ADvENS

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 Plant ADaptation versus ENvironnement & Stress

 

Research focuses

Unraveling molecular processes that underlie plant adaptive divergence and phenotypic plasticity is a crucial step towards identifying breeding strategies for maintenance of crop yield and quality under environmental constraint or predicting the adaptive potential of wild plant populations in the context of global change.

Our team aims at studying, through integrative approaches, the evolution of genomes, transcriptomes and metabolisms, in link with functional adaptive divergence and the regulation of specialized metabolisms. We intend to identify gene repertoires, modules of co-expressed genes and key metabolites associated with relevant ecological/economical functional traits. Our researches are mainly performed on tropical trees, with a special emphasis on their seeds that accumulate peculiar chemical compounds and exhibit high sensitivity to thermal and water stresses. The complementary skills of the team members enable the development of integrated research strategies coupling genomics, analytical chemistry and physiology.

Main activities and projects

Photo7 parcelle mr maillot langevin 2

Tropical tree adaptation to environmental changes

Understanding potential adaptation of forest tropical species to climate change remains a major challenging issue for biodiversity preservation of natural ecosystems. Following this objective, the project investigates the dynamism of genetic diversity of a forest tree species from Reunion Island (Coffea mauritiana), its plasticity mechanisms and adaptation to environmental perturbations. We will investigate the genomic differentiation among populations of C. mauritiana inhabiting along environmental gradients in Reunion island, whose is known for its wide range of microclimates with short geographic distances separating them. Integrative approaches relying on new tools provided by next-generation sequencing technologies, and including genomic, transcriptomic and ecophysiology, will be developed.

Funded by : EU, La Réunion Island regional council (FEDER, Cafediv project)

 

Functional plasticity associated with allopolyploidy

Allopolyploidization is a biological process that has played a major role in plant evolution giving rise to novel phenotypes and leading to ecological diversification. Genomic plasticity enables polyploids to combine two divergent genomes of the parental diploid species in the same cell, whereas functional plasticity of duplicate genes enables them to regulate gene expression to adapt to their environment. Using the Coffea genus and the species C. arabica as a model system, the project goals are i) to investigate the transcriptional dynamics and genome interplay in allopolyploid/hybrid, ii) to identify genetic and epigenetic determinants of diversification in allopolyploid/hybrid, and iii) to better understand the adaptive advantages associated with allopolyploidy.

Funded by: ANR (PuceCafe project), Agropolis Fondation ('GenomeHarvest' flagship project)

Key publications: Lashermes et al. (2016) G3 6:2937-48 , Lashermes et al. (2014) Plant Journal 78:674-85 ; Combes et al. (2013) New Phytologist 200:251-60 ; Combes et al. (2012) J Heredity 103:36-46

 

Coffea canephora genome sequencing and analysis

The project aimed at generating a highly continuous genome sequence that can be proposed as a reference for coffee genome analysis and other sequencing efforts and for broader comparative purposes. In the frame of the South Green Bioinformatics platform, a Coffee Genome Hub has been developed [http://coffee-genome.org/]. It’s an integrated web-based database providing centralized access to coffee community genomics, genetics and breeding data and analysis tools to facilitate basic, translational and applied research in coffee. Data available are the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics (ESTs, RNA-Seq), genetic markers and genetic maps. The hub provides also tools for easy querying, visualizing and downloading research data.

Partners: CEA genoscope-CIRAD-IRD

Funded by: ANR (Coffeaseq & GenomeCafe projects)

Key publications: Denoeud et al. (2014) Science 345:1181-4 ; Cenci et al. (2012) J Heredity 104:459-464 ; Dereeper et al. (2013) Plant Mol Biol 83:177-189 ; Dereeper et al. (2015) Nucleic Acids Research 43:D1028-35.

 

Lipid metabolism and longevity of oil palm seeds

The longevity of oil palm (Elaeis guineensis) seeds is particularly short, which constitutes a major constraint for oil palm seed companies. Oil palm seeds also accumulate large amounts of saturated medium-chain fatty acids (MCFA, from 8 to 14 carbons) which crystallization under storage may be involved in the rapid decline in viability of oil palm seeds. The project aimed at validating this hypothesis and at defining post-storage thermal processes that could be applied to seeds to enable complete melting of storage lipids prior to sowing. Besides, the project aimed at identifying the factors that determine the accumulation of these uncommon fatty acids in oil palm seeds. To gain insight into the mechanisms involved, lipid metabolism was compared during development in the three oil-storing tissues of oil palm, i.e. the embryo, endosperm and mesocarp. Taking advantage of recent transcriptomic technologies, we evidenced that MCFA accumulation in the endosperm of oil palm relies on tissue-specific up-regulation of few neofunctionalized paralogs.

Partners: F2F, PalmElit, INRAB

Funded by: PalmElit SAS

Key publications: Guérin et al., 2016. Plant J., 87:423-41 ; Dussert et al., 2013, Plant Physiol, 162:1337-58; Tranbarger et al., 2011. Plant Physiol 156:564-584

 

Environmental effects on transcriptome, composition and quality attributes of coffee seeds

Image coffee fruitAlthough cultivation of coffee trees under shade or at high elevation is known to favorably affect coffee quality, quantitative data describing the influence of climatic conditions on the chemical composition of the seed are still scarce. This project aimed at understanding environmental regulations of coffee seed metabolic pathways dedicated to the accumulation of aroma precursors. Using multienvironment designs displaying broad climatic variations, and parallel monitoring of gene expression levels and metabolite accumulation profiles, we showed how growth conditions - such as mean air temperature - influence, in a predictable way, fatty acid, sugar and chlorogenic acid metabolisms and alter the chemical composition of the mature seedthrough subtle transcriptional regulations during seed development. Progress in this area could ultimately help in developing robust genomics/metabolomics fingerprints of coffee bean origin and quality, and help in assisting breeding programs dedicated to coffee quality.

Partners: CIRAD

Funded by: UE, Région Réunion (FEADER)

Key publications: Joët et al. (2014) J Exp Bot 345:1181-4 ; Bertrand et al. (2012) Food Chem 135:2575-83 ; Joët et al. (2010) Plant Cell Env 33:1220-33; Joët et al. (2010) Food Chem 118: 693-701

Ecological significance of seed desiccation sensitivity

In most flowering plant species, seeds are in a dry quiescent state at maturity, which enables them to survive adverse environmental conditions after dispersal such as periods of cold or drought. However, more than 10% of higher plants produce non-orthodox (i.e. desiccation-sensitive) seeds, these plants prevailing in specific habitats such as tropical forests. This project aims at characterizing desiccation tolerance for different species of New-Caledonia biomes. This project also aims at identifying major environmental factors impairing post-dispersal seed survival and at determining if seed desiccation sensitivity is a direct correlate for predicting species distribution ranges along hydrological gradients.

Key publication:  Joët et al. (2016) Ann. Bot., 117:165-76 ; Joët et al. (2013) Ann. Bot., 111:693-701

 

Ex situ conservation

The Biological Resources Center for Coffea species (BRC Coffea) is managed by our team. The BRC Coffea contains about 750 accessions belonging to 35 wild species that represent the diversity of the genus Coffea throughout its natural range (Africa and Indian Ocean islands). It is maintained in the field at three locations that offer contrasted pedoclimatic conditions. All accessions are maintained in the main field collection (Southern Réunion Island). The two secondary field collections (Western and Northern Réunion Island) hold collections of smaller size but representative of the main collection. Finally, a cryobank has been established at Montpellier, to guarantee the long-term, safe and cost-effective conservation of this heritage of worldwide importance.

 

 

 

Team members

Non-permanent staff and students

  • Edith Garot, PhD thesis 2016-2019 (Université Montpellier)
  • Anna Stavrinides, Post-doc 2017-2018, IRD

Alumnis

  • Simon Foulquier, Master2, 2016 (Université Toulouse III)
  • Aldecinei SIQUEIRA BASTOS, Post-Doc 2014-2015, CNPq (Brésil, Embrapa Manaus)
  • Chloé GUERIN, PhD thesis 2013-2015, (UM, co-supervised with F2F)
  • Kheira ERROUANE, PhD thesis 2013-2015, (Université d’Oran)

 

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Coffeegenomehub 1

Other partners: CRF, Kenya; CEFE, CNRS; UNC, Nouvelle-Calédonie,CIRAD, Université de la Réunion