TY - JOUR
T1 - Development of nuclear and plastid SNP and INDEL markers for population genetic studies and timber traceability of Carapa species
AU - Tysklind, Niklas
AU - Blanc-Jolivet, Céline
AU - Mader, Malte
AU - Meyer-Sand, Barbara R.V.
AU - Paredes-Villanueva, Kathelyn
AU - Honorio Coronado, Eurídice N.
AU - García-Dávila, Carmen R.
AU - Sebbenn, Alexandre M.
AU - Caron, Henri
AU - Troispoux, Valerie
AU - Guichoux, Erwan
AU - Degen, Bernd
N1 - Funding Information:
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 For?ts, PGTB, and Th?nen Institute for their assistance during field and laboratory work.
Funding Information:
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.
Publisher Copyright:
© 2019, Springer Nature B.V.
PY - 2019/9/15
Y1 - 2019/9/15
N2 - 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.
AB - 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.
KW - Carapa guianensis
KW - Carapa surinamensis
KW - DNA-fingerprints
KW - Geographical origin
KW - MassARRAY
KW - MiSeq
KW - RADSeq
KW - Tropical timber
UR - http://www.scopus.com/inward/record.url?scp=85066884617&partnerID=8YFLogxK
U2 - 10.1007/s12686-019-01090-2
DO - 10.1007/s12686-019-01090-2
M3 - Article
AN - SCOPUS:85066884617
SN - 1877-7252
VL - 11
SP - 337
EP - 339
JO - Conservation Genetics Resources
JF - Conservation Genetics Resources
IS - 3
ER -