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Main publications

Each year, the projects supported by the Foundation are the source of very high level scientific publications. This section aims to highlight articles from projects supported by the Foundation that have appeared in high-impact journals. We will update it annually.

In 2019, the six best publications published in high-impact journals are as follows:

-* TE-GWAS in Rice

Carpentier MC, Manfroi E, Wei FJ, Wu HP, Lasserre E, Llauro C, Debladis E, Akakpo R, Hsing YI, Panaud O (2019). Retrotranspositional landscape of Asian rice revealed by 3000 genomes. Nature Communications. 11,88 10(1):24.
Abstract
The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.
Disponible en intégralité en open access sur https://go.nature.com/2WBgoLG

-* Projet GenomeHarvest

Franc-Christophe Baurens, Guillaume Martin, Catherine Hervouet, Frederic Salmon, David Yohome, Sebastien Ricci, Mathieu Rouard, Remy Habas, Arnaud Lemainque, Nabila Yahiaoui et Angelique D’Hont, 2019, Recombination and Large Structural Variations Shape Interspecific Edible Bananas Genomes, Molecular biology and evolution 14,797 36(1) 97-111 DOI: 10.1093/molbev/msy199
Abstract
Admixture and polyploidization are major recognized eukaryotic genome evolutionary processes. Their impacts on genome dynamics vary among systems and are still partially deciphered. Many banana cultivars are triploid (sometimes diploid) interspecific hybrids between Musa acuminata (A genome) and M. balbisiana (B genome). They have no or very low fertility, are vegetatively propagated and have been classified as “AB,” “AAB,” or “ABB” based on morphological characters. We used NGS sequence data to characterize the A versus B chromosome composition of nine diploid and triploid interspecific cultivars, to compare the chromosome structures of A and B genomes and analyze A/B chromosome segregations in a polyploid context. We showed that interspecific recombination occurred frequently between A and B chromosomes. We identified two large structural variations between A and B genomes, a reciprocal translocation and an inversion that locally affected recombination and led to segregation distortion and aneuploidy in a triploid progeny. Interspecific recombination and large structural variations explained the mosaic genomes observed in edible bananas. The unprecedented resolution in deciphering their genome structure allowed us to start revisiting the origins of banana cultivars and provided new information to gain insight into the impact of interspecificity on genome evolution. It will also facilitate much more effective assessment of breeding strategies.
Key words: banana, chromosomes, genome evolution, interspecific hybrids, Musa spp., polyploidy.
Disponible en intégralité en open access sur : bit.ly/2XezLdS

-* Projet ARCAD

Scarcelli N., Cubry P., Akakpo R., Thuillet AC, Obidiegwu J., Baco MN, Otoo E., Sonke B., Dansi A., Djedatin G., Mariac C., Couderc M., Causse S., Alix K., Chair H., Francois O., Vigouroux Y., 2019, Yam genomics supports West Africa as a major cradle of crop domestication Science Advances 12,804 5(5) DOI: 10.1126/sciadv.aaw1947 WoS
Abstract
While there has been progress in our understanding of the origin and history of agriculture in sub-Saharan Africa, a unified perspective is still lacking on where and how major crops were domesticated in the region. Here, we investigated the domestication of African yam (Dioscorea rotundata), a key crop in early African agriculture. Using whole-genome resequencing and statistical models, we show that cultivated yam was domesticated from a forest species. We infer that the expansion of African yam agriculture started in the Niger River basin. This result, alongside with the origins of African rice and pearl millet, supports the hypothesis that the vicinity of the Niger River was a major cradle of African agriculture.
Disponible en intégralité en open access sur : bit.ly/36DUVp8

-* Projet MooSciTIC - a shot of science

Atindehou, M. Adeoti, K. Loko, LEY, Beule, T; Paradis, E; Djedatin, G; Tranchant-Dubreuil C., Sabot F., Lagnika L., Jaligot E. 2019. MooSciTIC: Training of trainers in West African research and higher education PLOS Biology 8,386 17(6) OI: 10.1371/journal.pbio.3000312 WoS ;
Abstract
The MooSciTIC project is a capacity-building initiative targeting West African research scientists and higher education teachers. The project aimed to improve the self-reliance of researchers and upgrade research practices by providing on-site summer schools on trans-disciplinary topics such as scientific writing, communication, and integrity. Here, we explain how this program was designed and implemented and share the positive responses from our trainees, hoping to inspire similar initiatives.
Disponible en intégralité en open access sur : bit.ly/3ewn7gh

-* Projet Wood Formation Controls under Mineral and Water Stress on Eucalyptus

Raphael Ployet Mônica, T. Veneziano Labate, Thais Regiani Cataldi, Mathias Christina, Marie Morel, Hélène San Clemente, Marie Denis, Bénédicte Favreau, Mario Tomazello Filho, Jean‐Paul Laclau, Carlos Alberto Labate, Gilles Chaix, Jacqueline Grima‐Pettenati, Fabien Mounet, 2019. A systems biology view of wood formation in Eucalyptus grandis trees submitted to different potassium and water regimes New Phytologist 7,43 223 (2) 766-782 https://doi.org/10.1111/nph.15802 suivi/WoS ;
Abstract
Wood production in fast‐growing Eucalyptus grandis trees is highly dependent on both potassium (K) fertilization and water availability but the molecular processes underlying wood formation in response to the combined effects of these two limiting factors remain unknown.
E. grandis trees were submitted to four combinations of K‐fertilization and water supply. Weighted gene co‐expression network analysis and MixOmics‐based co‐regulation networks were used to integrate xylem transcriptome, metabolome and complex wood traits. Functional characterization of a candidate gene was performed in transgenic E. grandis hairy roots.
This integrated network‐based approach enabled us to identify meaningful biological processes and regulators impacted by K‐fertilization and/or water limitation. It revealed that modules of co‐regulated genes and metabolites strongly correlated to wood complex traits are in the heart of a complex trade‐off between biomass production and stress responses. Nested in these modules, potential new cell‐wall regulators were identified, as further confirmed by the functional characterization of EgMYB 137.
These findings provide new insights into the regulatory mechanisms of wood formation under stressful conditions, pointing out both known and new regulators co‐opted by K‐fertilization and/or water limitation that may potentially promote adaptive wood traits.

-* Projet Innovative Tools to Study Trans-generational Epigenetic Inheritance in Maize

Aguilar-Cruz, A; Grimanelli, D; Haseloff, J; Arteaga-Vazquez, MA 2019 DNA methylation in Marchantia polymorpha New Phytologist 7,43 223(2) 575-581 DOI: 10.1111/nph.15818 WoS.
Abstract
Methylation of DNA is an epigenetic mechanism for the control of gene expression. Alterations in the regulatory pathways involved in the establishment, perpetuation and removal of DNA methylation can lead to severe developmental alterations. Our understanding of the mechanistic aspects and relevance of DNA methylation comes from remarkable studies in well-established angiosperm plant models including maize and Arabidopsis. The study of plant models positioned at basal lineages opens exciting opportunities to expand our knowledge on the function and evolution of the components of DNA methylation. In this Tansley Insight, we summarize current progress in our understanding of the molecular basis and relevance of DNA methylation in the liverwort Marchantia polymorpha.
Keywords: DNA methylation; Marchantia polymorpha; RNA-directed DNA methylation (RdDM); epigenetic reprogramming; epigenetics.