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Conservation Genetics Resources

, Volume 11, Issue 3, pp 341–343 | Cite as

Nuclear and plastidial SNP and INDEL markers for genetic tracking studies of Jacaranda copaia

  • Alexandre M. Sebbenn
  • Celine Blanc-JolivetEmail author
  • Malte Mader
  • Barbara R. V. Meyer-Sand
  • Kathelyn Paredes-Villanueva
  • Eurídice N. Honorio Coronado
  • Carmen García-Dávila
  • Niklas Tysklind
  • Valerie Troispoux
  • Adline Delcamp
  • Bernd Degen
Technical Note
  • 27 Downloads

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.

Keywords

DNA fingerprints Geographical origin MiSeq RADSeq Tropical timber MassARRAY Jacaranda copaia 

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 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.

Supplementary material

12686_2019_1097_MOESM1_ESM.doc (1.1 mb)
Supplementary material 1 (DOC 1155 kb)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Alexandre M. Sebbenn
    • 1
  • Celine Blanc-Jolivet
    • 2
    Email author
  • Malte Mader
    • 2
  • Barbara R. V. Meyer-Sand
    • 3
  • Kathelyn Paredes-Villanueva
    • 4
  • Eurídice N. Honorio Coronado
    • 5
  • Carmen García-Dávila
    • 5
  • Niklas Tysklind
    • 6
  • Valerie Troispoux
    • 6
  • Adline Delcamp
    • 7
  • Bernd Degen
    • 2
  1. 1.Instituto Florestal de São PauloSão PauloBrazil
  2. 2.Thünen Institute of Forest GeneticsGrosshansdorfGermany
  3. 3.Departamento de Fitotecnia, Faculdade de Engenharia de Ilha SolteiraUniversidade Estadual PaulistaIlha 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.INRA, UMR0745 EcoFoG, AgroParisTech, Cirad, CNRS, Université des Antilles, Université de GuyaneKourou CedexFrance
  7. 7.BIOGECO, INRA, Univ. BordeauxCestasFrance

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