Nuclear and plastidial SNP and INDEL markers for genetic tracking studies of Jacaranda copaia
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TECHNICAL NOTE
Nuclear and plastidial SNP and INDEL markers for genetic tracking studies of Jacaranda copaia Alexandre M. Sebbenn1 · Celine Blanc‑Jolivet2 · Malte Mader2 · Barbara R. V. Meyer‑Sand3 · Kathelyn Paredes‑Villanueva4 · Eurídice N. Honorio Coronado5 · Carmen García‑Dávila5 · Niklas Tysklind6 · Valerie Troispoux6 · Adline Delcamp7 · Bernd Degen2 Received: 17 January 2019 / Accepted: 20 May 2019 © Springer Nature B.V. 2019
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 Jacaranda copaia (Aubl.) D. Don (Bignoniaceae) is a pioneer Neotropical tree found from Belize to Brazil (Vinson Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12686-019-01097-9) contains supplementary material, which is available to authorized users. * Celine Blanc‑Jolivet celine.blanc‑[email protected] 1
Instituto Florestal de São Paulo, CP 1322, São Paulo, SP 01059‑970, Brazil
2
Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
3
Departamento de Fitotecnia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brazil
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
5
Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. José A. Quiñones km 2.5, Iquitos, Peru
6
INRA, UMR0745 EcoFoG, AgroParisTech, Cirad, CNRS, Université des Antilles, Université de Guyane, Campus Agronomique, Avenue de France, BP97387, Kourou Cedex, France
7
BIOGECO, INRA, Univ. Bordeaux, 33610 Cestas, France
et al. 2014). The species is intensively harvested in the Amazon forest (Vinson et al. 2014), and as with other valuable species, the high occurrence of illegal logging activities in the Amazon basin commands the use of approaches to determine the geographic origin of the harvested wood. DNA fingerprints is a strong method to determine species identification and the geographic origin of timber (Jolivet and Degen 2012; Meyer-Sand et al. 2017; Blanc-Jolivet et al. 2018; Chaves et al. 2018). Here, we describe 407 new SNP and INDEL loci tested on J. copaia from which we selected 128 loci showing high geographical differentiation. Cambium
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