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Conservation Genetics Resources

, Volume 11, Issue 3, pp 337–339 | Cite as

Development of nuclear and plastid SNP and INDEL markers for population genetic studies and timber traceability of Carapa species

  • Niklas TysklindEmail author
  • Céline Blanc-Jolivet
  • Malte Mader
  • Barbara R. V. Meyer-Sand
  • Kathelyn Paredes-Villanueva
  • Eurídice N. Honorio Coronado
  • Carmen R. García-Dávila
  • Alexandre M. Sebbenn
  • Henri Caron
  • Valerie Troispoux
  • Erwan Guichoux
  • Bernd Degen
Technical Note

Abstract

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.

Keywords

DNA-fingerprints Geographical origin MiSeq RADSeq Tropical timber MassARRAY Carapa guianensis Carapa surinamensis 

Notes

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 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.

Supplementary material

12686_2019_1090_MOESM1_ESM.docx (110 kb)
Supplementary material 1 (DOCX 110 KB)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Niklas Tysklind
    • 1
    Email author
  • Céline Blanc-Jolivet
    • 2
  • Malte Mader
    • 2
  • Barbara R. V. Meyer-Sand
    • 3
  • Kathelyn Paredes-Villanueva
    • 4
  • Eurídice N. Honorio Coronado
    • 5
  • Carmen R. García-Dávila
    • 5
  • Alexandre M. Sebbenn
    • 6
  • Henri Caron
    • 1
  • Valerie Troispoux
    • 1
  • Erwan Guichoux
    • 7
  • Bernd Degen
    • 2
  1. 1.INRA, UMR0745 EcoFoG, AgroParisTech, Cirad, CNRS, Université des AntillesUniversité de GuyaneKourou CedexFrance
  2. 2.Thünen Institute of Forest GeneticsGrosshansdorfGermany
  3. 3.School of Natural Sciences and EngineeringSão Paulo State University (UNESP)Ilha SolteiraBrazil
  4. 4.Carrera de Ingeniería Forestal, Laboratorio de Dendrocronología, Facultad de Ciencias AgrícolasUniversidad Autónoma Gabriel René MorenoSanta CruzBolivia
  5. 5.Instituto de Investigaciones de la Amazonía Peruana (IIAP)IquitosPeru
  6. 6.Instituto Florestal de São PauloSão PauloBrazil
  7. 7.BIOGECO, INRA, University BordeauxCestasFrance

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