Development of new SNP and INDEL loci for the valuable African timber species Lophira alata

The timber of the species Lophira alata (azobe) is very popular for outdoor constructions, which favours its overexploitation and illegal logging. We sampled individuals from Liberia, Ivory Coast, Ghana, Nigeria, Cameroon, Gabon, Congo Brazzaville and Republic Democratic of Congo to discover new nuclear and plastidial SNP and INDEL loci through restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. From an initial set of 397 loci, a final set of 126 loci was selected for timber tracking purposes.

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

Swietenia species 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 for Swietenia sp., suitable for MassARRAY®iPLEX™ genotyping. These markers can be used for population genetic studies and timber tracking purposes.

Genetic Markers for Species Conservation and Timber Tracking: Development of Microsatellite Primers for the Tropical African Tree Species Prioria balsamifera and Prioria oxyphylla

Research Highlights: Two novel sets of polymorphic microsatellite markers were developed for Prioria balsamifera and Prioria oxyphylla through high-throughput sequencing. Validation in two populations of each species proved the utility of the developed primers to estimate genetic diversity at population level. Background and Objectives: Prioria balsamifera and Prioria oxyphylla are tropical tree species from Central Africa. They produce a high-quality, multi-purpose timber that is of great interest to the international market. Prioria balsamifera has been included as ‘endangered’ on the IUCN Red List of Threatened Species. In order to set up adequate management plans and facilitate timber tracking, knowledge on the genetic diversity at population level is needed. Therefore, we aim to develop microsatellite markers that can be used for species conservation, forensics, plant breeding and population genetics studies. Materials and Methods: Genomic DNA of P. balsamifera and P. oxyphylla was sequenced on an Illumina NextSeq platform (Illumina Inc., San Diego, CA, USA), generating 829,421 and 772,018 paired-end reads that contained 7148 and 7004 microsatellite sequences, respectively. The QDD-pipeline was used to design primers, which were tested for amplification in two populations of each species. Cross-species amplification was tested in all seven African Prioria species. Results: For P. balsamifera, 16 polymorphic microsatellite markers were developed and combined in three multiplexes. Inbreeding appeared to be absent but genetic diversity was low in both populations. For P. oxyphylla, 15 polymorphic microsatellite markers were developed and combined in three multiplexes. Genetic diversity was low in both populations and estimated null allele frequencies were high for multiple loci. Cross-species amplification tests demonstrated the occurrence of conserved loci that amplified for most of the African Prioria species. Conclusions: The microsatellite markers prove to be useful for estimating genetic diversity at population level. These novel markers can be used to study gene flow and spatial genetic structure in Prioria species, which is needed to set up proper conservation guidelines and to prevent genetic erosion.

Short note: Development of a new set of SNP markers to measure genetic diversity and genetic differentiation of Mongolian oak (Quercus mon­golica Fisch. ex Ledeb.) in the Far East of Russia

We developed a new set of 25 nuclear (nc), 12 chloroplast (cp) and 7 mitochondrial (mt) SNPs and used it to genotype 371 Mongolian oak (Quercus mongolica Fisch. ex Ledeb.) trees from seven locations in a 200 km by 400 km area in the Russian Far East. One of the locations in an area of 15 km by 25 km east of the city Ussuriusk was analyzed more intensively with 188 collected trees. The genetic differentiation at the nuclear SNPs was small to moderate and for the plastid SNPs it was high when considering all trees from the seven locations. The gene pool distances between locations were for 19 out of 21 pairs statistically highly significant. There was no correlation of genetic and spatial distances. Only three different multilocus-haplotypes could be identified and 42 two-loci-combinations of plastid SNPs could be used to identify them. Conclusions for the practical application such as timber tracking and gene conservation are discussed.

The Applicat ion of DNA methods to Timber Tracking and Origin Verificat ion

Molecular marker methods can be used at a variety of levels to identify wood, from species identification, through regional and concession source verification, down to tracking individual logs. This short review describes the most appropriate molecular marker methods currently being applied or developed for: species identification (DNA barcoding), verification of source, either at the regional scale (through phylogeographic methods) or concession (population genetic assignment), and for tracking individual logs or wood products (DNA fingerprinting). This review finds that for almost all applications, molecular marker methods offer tremendous promise for use in timber tracking at all levels and can be easily automated offering quick, cheap and high-volume processing and with an expressed statistical certainty of results. However, despite the promise of molecular marker methods, some problems remain, most notably in identifying variation at gene loci that distinguish between the scale of biological organization of interest (from species to individuals), and appropriate DNA extraction methods for dried wood and old tissue sources, and recent advances in these areas are reviewed.