Timber tracking of Jacaranda copaia from the Amazon forest using DNA fingerprinting

We investigated the utility of nuclear and cytoplasmic single nucleotide polymorphism (SNP) markers for timber tracking of the intensively logged and commercialized Amazonian tree Jacaranda copaia. Eight hundred and thirty-two trees were sampled (cambium or leaves) from 38 sampling sites in Bolivia, Brazil, French Guiana, and Peru. A total of 128 SNP markers (113 nuclear, 11 chloroplastic, and 4 mitochondrial) were used for genotyping the samples. Bayesian cluster analyses were carried out to group individuals into homogeneous genetic groups for tests to self-assign groups of individuals or individuals to their population of origin. Cluster analysis based on all the SNP markers detected seven main genetic groups. Genetic differentiation was high among populations (0.484) and among genetic groups (0.415), and populations showed a strong isolation-by-distance pattern. Self-assignment testing of the groups of individuals for all loci was able to determine the population origin of all the samples (accuracy = 100%). Self-assignment tests of individuals were able to assign the origin of 94.5%–100% of individuals (accuracy: 91.7%–100%). Our results show that the use of the 128 SNP markers is suitable to correctly determine the origin of J. copaia timber, and they should be considered a useful tool for customs and local and international police

Final protocols to monitor genetic diversity of Fagus sylvatica, Quercus spp, Picea abies and P. pinaster at pan-European scale : Deliverable D2.1

We conducted a pilot study on genetic monitoring of four European forest species. In each plot, adults, seedlings and seeds were sampled and genetically analysed at two types of molecular markers. Spatial configuration of stands, demographic parameters and geographic position were analysed together with genetic parameters to find correlates of genetic diversity. Results were discussed and recommendations could be provided to improve the existing protocols in a cost-effective way

Genotypes and geographic positions of 5797 European white oaks from 636 locations genotyped at 355 nuclear SNPs and 28 maternally inherited SNPs of the chloroplast and mitochondria

<p class="MsoNormal"><span>The data set is the result of genetic inventory on 5797 white oaks collected at 636 locations all over Europe. The oaks trees were assigned in forest inventories as <em>Quercus robur</em> </span><em>L.</em> <span>(3342), <em>Quercus petraea </em></span><em>Matt</em>. <span>(2090), <em>Quercus pubescens </em></span><em>Willd</em>. <span>(170) or as unspecified <em>Quercus</em>. spp. (195). The sampling had a focus on central and east Europe as well as the Black Sea and Caucasus region. All individuals were genotyped at 355 nuclear SNPs and 28 maternally inherited SNPs of the chloroplast and mitochondria. The combination of the maternally inherited SNPs resulted in 26 different haplotypes. </span></p> <p class="MsoNormal"><span>The genotype of each individual is one row in the csv-file "genotypes". The genotypes at the nuclear markers are diploid and represented by two columns per gene marker. The genetic information at the organelle genome is haploid. For each of these gene markers one column is used. Genotypes are coded by Arabic numbers. The meaning of the numbers is explained in the table "coding genotypes" in a second csv-file. Each Individual has a unique "Genotype_ID" and a "Thuenen_Sample_ID". The "Thuenen_Sample_ID" is a unique ID that serves to identify the sample in our depository at the Thuenen Institute of Forest Genetics. Each individual has data on the geographic origin given as "Longitude" and "Latitude" in decimal degrees. For each individual the putative oak species ("Putative species") as it has been assigned in the forest inventories is given. The numbers of the "Haplotype" represent the multilocus combination of the mitochondrial and chloroplast SNPs of that individual.</span></p><p>Funding provided by: Waldklimafonds<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100010297<br>Award Number: WKF-22WC4111 01</p><p>Funding provided by: Russian Science Foundation<br>Crossref Funder Registry ID: https://ror.org/03y2gwe85<br>Award Number: REC-RMG-2022</p><p class="MsoNormal"><span>We collected samples (cambium or leaves) from 5,797 white oak trees at 636 locations all over Europe. The majority of the samples came from central and eastern Europe as well as from the Black Sea and Caucasus region. As putative species, the samples included 3342 <em>Q. robur</em>, 2090 <em>Q. petraea</em>, 170 <em>Q. pubescens</em> and 195 unspecified white oak samples. The presumed species of the samples were derived from the species classification of the stands of origin done by forests experts in frame of forest inventories. The sample size varied be-tween 1 and 48 trees at each location. The vast majority (95%) of the samples were collected in forest stands, whereas few samples were taken from provenance trials. Most material is from adult trees with diameters at breast height above 20 cm.</span></p> <p class="MsoNormal"><span>For all samples, </span><span>355 nuclear SNPs and 28 maternally inherited chloroplast and mitochondria SNPs </span><span>were analysed based on targeted genotyping by sequencing. The details of the used gene markers are given by Degen et al. (2021).</span></p&gt

Development of SNP markers for the African timber species Nauclea diderrichii

The vulnerable African timber species Nauclea diderrichii is threatened because of its overexploitation and illegal trade. We sampled individuals across Ghana, Nigeria, Cameroon, Congo Brazzaville, Gabon and Democratic Republic of Congo and performed restriction associated DNA sequencing and low coverage MiSeq genome sequencing to discover SNP and INDEL loci. After MassARRAY genotyping of 95 individuals covering the sampled distribution range at 205 loci, a set of 88 loci were selected according to their differentiation among geographical regions. It is the first time that molecular markers are described for N. diderrichii and it should encourage genetic studies in this valuable species.Plateforme d'Innovation " Forêt-Bois-Fibre-Biomasse du Futur

Development of set of SNP markers for population genetics studies of lpe (Handroanthus sp.), a valuable tree genus from Latin America

A combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing was used for the development of single nucleotide polymorphisms (SNP) and INDEL (insertion/deletions) genetic markers for Ipe (Handroanthus sp.). Of the 402 putative loci identified, 389 SNPs and INDELs (315 nuclear SPNs, six chloroplast INDELs, 15 chloroplast SNPs, 12 mitochondrial INDELs and 41 mitochondrial SNPs) were successfully genotyped at 93 individuals from Brazil, Bolivia and French Guiana using a MassARRAY® iPLEX™ platform. This set of markers will be invaluable for population genetics, phylogeography and DNA fingerprinting studie

Development of nuclear SNP markers for Mahogany (Swietenia spp.)

Swieteniaspecies are the most valuable American tropical timbers and have been heavily overexploited for decades. The three species are listed as either vulnerable or endangered by IUCN and are included on Appendix II of CITES, yet illegal exploitation continues. Here, we used restriction associated DNA sequencing to develop a new set of 120 SNP markers forSwieteniasp., suitable for MassARRAY (R) iPLEX (TM) genotyping. These markers can be used for population genetic studies and timber tracking purposes.Plateforme d'Innovation " Forêt-Bois-Fibre-Biomasse du Futur "CEnter of the study of Biodiversity in Amazoni

Nuclear and plastid SNP markers for tracing Cedrela timber in the tropics

Illegal logging and trade of timber are major worldwide concerns, resulting in biodiversity and economic losses. Tropical tree species in the genus Cedrela, which have historically been heavily exploited, are still often illegally traded and there is an urgent need to develop tools to verify the origin of Cedrela products. A set of 351 SNP loci for Cedrela species from Bolivia, Brazil, Costa Rica, Cuba, Ecuador, French Guiana, Mexico, and Peru was developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing, and adapted for MassARRAY genotyping. After screening of 94 individuals covering most of the distribution of Cedrela, a final set of 136 SNP loci which included 92 nuclear SNPs, 22 chloroplast markers (20 SNPs and 2 INDELs), and 22 mitochondrial markers (19 SNPs and 3 INDELs) was selected and tested for potential to verify Cedrela timber origin

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

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

Development of nuclear and plastid SNP and INDEL markers for population genetic studies and timber traceability of Carapa species

Low coverage MiSeq genome sequencing and restriction associated DNA sequencing (RADseq) were used to identify nuclear and plastid SNP and INDEL genetic markers in Carapa guianensis. 261 genetic markers including 237 nuclear SNPs, 22 plastid SNPs, and 2 plastid INDELs are described based on 96 genotyped individuals from French Guiana, Brazil, Peru, and Bolivia. The best 117 SNPs for identifying population structure and performing individual assignment are assembled into four multiplexes for MassARRAY genotyping