The giant diploid faba genome unlocks variation in a global protein crop

Publisher Copyright: © 2023, The Author(s).Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.Peer reviewe

Services rendus par les microorganismes du sol pour l’amélioration de la nutrition phosphatée des plantes

Since the first Green Revolution, agricultural practices have been based on the massive use of synthetic fertilisers and plant protection products. Since then, global consumption of phosphate fertilisers has more than tripled, reaching 47 million tonnes in 2019. Current projections estimate that phosphate rock stocks (natural phosphorus resources for fertiliser production) could be depleted within the next century, leading us to change our agricultural practices. In soils, P is mainly present in complexed forms that are not easily accessible to plants. To reduce the use of phosphate fertilisers, it is necessary to make this complexed phosphate accessible to plants. This can be done by beneficial microorganisms such as arbuscular mycorrhizal fungi (AMF) and plant growth promoting rhizobacteria (PGPR). These soil microorganisms are of increasing interest as agro-ecosystem service providers that can maintain crop productivity and quality while reducing synthetic fertiliser inputs. The main objective of the thesis was to study, using potato as the agronomic plant of interest, the potential valorisation of AMF and PGPR associations for plant growth and nutrition while limiting P inputs. As a first step, we developed biotests to characterise and select bacteria with plant growth stimulating capacities that can interact with AMF. We tested these biotests on a Premier Tech collection of 26 bacterial isolates. Based on these tests, we developed a bacterial consortium from the above- mentioned collection that we inoculated in the greenhouse on potatoes planted in pots containing agricultural soil. We observed that inoculation of the consortium improved the phosphate nutrition and tuber yield of the plant as well as the rate of colonisation by native AMF. In parallel, we conducted a field trial in which we tested the effect of AMF inoculation on different potato cultivars. Our results suggest that the contribution of inoculation is highly dependent on the cultivar. It should be noted that inoculation, whether performed in the field or under controlled conditions, did not alter the native microbial communities.A partir de la première révolution verte, les pratiques agricoles ont reposé sur l'utilisation massive d'engrais de synthèse et de produits phytosanitaires. Depuis lors, la consommation mondiale d'engrais phosphatés a plus que triplé, pour atteindre 47 millions de tonnes en 2019. Les projections actuelles estiment que les stocks de roches phosphatées (ressources naturelles en phosphore pour la production d'engrais) pourraient être épuisées au cours du siècle prochain, ce qui nous amène à modifier nos pratiques agricoles. Dans les sols, le P est principalement présent sous des formes complexées qui ne sont pas facilement accessibles aux plantes. Pour réduire l'utilisation d'engrais phosphatés, il est nécessaire de rendre ce phosphate complexé accessible aux plantes. Cela peut se faire grâce à des microorganismes bénéfiques tels que les champignons mycorhiziens à arbuscules (CMA) et les rhizobactéries favorisant la croissance des plantes (RFCP). Ces micro-organismes du sol présentent un intérêt croissant en tant que fournisseurs de services agro- écosystémiques qui peuvent maintenir la productivité et la qualité des cultures tout en réduisant les apports synthétiques. d'engrais L'objectif principal de la thèse était d'étudier, en utilisant la pomme de terre comme plante agronomique d'intérêt, la valorisation potentielle des associations CMA et RFCP pour la croissance et la nutrition des plantes tout en limitant les apports de P. Dans un premier temps, nous avons développé des biotests pour caractériser et sélectionner des bactéries ayant des capacités de stimulation de la croissance des plantes et pouvant interagir avec les CMA. Biotests que nous avons testés sur une collection de Premier Tech composée de 26 isolats bactériens. À partir de ces tests, nous avons développé un consortium bactérien à partir de la collection susmentionnée que nous avons inoculé en serre sur des pommes de terre plantées dans des pots contenant du sol agricole. Nous avons pu observer que l'inoculation du consortium améliorait la nutrition phosphatée et le rendement en tubercules de la plante ainsi que le taux de colonisation par les CMA indigènes. En parallèle, nous avons mené un essai en champ dans lequel nous avons testé l'effet de l'inoculation des CMA sur différents cultivars de pommes de terre. Nos résultats suggèrent que l'apport de l'inoculation dépend fortement du cultivar. Il est à noter que l'inoculation, qu'elle soit effectuée au champ ou en conditions contrôlées, n'a pas modifié les communautés microbiennes indigènes

Le coup de crayon qui nous rend tous un peu scientifiques. Article sur la bande déssinée "Voyage au centre de la Pomme de terre"

National audienc

The hidden side of interaction: microbes and roots get together to improve plant resilience

ABSTRACTPlants have evolved various belowground traits to adapt to the changing environments, and root-associated soil microbes play a crucial role in the response, adaptation, and resilience to adverse environmental conditions. This comprehensive review explores the diverse interactions between plants and soil microbes, focusing on the role of root-associated microbiota, with a particular emphasis on arbuscular mycorrhizal fungi, in plant responses to diverse environmental conditions. How plant genotype, root traits, and growth environments influence these interactions, and consequently plant resilience and productivity, are discussed. Recent advances in root phenotyping, including traditional and machine learning-based methods are also presented as an innovative tool to study and characterize root-microbe interactions. Overall, these studies highlight the importance of considering the hidden side of the interactions between roots and microbes to improve plant nutrition and protection in the context of sustainable agriculture in the face of climate change

Bacillus consortium positively impacts arbuscular mycorrhizal fungi community, plant phosphate nutrition and potato yield in Solanum tuberosum cv. Jazzy

International audienceMany agricultural soils are naturally poor in plant available phosphorus (P), although total P stocks can exceed plant requirements by more than 100-fold. The reason for such apparent contradiction is that P is complexed under organic and inorganic forms, but only free inorganic orthophosphate (Pi) ions are available to plants and soil organisms. The high immobility of Pi in soil, the low soil solution circulation associated with a rapid root absorption lead to the development of a depletion zone around the roots. As a consequence, P is frequently a limiting factor for plant growth and development.Arbuscular mycorrhizal (AM) fungi are estimated to colonize the vast majority of crop plants and can provide up to 90% of the P required by plants. The hyphae produced by AM fungi and emanating from the roots forms an extremely dense hyphal network. Although those hyphae are efficient to translocate phosphate to their host, they can only absorb Pi from soil solution but are less able to degrade P complexes, contrary to P-degrading bacteria that are effective in the degradation of inorganic (i.e. Phosphate-solubilising bacteria) and organic (i.e. Phosphate-moblizsing bacteria) P. In this context, the synergetic interaction between P-degrading bacteria and AMF should allow AM fungi to take-up and translocate P to their host plants to promote their growth. Using Solanum tuberosum cv. Jazzy, we have investigated the impact of bacterial inoculation on AMF community, plant phosphate nutrition and potato yield. We have developed and characterized in-vitro an inoculum composed of two Bacillus species for their PGPR capacity. In non-sterile soil, we have shown that the inoculation with those 2 strains improves indigenous mycorrhizal colonization, plant P nutrition and potato yield. Taken together our results suggest that the bacterial inoculum synergically interacts with AMF community to improve plant nutrition and yield

Impact of double symbiosis (arbuscular mycorrhiza and nodulation) on nitrogen uptake in the Papilionoideae subfamily

International audienceThe study of plant-microbe associations through nutrient exchanges has significantly improved our understanding of plant microbiome. Leguminous plants establish mutualistic associations with both rhizobial bacteria and arbuscular mycorrhizal fungi. These symbioses improve mineral plant nutrition and increase plant resistance against biotic and abiotic stresses. Plant-microbe associations provide key features for the current agricultural and environmental challenges.In Poaceae plant, inductions of specific ammonium transporters (AMT) genes and nitrogen/peptide transporters (NRF) genes have already been described during arbuscular mycorrhiza symbiosis. Similarly, in Papilionoideae, AMT and NRF genes were shown to be regulated in mycorrhizal roots or in nodulated roots. However, little is known, in terms of efficiency and mechanisms, about the impact of the simultaneous presence of the two symbioses on the plant's nitrogen nutrition. Especially, nitrogen translocation mechanisms from the fungal and rhizobial symbiotic interfaces to the plant are not well-defined yet. We have investigated the impact of simultaneous symbiosis on nitrogen acquisition by host plants, and in particular, whether ammonium transporters were conserved throughout evolution among Papilionoideae, and if so, whether similar patterns of expression are shared. Phylogenetic analysis has revealed an organisation of AMT gene in orthologous clusters. Considering the effect of both symbioses on genes encoding proteins involved in nitrogen uptake, we have highlighted novel positively regulated genes during arbuscular mycorrhiza and/or rhizobia symbiosis. Our results identified new key proteins from mycorrhizal and rhizobial transcriptome and gives new insights on the regulation patterns determined by plant/microbe interaction

A historical perspective on mycorrhizal mutualism emphasizing arbuscular mycorrhizas and their emerging challenges

International audienceArbuscular mycorrhiza, one of the oldest interactions on earth (~ 450 million years old) and a first-class partner for plants to colonize emerged land, is considered one of the most pervasive ecological relationships on the globe. Despite how important and old this interaction is, its discovery was very recent compared to the long story of land plant evolution. The story of the arbuscular mycorrhiza cannot be addressed apart from the history, controversies, and speculations about mycorrhiza in its broad sense. The chronicle of mycorrhizal research is marked by multiple key milestones such as the initial description of a “persistent epiderm and pellicular wall structure” by Hartig; the introduction of the “Symbiotismus” and “Mycorrhiza” concepts by Frank; the description of diverse root-fungal morphologies; the first description of arbuscules by Gallaud; Mosse’s pivotal statement of the beneficial nature of the arbuscular mycorrhizal symbiosis; the impact of molecular tools on the taxonomy of mycorrhizal fungi as well as the development of in vitro root organ cultures for producing axenic arbuscular mycorrhizal fungi (AMF). An appreciation of the story – full of twists and turns – of the arbuscular mycorrhiza, going from the roots of mycorrhiza history, along with the discovery of different mycorrhiza types such as ectomycorrhiza, can improve research to help face our days’ challenge of developing sustainable agriculture that integrates the arbuscular mycorrhiza and its ecosystem services

Correction to: A historical perspective on mycorrhizal mutualism emphasizing arbuscular mycorrhizas and their emerging challenges

International audienc

Identification of putative interactors of arabidopsis sugar transporters

National audienc

The giant diploid faba genome unlocks variation in a global protein crop

International audienceIncreasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones