ir.library.oregonstate.edu/concern/articles/jm214q54g

Supporting Information is available online at:  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158221#sec017

Data Availability Statement: DNA sequences from Sanger sequencing of the indel containing fragments derived from this study have been deposited in GenBank (Accession numbers: KU201020- KU201034). Next-generation sequences supporting this study are available from the NCBI GenBank as BioProject PRJNA269970 (SRA Accessions SRS954648, SRS954649, and SRS954650, SRX1050444-1050539). SRA accession numbers of the next-generation sequencing data of the two DNApools are SRR3624658 (Q. robur) and SRR3624680 (Q. mongolica). Draft chloroplast genome references will be submitted to Dryad soon. The open source software Variant Tools is available on  https://github. com/ThuenenFG/varianttools.

To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article was published by the Public Library of Science and is in the public domain. The published article can be found at:  http://www.plosone.org/

Descriptions

Attribute NameValues
Creator
Abstract or Summary
  • To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of Asian Q. mongolica as a reference, we identified 861 variant sites (672 single nucleotide polymorphisms (SNPs); 189 insertion/deletion (indel) polymorphism) from representative species of three continents (Q. mongolica from Asia; Q. petraea and Q. robur from Europe; Q. alba from North America), and we identified additional chloroplast polymorphisms in pools of 20 individuals each from Q. mongolica (789 variant sites) and Q. robur (346 variant sites). Genome sequences were screened for indels to develop markers that identify continental origin of oak species, and that can be easily evaluated using a variety of detection methods. We identified five indels and one SNP that reliably identify continent-of-origin, based on evaluations of up to 1078 individuals representing 13 white oak species and three continents. Due to the size of length polymorphisms revealed, this marker set can be visualized using capillary electrophoresis or high resolution gel (acrylamide or agarose) electrophoresis. With these markers, we provide the wood trading market with an instrument to comply with the U.S. and European laws that require timber companies to avoid the trade of illegally harvested timber.
Resource Type
DOI
Date Available
Date Issued
Citation
  • Schroeder, H., Cronn, R., Yanbaev, Y., Jennings, T., Mader, M., Degen, B., & Kersten, B. (2016). Development of molecular markers for determining continental origin of wood from white oaks (Quercus L. sect. Quercus). PLoS ONE, 11(6), e0158221. doi:10.1371/journal.pone.0158221
Series
Rights Statement
Funding Statement (additional comments about funding)
Publisher
Peer Reviewed
Language
Replaces
Additional Information
  • description.provenance : Made available in DSpace on 2016-08-11T17:44:59Z (GMT). No. of bitstreams: 2 license_rdf: 1089 bytes, checksum: 0a703d871bf062c5fdc7850b1496693b (MD5) SchroederDevelopmentMolecularMarkers.PDF: 1530784 bytes, checksum: 3d986341214f4083e67f66254f3a2a2e (MD5) Previous issue date: 2016-06-28
  • description.provenance : Approved for entry into archive by Patricia Black(patricia.black@oregonstate.edu) on 2016-08-11T17:44:59Z (GMT) No. of bitstreams: 2 license_rdf: 1089 bytes, checksum: 0a703d871bf062c5fdc7850b1496693b (MD5) SchroederDevelopmentMolecularMarkers.PDF: 1530784 bytes, checksum: 3d986341214f4083e67f66254f3a2a2e (MD5)
  • description.provenance : Submitted by Patricia Black (patricia.black@oregonstate.edu) on 2016-08-11T17:44:37Z No. of bitstreams: 2 license_rdf: 1089 bytes, checksum: 0a703d871bf062c5fdc7850b1496693b (MD5) SchroederDevelopmentMolecularMarkers.PDF: 1530784 bytes, checksum: 3d986341214f4083e67f66254f3a2a2e (MD5)

Relationships

In Administrative Set:
Last modified: 07/26/2017

Downloadable Content

Download PDF
Citations:

EndNote | Zotero | Mendeley

Items