Development of nuclear and plastid SNP and INDEL markers for population genetic studies and timber traceability of Carapa species
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Low coverage MiSeq genome sequencing and restriction associated DNA sequencing (RADseq) were used to identify nuclear and plastid SNP and INDEL genetic markers in Carapa guianensis. 261 genetic markers including 237 nuclear SNPs, 22 plastid SNPs, and 2 plastid INDELs are described based on 96 genotyped individuals from French Guiana, Brazil, Peru, and Bolivia. The best 117 SNPs for identifying population structure and performing individual assignment are assembled into four multiplexes for MassARRAY genotyping.
KeywordsDNA-fingerprints Geographical origin MiSeq RADSeq Tropical timber MassARRAY Carapa guianensis Carapa surinamensis
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 Genome Transcriptome Facility of Bordeaux (PGTB) (Grants from the Conseil Regional d’Aquitaine No. 20030304002FA and 20040305003FA, the European Union, FEDER No. 2003227, and Investissements d’avenir, No. ANR-10-EQPX-16-01). Support for the UMR EcoFoG was provided by CEBA: ANR-10-LABX-25-01. Permits ICMBIO Nos. 47960, 49369, registration SisGen No. A16E4DA (Brazil), MMAYA/VMABCCGDF/DGBAP/MEG No. 0280/2016 (Bolivia), R.D. No. 001-2016- SERNANP-DGANP, R.D. No. 230-2016-SERFOR-DGGSPFFS, Contrato No. 001-2016-SERFOR-DGGSPFFS-DGSPF (Peru) were granted for field work 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, PGTB, and Thünen Institute for their assistance during field and laboratory work.
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