Development of nuclear and plastid SNP markers for genetic studies of Dipteryx tree species in Amazonia
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We developed nuclear and plastid single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) markers for Dipteryx species using a combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. Of the total 315 loci genotyped using a MassARRAY platform, 292 loci were variable and polymorphic among the 73 sampled individuals from French Guiana, Brasil, Peru, and Bolivia. A final set of 56 nuclear SNPs, 26 chloroplast SNPs, 2 chloroplast INDELs, and 32 mitochondrial SNPs identifying significant population structure was developed. This set of loci will be useful for studies on population genetics of Dipteryx species in Amazonia.
KeywordsCumaru Timber species SNP MassARRAY
This research was supported by the German Federal Ministry of Food and Agriculture (BMEL) and the Programa Nacional de Innovación para la Competitividad y Productividad (Innóvate Perú—contract 381-PNICP-PIAP-2014). Genotyping was performed at the Genomic and Sequencing Facility of Bordeaux (Grants from the Conseil Regional d’Aquitaine Nos. 20030304002FA and 20040305003FA, the European Union, FEDER No. 2003227 and Investissements d’avenir, No. ANR-10-EQPX-16-01 and CEBA: ANR-10-LABX-25-01 to the UMR EcoFoG). Permits ICMBIO Nos. 4760, 49369, registration CGen No. A16E4DA (Brazil), MAYA/VMABCCGDF/DGBAP/MEG No. 0280/2016 (Bolivia), R.D. No. 001-2016-SERNANP-DGANP, R.D. No. 001A-2015-SERFOR-DGGSPFFS-DGSPF, and Contrato No. 001-2016-SERFOR-DGGSPFFS-DGSPF (Peru) were granted for the collection, transport and genetic analyses of samples. We are also 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.
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