Abstract
Nuclear and plastidial single nucleotide polymorphism (SNP) and INDEL markers were developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing for population genetics and timber tracking purposes in the Neotropical timber species Jacaranda copaia. We used 407 nuclear SNPs, 29 chloroplast, and 31 mitochondrial loci to genotype 92 individuals from Brazil, Bolivia, French Guiana, and Peru. Based on high amplification rates and genetic differentiation among populations, 113 nuclear SNPs, 11 chloroplast, and 4 mitochondrial loci were selected, and their use validated for genetic tracking of timber origin.
References
Blanc-Jolivet C, Yanbaev Y, Kersten B, Degen B (2018) A set of SNP markers for timber tracking of Larix spp. in Europe and Russia. Forestry 91(5):614–628
Chaves CL, Degen B, Pakull B, Mader M, Honorio E, Ruas P, Tysklind N, Sebbenn AM (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
Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59:1633–1638
Jolivet C, Degen B (2012) Use of DNA fingerprints to control the origin of sapelli timber (Entandrophragma cylindricum) at the forest concession level in Cameroon. Forensic Sci Int 6:487–492
Meyer-Sand BRV, Blanc-Jolivet C, Mader M, Paredes-Villanueva K, Tysklind N, Sebbenn AM, Guichoux E, Degen B (2017) 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
Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin L, Estoup A (2004) GENECLASS 2: a software for genetic assignment and first generation migrant detection. J Hered 95:536–539
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
Vinson C, Kanashiro M, Sebbenn AM, Williams T, Harris S, Boshier D (2014) Long-term impacts of selective logging on two Amazonian tree species with contrasting ecological and reproductive characteristics: inferences from Eco-gene model simulations. Heredity 115:130–139
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 to the UMR EcoFoG). Permits ICMBIO n° 47960, 49369, registration SisGen n° A16E4DA (Brazil), MAYA/VMABCCGDF/DGBAP/MEG n° 0280/2016 (Bolivia), R.D. n° 001-2016-SERNANP-DGANP, R.D. n° 001A-2015-SERFOR-DGGSPFFS-DGSPF, and Contrato n° 001-2016-SERFOR-DGGSPFFS-DGSPF (Peru) were granted for the collection, transport, and genetic analyses of samples. We are grateful to colleagues from IIAP, INRA French Guiana, Cirad Paracou Station, Office National des Forêts, and Thünen Institute for their assistance during field work and laboratory work. In Bolivia, samples were identified by Museo de Historia Natural Noel Kempff Mercado.
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Sebbenn, A.M., Blanc-Jolivet, C., Mader, M. et al. Nuclear and plastidial SNP and INDEL markers for genetic tracking studies of Jacaranda copaia. Conservation Genet Resour 11, 341–343 (2019). https://doi.org/10.1007/s12686-019-01097-9
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DOI: https://doi.org/10.1007/s12686-019-01097-9