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

Abstract

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.

A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny

“…Individual DNA aliquots (0.5-1 g) were sheared to a median length of ϳ300 bp and converted into individually indexed sequencing libraries using Illumina TruSeq v.2 kits at the USDA Forest Service (Corvallis, Oreg., USA), as described in Schroeder et al (2016). Briefly, sequencing was performed using the Illumina MiSeq with 2 × 150 bp paired-end reads to produce individual de novo genome reference assemblies for representative North American, European, and Asian species (Q. alba, Q. petraea, and Q. mongolica, respectively); and the Illumina HiSeq with 100 bp singleend reads to sequence individual samples for reference-guided read mapping and genome assembly.…”

“…Raw read quality filtering, de novo assembly, and referenceguided assembly for these samples are described in Schroeder et al (2016). Briefly, raw read quality filtering was accomplished using Trimmomatic v0.30 (Bolger et al 2014) to remove reads with a mean Phred score less than 33.…”

“…Briefly, raw read quality filtering was accomplished using Trimmomatic v0.30 (Bolger et al 2014) to remove reads with a mean Phred score less than 33. Reference-guided read mapping and plastome assembly were performed using CLC Genomics Workbench v. 7.5.1 (CLC-Bio; Aarhus, Denmark) and the 135 258 bp Q. mongolica draft plastid genome reference (accession MOR360/ QUMO5_CH_1; Schroeder et al 2016). This chloroplast genome reference contains only one of the two inverted repeat regions that are present in red oak chloroplast genomes (Alexander and Woeste 2014), so our reference size (135.2 kb) is smaller than a complete oak chloroplast genome (ϳ161 kb).…”

Multi‐variable approach pinpoints origin of oak wood with higher precision

“…wood density [Wilson et al., ]; parenchyma fractions [Morris et al., ]) should be explored. Moreover, as ring‐porous oak species in Northern Spain exhibit specific biogeographical distributions, integration of DNA analyses for species identification or genome sequencing (Schroeder et al., ) could further supplement the tool‐box for dendroprovenancing. We believe that with a multi‐variable approach we achieve a higher precision in dendroprovenancing and pinpoint origin of timber on a finer scale.…”

Improved recovery of ancient DNA from subfossil wood – application to the world's oldest Late Glacial pine forest

“…As an example, Schroeder et al . () could successfully genotype only 58% of their analysed > 200 processed and treated timber samples. In our case, four out of 12 pine samples dated to > 13 000 yr bp yielded authentic Pinus aDNA for the 84‐bp trn L region (including 39 bp of primers).…”