Development of nuclear and plastid SNP markers for genetic studies of Dipteryx tree species in Amazonia
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TECHNICAL NOTE
Development of nuclear and plastid SNP markers for genetic studies of Dipteryx tree species in Amazonia Eurídice N. Honorio Coronado1 · Céline Blanc‑Jolivet2 · Malte Mader2 · Carmen R. García‑Dávila1 · Alexandre M. Sebbenn3 · Barbara R. V. Meyer‑Sand4 · Kathelyn Paredes‑Villanueva5 · Niklas Tysklind6 · Valerie Troispoux6 · Marie Massot7 · Bernd Degen2 Received: 24 November 2018 / Accepted: 6 January 2019 © Springer Nature B.V. 2019
Abstract We developed nuclear and plastid single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) markers for Dipteryx species using a combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. Of the total 315 loci genotyped using a MassARRAY platform, 292 loci were variable and polymorphic among the 73 sampled individuals from French Guiana, Brasil, Peru, and Bolivia. A final set of 56 nuclear SNPs, 26 chloroplast SNPs, 2 chloroplast INDELs, and 32 mitochondrial SNPs identifying significant population structure was developed. This set of loci will be useful for studies on population genetics of Dipteryx species in Amazonia. Keywords Cumaru · Timber species · SNP · MassARRAY Dipteryx Schreb. (Fabaceae) is a Neotropical genus of nine accepted tree species distributed across South America, Central America, and the Caribbean. Dipteryx timber is heavy, dense, and resistant to moisture and pest attack, and has been exploited heavily over the last decade in response to the increasing international demand of hardwood (Putzel et al. 2011). The seeds, known as tonka beans, are fragrant and valuable in the perfume industry. Two species, D. odorata (Aubl.) Willd and D. charapilla J.F. Macbr. Ducke are classified as vulnerable in the IUCN Red List of Threatened Species (IUCN 2018). Nuclear microsatellites (nSSRs) have Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12686-019-01081-3) contains supplementary material, which is available to authorized users. * Eurídice N. Honorio Coronado [email protected] 1
Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. José A. Quiñones km 2.5, Iquitos, Peru
2
Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
3
Instituto Florestal de São Paulo, CP 1322, São Paulo, SP 01059‑970, Brazil
4
Departamento de Fitotecnia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brazil
been developed to study gene flow of D. odorata (Vinson et al. 2009) and D. alata Vog. (Soares et al. 2012). However, the amplification and scoring of microsatellite loci from timber material is problematic due to the low quality and quantity of DNA which can be recovered. New sets of single nucleotide polymorphisms (SNP) have been recently developed for valuable tropical timber species and have been successfully amplified in DNA of timber in South America (Chaves et al. 2018; Meyer-Sand et al. 2018) and Africa (Blanc-Jolivet et al. 2017; Jardine et al. 2016; Pa
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