Abstract
Illegal logging and trade of timber are major worldwide concerns, resulting in biodiversity and economic losses. Tropical tree species in the genus Cedrela, which have historically been heavily exploited, are still often illegally traded and there is an urgent need to develop tools to verify the origin of Cedrela products. A set of 351 SNP loci for Cedrela species from Bolivia, Brazil, Costa Rica, Cuba, Ecuador, French Guiana, Mexico, and Peru was developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing, and adapted for MassARRAY genotyping. After screening of 94 individuals covering most of the distribution of Cedrela, a final set of 136 SNP loci which included 92 nuclear SNPs, 22 chloroplast markers (20 SNPs and 2 INDELs), and 22 mitochondrial markers (19 SNPs and 3 INDELs) was selected and tested for potential to verify Cedrela timber origin.
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References
Chaplin GE (1980) Progress with provenance exploration and seed collection of Cedrela spp. In: Proceedings of the 11th Commonwealth forestry conference. Commonwealth Forestry Institute, Oxford
Chaves CL et al (2018) Assessing the ability of chloroplast and nuclear DNA gene markers to verify the geographic origin of Jatoba (Hymenaea courbaril L.) timber. J Hered 109:543–552. https://doi.org/10.1093/jhered/esy017
CITES (2017) Convention on International Trade in Endangered Species of Wild Fauna and Flora. Appendices I, II and III. Convention on International Trade in Endangered Species of Wild Fauna and Flora. https://cites.org/eng/app/appendices.php. Accessed 9 Dec 2017
Compt J, Christy T (2008) The 14th meeting of the conference of the parties to CITES. Traffic Bull 21:101
Degen B, Blanc L, Caron H, Maggia L, Kremer A, Gourlet-Fleury S (2006) Impact of selective logging on genetic composition and demographic structure of four tropical tree species. Biol Conserv 131:386–401. https://doi.org/10.1016/j.biocon.2006.02.014
Degen B, Ward S, Lemes M, Navarro C, Cavers S, Sebbenn A (2013) Verifying the geographic origin of mahogany (Swietenia macrophylla King) with DNA-fingerprints. Forensic Sci Int Genet 7:55–62
Dumolin S, Demesure B, Petit RJ (1995) Inheritance of chloroplast and mitochondrial genomes in pedunculate oak investigated with an efficient PCR method. Theor Appl Genet 91:1253–1256. https://doi.org/10.1007/bf00220937
Francis J, Lowe C (2000) Bioecología de árboles nativos y exóticos de Puerto Rico y las Indias Occidentales. Reporte Técnico General IITF-15. USDA, Servicio Forestal, Departamento de Agricultura de los Estados Unidos, Instituto Internacional de Dasonomía Tropical, Río Piedras
Gregorius HR (1987) The relationship between the concepts of genetic diversity and differentiation, vol 74. https://doi.org/10.1007/bf00274724
Honorio Coronado EN et al (2019) Development of nuclear and plastid SNP markers for genetic studies of Dipteryx tree species in Amazonia. Conserv Genet Resour. https://doi.org/10.1007/s12686-019-01081-3
Lowe AJ et al (2016) Opportunities for improved transparency in the timber trade through scientific verification. Bioscience 66:990–998. https://doi.org/10.1093/biosci/biw129
Meyer-Sand BR et al (2018) Development of a set of SNP markers for population genetics studies of Ipe (Handroanthus sp.), a valuable tree genus from Latin America. Conserv Genet Resour 10:779–781
Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–248
Mostacedo B, Fredericksen TS (1999) Regeneration status of important tropical forest tree species in Bolivia: assessment and recommendations. For Ecol Manag 124:263–273. https://doi.org/10.1016/S0378-1127(99)00076-6
Paredes-Villanueva K, de Groot GA, Laros I, Bovenschen J, Bongers F, Zuidema PA (2019) Genetic differences among Cedrela odorata sites in Bolivia provide limited potential for fine-scale timber tracing. Tree Genet Genomes 15:33. https://doi.org/10.1007/s11295-019-1339-4
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Richter H, Dallwitz M (2000) Commercial timbers: descriptions, illustrations, identification, and information retrieval. In English, French, German, Portuguese, and Spanish. Version: 25th June 2009. http://delta-intkey.com. Accessed 11 April 2018
Straub SC, Parks M, Weitemier K, Fishbein M, Cronn RC, Liston A (2012) Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics. Am J Bot 99:349–364
Toledo M, Chevallier B, Villarroel D, Mostacedo B (2008) Ecología y silvicultura de especies menos conocidas Cedro, Cedrela spp. Instituto Boliviano de Investigación Forestal, Santa Cruz
United Nations Office on Drugs and Crime, UNODC (2016) Best practice guide for forensic timber identification. International Consortium on Combating Wildlife Crime, New York
Acknowledgements
This research was supported by the German Federal Ministry of Food and Agriculture in the Frame of the “Large scale project on genetic timber verification”. Genotyping was performed at the Genomic and Sequencing Facility of Bordeaux (Grants from the Conseil Regional d’Aquitaine n° 20030304002FA and 20040305003FA, the European Union, FEDER N° 2003227, and Investissements d’avenir, n° ANR-10-EQPX-16-01 and CEBA: ANR-10-LABX-25-01). Permits ICMBIO N° 47960 and 49369, Registration SisGen N° A16E4DA (Brazil), MMAYA/VMABCCGDF/DGBAP/MEG N° 0280/2016 (Bolivia), R.D. N° 001-2016-SERNANP-DGANP, R.D. N° 001A-2015-SERFOR-DGGSPFFS-DGSPF, Contrato N° 001-2016-SERFOR-DGGSPFFS-DGSPF (Peru) were granted for collection, transport and genetic analyses. We are grateful to colleagues from IIAP, Museo de Historia Natural Noel Kempff Mercado, INRA French Guiana, Cirad Paracou Station, Office National des Forêts, and Thünen Institute for their assistance during field and laboratory work.
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Paredes-Villanueva, K., Blanc-Jolivet, C., Mader, M. et al. Nuclear and plastid SNP markers for tracing Cedrela timber in the tropics. Conservation Genet Resour 12, 239–244 (2020). https://doi.org/10.1007/s12686-019-01110-1
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DOI: https://doi.org/10.1007/s12686-019-01110-1