Development of molecular markers for determining continental origin of wood from white oaks (QuercusL. 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.

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

“…We found 82 SSRs in the Q. bawanglingensis cp genome that were mostly distributed in the LSC (62, 75.61%) and intergenic spaces (64, 78.04%). Efficient molecular markers might be selected by using auxiliary information from the uneven distribution of cpSSRs for phylogenetic and phylogeographical studies [38,96,97]. In addition, the majority of cpSSRs in the Q. bawanglingensis cp genome mononucleotides and dinucleotides are formed by A and T, which might be related to the high AT richness in the nucleotide composition, similar to the results found for other cp genomes [39,43,46,98].…”

Short note: Development of a new set of SNP markers to measure genetic diversity and genetic differentiation of Mongolian oak (Quercus mon­golica Fisch. ex Ledeb.) in the Far East of Russia

“…The individuals for the pool were chosen from 10 locations in the Far East of Russia with two individuals per location (Schroeder et al, 2018). The reads from the Q. mongolica pool were trimmed and then mapped against a nearly complete reference chloroplast DNA sequence of a Q. mongolica reference individual (Schroeder et al, 2016a). Read trimming, reference guided read mapping as well as the following polymorphism detection were performed using CLC…”

“…So far, mostly microsatellites have been applied to study the genetic differentiation of Mongolian oak populations and genetic differences to and hybridisation with other Asian white oak species in China and Japan (Lyu et al, 2018;Tamaki and Okada, 2014;Zeng et al, 2015). Because of their even distribution across the genome, higher number, and higher reproducibility during genotyping nuclear and plastid SNPs are increasingly used for population genetic analysis, tracking of origin and species identification for tree species (Blanc-Jolivet et al, 2018;Pakull et al, 2016;Schroeder et al, 2016a).…”

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

“…Samples therefore often fail to provide enough DNA to ensure successful genetic analysis (Rachmayanti et al, 2009). As an example, Schroeder et al (2016) 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 84bp trnL region (including 39 bp of primers).…”