Céline Blanc-Jolivet's research while affiliated with Thünen Institute and other places

Publications (38)

Article
Full-text available
We used Double Digest Restriction site associated DNA sequencing (ddRADseq), exome sequencing (exome-seq) and targeted genotyping by sequencing (GBS) to develop new geographically informative nuclear SNP markers in Picea abies . This set of 518 loci consists of 397 loci specifically designed for the geographic differentiation of populations and 121...
Article
Pedunculate oak is seen as an alternative to other tree species for reforestation and mitigation programs in the face of climate change. Thus, the identification of suitable, well-adapted seed sources is of high priority. We perform a genetic inventory on 970 trees from 97 locations in Russia, Belarus, Ukraine and Latvia representing the eastern pa...
Article
Full-text available
The large-scale spatial genetic structure of European beech, Fagus sylvatica, has been until now poorly studied. We conducted double digest RAD sequencing (ddRADseq) on 54 beech individuals stemming from 36 provenances to discover spatially informative nuclear SNP loci. In addition, two pools derived from 14 early and 14 late flushing individuals e...
Article
Full-text available
As for most other temperate broadleaved tree species, large-scale genetic inventories of pedun-culate oak (Quercus robur L.) have focused on the plastidial genome, which showed the impact of post-glacial recolonization and manmade seed transfer. However, how have pollen mediated gene flow and introgression impacted the large-scale genetic structure...
Article
Full-text available
We used Double Digest Restriction site associated DNA sequencing (ddRAD) and Miseq to develop new geographically informative nuclear and plastid SNP and indel loci in Quercus robur and Q. petraea . Genotypes derived from sequence data of 95 individuals and two pools of 20 individuals each of Q. robur and Q. mongolica covering the distribution range...
Article
Full-text available
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 res...
Article
Full-text available
Genetic diversity and the optimal genetic composition are essential for the adaptability and adaptation of tree populations. Artificial regeneration of stands might reduce the genetic diversity and increase family structures if the seeds were collected from a limited number of mother trees. We did a genetic inventory in 12 pedunculate oak stands in...
Article
Full-text available
We used double digest restriction site associated DNA sequencing (ddRAD) to develop new geographically informative nuclear SNP loci in Quercus robur and Quercus petraea. Genotypes derived from sequence data of 95 individuals covering the distribution range of the species were analysed to select geographically informative and polymorphic loci within...
Article
Full-text available
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 m...
Article
Full-text available
The legality of wood products often depends on their origin, creating a need for forensic tools that verify claims of provenance for wood products. The neotropical tree species Cedrela odorata (Spanish cedar) is economically valuable for its wood and faces threats of overexploitation. We developed a 140 SNP assay for geographic localization of C. o...
Method
Full-text available
Today we have five types of timber tracking tools available. Each has its own strengths and limitations (see the Timber Tracking Tool Infogram), but together they offer a broad range of methods that can assist us in identifying the botanical as well as the geographic origin (provenance) of most kinds of timber samples, even those smaller than 1 cm³...
Article
Dipteryx timber has been heavily exploited in South America since 2000's due to the increasing international demand for hardwood. Developing tools for the genetic identification of Dipteryx species and their geographical origin can help to promote legal trading of timber. A collection of 800 individual trees, belonging to six different Dipteryx spe...
Article
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...
Technical Report
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...
Article
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...
Article
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 mitochond...
Article
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,...
Article
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,...
Method
Full-text available
This is a guide for the collection of reference samples of trees to enable the identification of species and/or geographical origin of woody material. To enable the implementation of the different laws regulating the trade in illegal wood, reference databases for various timber tracking tools are urgently needed for at least the most traded and e...
Article
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...
Article
The verification of the geographical origin of timber is of increasing importance with the entry into force of new regulations having become effective (EU Timber Regulation, US Lacey Act and Australia Illegal Logging Prohibition Act) that regulate the trade of timber. Larch timber represents a significant portion of timber traded on the European ma...
Article
Full-text available
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 l...
Article
Full-text available
The Meliaceae family mainly consists of trees and shrubs with a pantropical distribution. In this study, the complete chloroplast genomes of four Meliaceae species were sequenced and compared with each other and with the previously publishedAzadirachta indicaplastome. The five plastomes are circular and exhibit a quadripartite structure with high c...
Article
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,...
Article
We describe the development of new nuclear SNP markers for the genetic timber tracking of the geographical origin of Sapelli, Entandrophragma cylindricum (Meliaceae). Restriction associated DNA sequencing (RADseq) of two reference individuals yielded 1131 putative SNPs. Among those, 131 were selected to design four MassARRAY multiplexes and screene...
Conference Paper
Key words: next generation sequencing (NGS), genome skimming, SNPs, InDels, marker assisted selection The rapid development of NGS technologies and bioinformatic tools has paved the way for the assembly of complete genome sequences which may serve as references for the efficient development of molecular markers for different traits or the determin...
Article
Full-text available
DNA-based techniques are helpful in characterising hybridisation patterns in plant species. To be efficient in disentangling species boundaries and interspecific gene flow, it is recommended to combine various methodologies and types of markers. Here, we used different analytical tools (algorithms implemented in Structure, Tess, NewHybrids and HIes...
Article
Restriction associated DNA sequencing was conducted on two genetically independent individuals of Iroko, Milicia excelsa, for the discovery of nuclear SNPs. Ninety-four samples, well-distributed over the natural range and including timber DNA, were screened at 138 loci on a MassARRAY iPLEX system. Amplification success was high and 77 loci were sel...
Article
Full-text available
Background Species delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus...
Article
During the past decade, the use of DNA for forensic applications has been extensively implemented for plant and animal species, as well as in humans. Tracing back the geographical origin of an individual usually requires genetic assignment analysis. These approaches are based on reference samples that are grouped into populations or other aggregate...
Preprint
During the past decade, the use of DNA for forensic applications has been extensively implemented for plant and animal species, as well as in humans. Tracing back the geographical origin of an individual usually requires genetic assignment analysis. These approaches are based on reference samples that are grouped into populations or other aggregate...
Article
182 SNP markers were developed for Ayous (Triplochiton scleroxylon K. Schum) by incorporating information from two next generation sequencing approaches (RADseq Floragenex and AFLPseq IonTorrent PGM) into a single genotyping panel for MassARRAY® iPLEX™. This set of markers was successfully used to genotype 753 individuals from 43 populations in fiv...
Article
Full-text available
Traceability of forest material has received recently increasing interest and European regulations already apply on forest reproductive material and timber. DNA fingerprinting methods allow identification of species and control of geographic origin, providing that genetic reference data is available. In this review, we focus on the two economically...
Technical Report
Full-text available
Project no. 284181 - Trees4Future - Designing Trees for the Future This report will specify which methods have already been tried successfully in different labs, and where researchers and practitioners see the greatest needs for new marker development. http://www.trees4future.eu/uploads/t4fdeliverables/284181_T4F_D7.1_Methods_identification_web.pd...

Citations

... An overview of the program features is given in Table 1. The program can handle data of up to a few hundred populations and a few hundred genetic markers (see as an example Degen et al. (2021)). GDA-NT 2021 is well suited for conservation genetics studies, where typical datasets involve the screening of many populations with a specifically selected subset of informative genetic markers. ...
... At the same time, genetic diversity and population structure of Q. robur is well investigated in Western and Central Europe (Petit et al. 2002) and, in the last years, in the Russian part of the distribution range, including the Southern Urals. (Bushbom et al. 2011;Degen et al. 2019Degen et al. , 2021aDegen et al. , 2021bDegen et al. , 2021cBlanc-Jolivet et al. 2020;Semerikova et al. 2021). Having got results on genetic diversity of A. platanoides, it seems important to compare genetic diversity of these two associate representatives of broadleaved forests from theoretical and practical points of view. ...
... Currently, single-nucleotide polymorphisms (SNPs) technology is available for the genus Swietenia spp. [14]. RAPDs were the first molecular markers used to investigate the genetic structure of natural mahogany tree populations from Panama, Guatemala, Costa Rica, Nicaragua, Honduras, and México. ...
... and Diospyros spp.) have been undertaken since 2014, and resulted in collection of new plant material in the field using a standardized sampling protocol that includes sampling of heartwood and herbarium voucher specimens, taxonomic investigations, and conservation assessments. In parallel, these resources have also been used to develop reference collections and databases for various forensic timber identification methods (reviewed in Dormontt et al. 2015 andSchmitz et al. 2020). ...
... In the present study, we add a historic level to the species monitoring of the flowering plant species, Dracocephalum ruyschiana L. (northern dragonhead; Lamiaceae) by testing a microfluidic-based SNP genotyping array on old herbarium specimens. This approach has recently been applied by others to historical materials of, for example, tropical tree species and salmon (Finch et al., 2020;Johnston et al., 2013;Östergren et al., 2021). ...
... For the number of close neighbours, we buffered each island by 100km and counted the number of neighbouring islands within this zone. This distance was chosen as previous studies on nearest neighbour metrics in both marine (Manel et al., 2019;Mellin et al., 2010) and terrestrial (Honorio Coronado et al., 2020;Marrotte et al., 2020) ecosystems used 100 km as a metric of determining independence between populations. Then, using these neighbours' areas and distances to the target island, we estimated the effect of neighbour sizes on an island in relation to its level of isolation. ...
... At the same time, genetic diversity and population structure of Q. robur is well investigated in Western and Central Europe (Petit et al. 2002) and, in the last years, in the Russian part of the distribution range, including the Southern Urals. (Bushbom et al. 2011;Degen et al. 2019Degen et al. , 2021aDegen et al. , 2021bDegen et al. , 2021cBlanc-Jolivet et al. 2020;Semerikova et al. 2021). Having got results on genetic diversity of A. platanoides, it seems important to compare genetic diversity of these two associate representatives of broadleaved forests from theoretical and practical points of view. ...
... SSR is also often used in genetic diversity and population structure analysis of species 14,19 , and can further predict the geographic provenance and distribution of species. Genetic methods have been applied to con rm the source and trade routes of protected species 20,21 . However, ling the DNA of every individual is not feasible even if C. formosensis has been listed as an endangered species. ...
... Because indel regions are relatively easy to detect, they are often used to develop markers for identifying species [50]. The genus Acer comprises more than 200 species grown in China [2,51]; however, the highly similar shapes of some species present a challenge for identification, and a molecular approach would be beneficial. ...
... InDel markers have been used to identify the specificity of germplasm resources and provide information for breeding in chickpea (Cicer arietinum L.) [28], cotton (Gossypium hirsutum L.) [74], pepper (Capsicum spp. L.) [26], Carapa guianensis [63], mung bean (Vigna radiata (L.) Wilczek) [35], and cucumber (Cucumis sativus L.) [36]. In addition, InDel markers have been successfully used to distinguish somatic variations in apple [33], although InDel markers have not been as widely used in apple as SSRs and SNPs. ...