Valerie Poncet

Valerie Poncet
Institute of Research for Development | IRD · 232 - Diversity, Adaptation and Development of Cultivated Plants (DIADE)

PhD

About

159
Publications
35,166
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2,795
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Publications

Publications (159)
Chapter
Full-text available
The ultimately main purpose of studying coffee genetics and genomics using molecular markers is to preserve and enhance the gene pool of high-quality coffee varieties and improve or produce varieties with desirable traits. Studying coffee evolution is important to understand their mechanism of adaptation to the changing environment and predict thei...
Preprint
Full-text available
Uganda lies within the drier end of the natural distribution range of Coffea canephora and contains unexplored genetic material that could be drought-adapted and useful for developing climate-resilient varieties. Using experimental treatments, (i) ample and (ii) restricted-water, response of 148 genotypes were studied comprising wild, feral and cul...
Article
The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant re...
Article
Full-text available
Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programs. To this end, landscape genomics is a useful approach for assessing putative adaptations to future climatic conditions, especially in long‐lived species such as trees. We conducted a p...
Preprint
Full-text available
We assessed and optimized a capture protocol in 20 different species from 6 different plant genus using kits from 20,000 to 200,000 baits targeting from 300 to 32,000 genes. We evaluated both the effectiveness of the capture protocol and the fold enrichment in targeted sequences. We proposed a protocol with multiplexing up to 96 samples in a single...
Poster
Full-text available
As a consequence of climate change, Vietnam, the world's largest Robusta producer, is facing the risk of losing 50% suitable area for growing Robusta by 2050 (Bunn et al., 2015). To deal with the ongoing challenge, it is therefore important to understand the genetic makeup and diversity of Coffea canephora clones cultivated in Vietnam. As a prelimi...
Article
Full-text available
Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to ex...
Poster
Full-text available
Targeted-sequence capture coupled to high-throughput sequencing has become a powerful method for the study of genome-wide sequence variation. Using the available genome of C. canephora (estimated size of 710 Mb/haploid) as a reference, we designed probes for the 323 selected candidate genes (CGs) to capture their homeologs in 293 accessions of C. c...
Poster
Full-text available
Testing whether and how natural populations are adapted to their local environment and predicting their responses to future habitat alterations is of key importance in the face of climate change. This is particularly the case for coffee trees for which the pace of climate change could be too fast and drastic for adaptation of populations. Using the...
Chapter
Full-text available
Amborella trichopoda (Amborellaceae) is a shrub endemic to New Caledonia in the Southwest Pacific region. This plant suddenly became famous when molecular phylogenetic studies revealed that this sole species is likely the sister taxon to all other angiosperms. It has thus been a prime research model for reconstructing plant evolution and gaining in...
Book
Full-text available
Simposio de Pesquisa dos Cafés do Brasil, Vitória, BRA, 08-/10/2019 - 10/10/2019
Book
Full-text available
Simposio de Pesquisa dos Cafés do Brasil, Vitória, BRA, 08-/10/2019 - 10/10/2019
Article
Full-text available
Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n=4x=44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n= 2x=22). Interestingly, these progenitor species harbor a gre...
Article
Full-text available
Inferring the mode and tempo of natural selection helps further our understanding of adaptation to past environmental changes. Here we introduce McSwan, a method to detect and date past and recent natural selection events in the case of a hard sweep. The method is based on the comparison of site frequency spectra obtained under various demographic...
Conference Paper
Full-text available
In the light of adaptation, understanding how organisms respond to their environment, by altering physiological processes, will increase our capacity to make predictions about adaptation to global climate change. Adaptive clines have been increasingly studied in plant species within temperate zones to understand adaptation of organism in natural po...
Conference Paper
Full-text available
Like many other crops, coffee production is threatened by climate changes. Therefore, research on coffee adaptation to abiotic stresses as well as alternative faster breeding programs are priorities in many coffee growing countries. During the last decade, studies have been focused on identifying the physiological, molecular and genetic determinism...
Poster
Full-text available
Coffea canephora, (Robusta), provides 33% of worldwide coffee production, 80% and 22% of Ugandan and Brazilian coffee production, respectively. Abiotic stress such as temperature variations or drought periods, aggravated by climate changes, are factors that affect this production. This sensitivity threatens both the steady supply of quality coffees...
Data
Fig 3 – Putative Amborella ancestral population locations at 12,800 years BP, as inferred from the spatially explicit modelling. Solid curves define the envelope containing 50% of the posterior location density for each ancestral population, while dotted curves define the 95% envelopes. Diamonds indicate the location with maximum posterior probabil...
Data
Bioinformatic data pre-processing. (PDF)
Data
Parameter estimation for the most likely demo-genomic model (2M). (PDF)
Data
Posterior parameter distributions of the spatial demo-genetic inference. Prior densities (grey-filled) and marginal posterior densities (red-filled) for 16 parameters of the spatially explicit demo-genetic modelling. The geographical coordinates of the ancestral populations are the COORD_* parameters. (TIF)
Data
MaxEnt estimated probabilities of Amborella trichopoda paleo-occurrence. Maps of paleo-occurrence probabilities during the mid-Holocene (6,000 years BP) and during the Last Glacial Maximum (21,000 BP), based on the simulations of four different global circulation models: CCSM4 (CC), MPI-ESM-P (ME), MIROC-ESM (MR) and IPSL-CM5A-LR (IP). (A) Continuo...
Data
Predictive check of the adjusted 2M demo-genomic model. Genetic summary statistics derived from the observed probabilistic SFS vs. their prediction under the adjusted 2M scenario. (PDF)
Data
Mean posterior estimates for key parameters of the spatially explicit demo-genetic model. (PDF)
Data
Genetic structure. (A; C) Inference using the ADMIXTURE software; (B; D) using the sNMF software; (E) using the full-genotype likelihood software NGSAdmix. (TIF)
Data
Posterior predictive check for the spatial demo-genetic modelling. The observed dataset (red cross) represented in the space of the first two principal components computed over the 159 summary statistics from the 2,850 posterior simulations under the adjusted spatially explicit demo-genetic model. The envelope contains 90% of the simulated datasets...
Data
Matrix of pairwise allele sharing distances. (PDF)
Data
Typology of the non-spatial demo-genomic models. (PDF)
Data
Non spatial demo-genomic model comparison. Maximum composite likelihoods, AICs and evidence ratios for the 13 tested demo-genomic models. (PDF)
Data
Mean-standardized root-mean-square error (SRMSE) of parameter estimation for the spatial coalescent model. (PDF)
Article
Full-text available
Past climate fluctuations shaped the population dynamics of organisms in space and time, and have impacted their present intra-specific genetic structure. Demo-genetic modelling allows inferring the way past demographic and migration dynamics have determined this structure. Amborella trichopoda is an emblematic relict species endemic to New Caledon...
Article
Full-text available
Aim. The frequency of plant species introductions has increased in a highly connected world, modifying species distribution patterns to include areas outside their natural ranges. These introductions provide the opportunity to gain new insight into the importance of flowering phenology as a component of adaptation to a new environment. Three Coffea...