Development of DNA-based methods to identify CITES-protected timber species: a case study in the Meliaceae family

Abstract

Violation of CITES regulations in tropical timber trade necessitates the development of accurate species identification systems. The application of available methods, mostly based on visual illustrations and descriptions of wood anatomical characteristics, proved to be difficult or even impossible, particularly on lower taxonomic levels. Further, because most of the chain-of-custody documents are externally applied marks which can easily be manipulated, control methods should be based on wood features which are inherent in the wood itself. In a case study on five closely-related genera of the Meliaceae (mahogany) family, including Swietenia sp. (listed on CITES appendix II), Khaya, Entandrophragma, and Carapa sp. (legal trade timbers), this study demonstrates the process of developing DNA markers for identification purposes. A detailed sequence analysis of several non-coding cpDNA regions resulted in an assay of seven genus-specific SNP (single nucleotide polymorphism) markers. Tools have been designed that could be applied with lowcost equipment on the basis of PCR-RFLPs without the need for sequencing or capillary electrophoresis techniques. In addition, the application of the method to wood material with degraded DNA of low overall quantity is highlighted.

Comparative Analysis of two DNA Extraction Protocols from Fresh and Dried wood of Cunninghamia Lanceolata (Taxodiaceae)

“…The chloroplast genome has a highly conserved sequence, a uniparental inheritance (usually maternal in angiosperms and paternal in gymnosperms) and no recombination (Tang et al 2011). Moreover, the chloroplast gene for DNA barcoding is appropriate for the taxonomic identification of a species (Kress & Erickson 2007;Taberlet et al 2007;Lahaye et al 2008;Höltken et al 2012). In higher plants, plastids originate from proplastids in the cells of the meristem and they take on different forms, such as chloroplasts, chromoplasts, leucoplasts and amyloplasts, according to their cellular function, biochemistry and storage capacity.…”

Des confusions entre espèces préjudiciables à la gestion durable des essences forestières : l’exemple des acajous d’Afrique (Khaya, Meliaceae)

“…Outre le développement de marqueurs polymorphes, de microsatellites et de SNP (Single Nucleotide Polymorphisms) propres à l'espèce (Li et al, 2010 ;Sexton et al, 2010 ;Höltken et al, 2012 ;Karan et al, 2012), K. senegalensis présente un niveau de transférabilité très élevé des microsatellites de Swietenia mahagoni (L.) Jacq. (Lemes et al, 2011).…”

“…Les marqueurs RAPD, microsatellites et SNP (Chalmers et al, 1994 ;Li et al, 2010 ;Sexton et al, 2010 ;Höltken et al, 2012 ;Karan et al, 2012 ;Pakull et al, 2016) déjà développés pourraient ainsi servir pour étudier les questions de délimitation des espèces et de l'existence des hybrides au sein des acajous d'Afrique via les méthodes d'assignation bayésienne. Ces méthodes ont déjà été utilisées avec succès sur certains groupes tropicaux présentant les mêmes difficultés taxonomiques que les acajous d'Afrique ; c'est le cas des genres Santiria Blume (Ikabanga et al, 2017) et Milicia T.R.…”

SmartWoodID—an image collection of large end-grain surfaces to support wood identification systems

“…NIRS can potentially distinguish between species by differences in near-infrared absorption ( 13–15 ), although it still requires more development before becoming a common method in forensic research ( 16 ). Genetic techniques use deoxyribonucleic acid (DNA)-based approaches and can track individual logs throughout the supply chain ( 17 ), but extracting high-quality DNA from timber is difficult, especially when dried or processed ( 18–21 ). Mass spectrometry, specifically DART TOFMS, produces a chemical fingerprint indicative of a wood species, but challenges include the need for reference databases ( 15 , 16 , 22 ).…”