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Nuclear and chloroplastic SNP markers for genetic studies of timber origin for Hymenaea trees

  • Camila L. Chaves
  • Celine Blanc-JolivetEmail author
  • Alexandre M. Sebbenn
  • Malte Mader
  • Barbara R. V. Meyer-Sand
  • Kathelyn Paredes-Villanueva
  • Euridice N. Honorio Coronado
  • Carmen Garcia-Davila
  • Niklas Tysklind
  • Valerie Troispoux
  • Marie Massot
  • Bernd Degen
Technical Note

Abstract

We developed nuclear and chloroplastic single nucleotide polymorphism (SNP) and INDEL (insertion/deletion) markers using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing to set up a genetic tracking method of the geographical origin of Hymenaea sp. From two initial sets of 358 and 32 loci used to genotype at least 94 individuals, a final set of 75 nSNPs, 50 cpSNPs and 6 INDELs identifying significant population structure was developed.

Keywords

DNA fingerprints Geographical origin MiSeq RADSeq 

Notes

Acknowledgements

This research was supported by the German Federal Ministry of Food and Agriculture (BMEL) with the program International Sustainable Forest Management and the Conselho Nacional de Ciência e Tecnologia (CAPES) that granted a PhD scholarship to C.L Chaves. Genotyping was performed at the Genome Transcriptome Facility of Bordeaux (Grants from Investissements d’Avenir, Convention attributive d’aide EquipEx Xyloforest ANR-10-EQPX-16-01, 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). Sampling permits n49369 (Chico Mendes Biodiversity Institute, Brasil), MMAYA/VMABCCGDF/ DGBAP/MEG No. 0280/2016 (Bolivia), R.D. No. 001-2016- SERNANP-DGANP, R.D. No. 109-2015-SERFOR-DGGSPFFS, R.D. No. 230-2016-SERFOR-DGGSPFFS, Contrato No. 001-2016-SERFOR-DGGSPFFS-DGSPF (Peru) were granted for field work. We are also grateful to colleagues from IIAP, INRA French Guiana, Office National des Forêts and Thuenen for their assistance during field and laboratory work.

Supplementary material

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Supplementary material 1 (DOCX 52 KB)
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Supplementary material 2 (DOC 225 KB)
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Supplementary material 3 (DOCX 33 KB)

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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Camila L. Chaves
    • 1
  • Celine Blanc-Jolivet
    • 2
    Email author
  • Alexandre M. Sebbenn
    • 3
  • Malte Mader
    • 2
  • Barbara R. V. Meyer-Sand
    • 8
  • Kathelyn Paredes-Villanueva
    • 4
  • Euridice N. Honorio Coronado
    • 5
  • Carmen Garcia-Davila
    • 5
  • Niklas Tysklind
    • 6
  • Valerie Troispoux
    • 6
  • Marie Massot
    • 7
  • Bernd Degen
    • 2
  1. 1.Department of Forest Sciences, Luiz de Queiroz College of AgricultureUniversity of São PauloPiracicabaBrazil
  2. 2.Thünen Institute of Forest GeneticsGrosshansdorfGermany
  3. 3.Instituto Florestal de São PauloSão PauloBrazil
  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), Laboratorio de Biología y Genética Molecular (LBGM)IquitosPeru
  6. 6.INRA, UMR0745 EcoFoG, AgroParisTech, Cirad, CNRS, Université des Antilles, Université de GuyaneKourou CedexFrance
  7. 7.BIOGECO, INRA, Univ. BordeauxCestasFrance
  8. 8.Departamento de Fitotecnia, Faculdade de Engenharia de Ilha SolteiraUniversidade Estadual PaulistaIlha SolteiraBrazil

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