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

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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.

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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.

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Authors and Affiliations

  1. Department of Forest Sciences, Luiz de Queiroz College of Agriculture, University of São Paulo, Av. Pádua Dias, 11, PO Box 9, Piracicaba, São Paulo, 13418-900, Brazil

    Camila L. Chaves

  2. Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927, Grosshansdorf, Germany

    Celine Blanc-Jolivet, Malte Mader & Bernd Degen

  3. Instituto Florestal de São Paulo, CP 1322, São Paulo, SP, 01059-970, Brazil

    Alexandre M. Sebbenn

  4. Carrera de Ingeniería Forestal, Laboratorio de Dendrocronología, Facultad de Ciencias Agrícolas, Universidad Autónoma Gabriel René Moreno, Km 9 carretera al Norte, El Vallecito, Santa Cruz, Bolivia

    Kathelyn Paredes-Villanueva

  5. Instituto de Investigaciones de la Amazonía Peruana (IIAP), Laboratorio de Biología y Genética Molecular (LBGM), Av. José A. Quiñones km 2.5, Iquitos, Peru

    Euridice N. Honorio Coronado & Carmen Garcia-Davila

  6. INRA, UMR0745 EcoFoG, AgroParisTech, Cirad, CNRS, Université des Antilles, Université de Guyane, Campus Agronomique, Avenue de France, BP97387, Kourou Cedex, France

    Niklas Tysklind & Valerie Troispoux

  7. BIOGECO, INRA, Univ. Bordeaux, 69 route d’Arcachon, 33610, Cestas, France

    Marie Massot

  8. Departamento de Fitotecnia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brazil

    Barbara R. V. Meyer-Sand

Authors
  1. Camila L. Chaves
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  2. Celine Blanc-Jolivet
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  3. Alexandre M. Sebbenn
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  4. Malte Mader
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  5. Barbara R. V. Meyer-Sand
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  6. Kathelyn Paredes-Villanueva
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  7. Euridice N. Honorio Coronado
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  8. Carmen Garcia-Davila
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  9. Niklas Tysklind
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  10. Valerie Troispoux
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  11. Marie Massot
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  12. Bernd Degen
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Corresponding author

Correspondence to Celine Blanc-Jolivet.

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Chaves, C.L., Blanc-Jolivet, C., Sebbenn, A.M. et al. Nuclear and chloroplastic SNP markers for genetic studies of timber origin for Hymenaea trees. Conservation Genet Resour 11, 329–331 (2019). https://doi.org/10.1007/s12686-018-1077-1

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  • DOI: https://doi.org/10.1007/s12686-018-1077-1

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