Joan Doidy

Medicago truncatula: Pas de résumé en français

Transcription factors (TF) are the primary regulators of genome-wide transcriptional changes. With the recent release of the pea genome, a systems analysis of TF is now possible in this important legume crop. Here, we used the TF prediction server available at the Plant TF Database to uncover TF genes in Pisum sativum. By this means, we identified a dataset of 1807 TFs in the pea genome belonging to respective TF families. This pea TF dataset was compared with TF repertoires from model species Medicago truncatula and Arabidopsis thaliana. While higher number of TFs could be observed in legume genomes, Arabidopsis showed a higher proportion of TF in its genome when reported to the total number of genes. We also described the family distribution in respective plant genomes including the well-known families of MYB, bHLH, bZIP and WRKY. In brief, this TF dataset represents a promising genetic resource to exploit in breeding programs of legume crops. This resource will also serve as a basis for further analysis on transcriptional regulation, in the field of transcriptomics and for building gene regulatory networks in systems biology.

Pea is a model organism in biology and an agronomic crop, entering the genomics era. Although RNA‐sequencing (RNA‐seq) has become the main transcriptomic approach in biology, there is currently no genome‐wide expression atlas covering a wide range of biological conditions for this species. Here, we generate a transcriptomic atlas in Pisum sativum by integrating 149 publicly available RNA‐seq libraries, covering 10 cultivars, and a comprehensive collection of plant organs and several environmental stress conditions (heat, low temperature, nutrient, and water deficit). As proof of concept, we first verified the expression profiles of key gene families, such as sugar transporters and transcription factors (TF), across this transcriptomic atlas. Using a systems biology approach, we then inferred a regulatory network of genes responsive to water deficit, from which we predicted putative TF‐target interactions, including genes encoding monosaccharide transporter PsSTP13.2 and sugar facilitator PsSWEET6 . Finally, we exploited our meta‐analysis to identify new reference genes with stable expression based on their coefficient of variation. Ten reference genes were validated by quantitative PCR across various biological samples, including different pea varieties, organs, and stress conditions (water deficit and fungal pathogen infection). Three reference genes ( Psat6g102320 , Psat6g163160 , and Psat7g253080 ) outperformed the expression stability of common housekeeping genes ( TFIIA , PPIIA , and β‐tubulin ). Altogether, this atlas opens new avenues of integrative research in the genomics and systems biology era of legume crops.

Factors controlling plant photosynthesis and primary production include parameters dictating photosynthetic activity together with export and allocation properties. In fact, phloem loading activity as well as phloem sap redistribution and velocity are considered as important players in plant carbon acquisition. But surprisingly, there is almost no information about how phloem sap properties such as sugar concentration and velocity, are controlled by photosynthetic rate. Here, we carried out gas exchange experiments coupled to isotopic labelling on sunflower leaves to monitor photosynthate export rate when photosynthesis was varied with CO ₂ mole fraction. We took advantage of a compartmental isotope model to obtain an experimental estimate of phloem sugar pool size and thus sap concentration and velocity. Phloem sugar concentration was found to increase relatively slowly (from very low values to about 1 mol L ^{− 1} ) with photosynthesis and export rate, while sap velocity remained in the same order of magnitude (0.2–0.6 mm s ⁻¹ ). This phenomenon could be explained using a simple one‐dimensional model of phloem sap generation and movement suggesting that at fixed photosynthesis, phloem sap was in a steady‐state reflecting the balance between xylem‐to‐phloem and sieve tube hydraulic conductance, turgor pressure and osmotic pressure due to loading. Our study also shows that phloem sap composition was not invariant with photosynthetic conditions but rather, adjusted to leaf export while maintaining sap flow even at very low CO ₂ .

Factors controlling plant photosynthesis and primary production include parameters dictating photosynthetic activity together with export and allocation properties. In fact, phloem loading activity as well as phloem sap redistribution and velocity are considered as important players in plant carbon acquisition. But surprisingly, there is almost no information about how phloem sap properties such as sugar concentration and velocity, are controlled by photosynthetic rate. Here, we carried out gas exchange experiments coupled to isotopic labelling on sunflower leaves to monitor photosynthate export rate when photosynthesis was varied with CO ₂ mole fraction. We took advantage of a compartmental isotope model to obtain an experimental estimate of phloem sugar pool size and thus sap concentration and velocity. Phloem sugar concentration was found to increase relatively slowly (from very low values to about 1 mol L ^-1 ) with photosynthesis and export rate, while sap velocity remained in the same order of magnitude (0.2-0.6 mm s ^-1 ). This phenomenon could be explained using a simple one-dimensional model of phloem sap generation and movement suggesting that at fixed photosynthesis, phloem sap was in a steady-state reflecting the balance between xylem-to-phloem and sieve tube hydraulic conductance, turgor pressure and osmotic pressure due to loading. Our study also shows that phloem sap composition was not invariant with photosynthetic conditions but rather, adjusted to leaf export while maintaining sap flow even at very low CO ₂ .

Factors controlling plant photosynthesis and primary production include parameters dictating photosynthetic activity together with export and allocation properties. In fact, phloem loading activity as well as phloem sap redistribution and velocity are considered as important players in plant carbon acquisition. But surprisingly, there is almost no information about how phloem sap properties such as sugar concentration and velocity, are controlled by photosynthetic rate. Here, we carried out gas exchange experiments coupled to isotopic labelling on sunflower leaves to monitor photosynthate export rate when photosynthesis was varied with CO ₂ mole fraction. We took advantage of a compartmental isotope model to obtain an experimental estimate of phloem sugar pool size and thus sap concentration and velocity. Phloem sugar concentration was found to increase relatively slowly (from very low values to about 1 mol L ^-1 ) with photosynthesis and export rate, while sap velocity remained in the same order of magnitude (0.2-0.6 mm s ^-1 ). This phenomenon could be explained using a simple one-dimensional model of phloem sap generation and movement suggesting that at fixed photosynthesis, phloem sap was in a steady-state reflecting the balance between xylem-to-phloem and sieve tube hydraulic conductance, turgor pressure and osmotic pressure due to loading. Our study also shows that phloem sap composition was not invariant with photosynthetic conditions but rather, adjusted to leaf export while maintaining sap flow even at very low CO ₂ .

The source–sink relationship is critical for proper plant growth and development, particularly for vegetative axillary buds, whose activity shapes the branching pattern and ultimately the plant architecture. Once formed from axillary meristems, axillary buds remain dormant or become active to grow into new branches. This transition is notably driven by the regulation of the bud sink strength, which is reflected in the ability to unload, metabolize and store photoassimilates. Plants have so far developed two main mechanisms for unloading sugars (sucrose) towards sink organs, a symplasmic pathway and an apoplasmic pathway, but so far limited investigations have been reported about the modes of sugar uptake during the transition from the dormant to the active outgrowth state of the bud. The available data indicate that the switch from dormant bud to active outgrowing state, requires sugar and is shortly preceded by an increase in bud metabolic activity and a remobilization of the stem starch reserves in favor of growing buds. This activation of the bud sink strength is accompanied by an up-regulation of the main markers of apoplasmic unloading, such as sugar transporters (sucrose transporters—SUTs; sugar will eventually be exported transporters—SWEETs), sucrose hydrolyzing enzymes (cell wall invertase—CWINV) and sugar metabolic pathways (glycolysis/tricarboxylic cycle—TCA; oxidative pentose phosphate pathway—OPPP). As these results are limited to a few species, they are not sufficient to provide a complete and accurate picture of the mode(s) of sugar unloading toward axillary buds and deserve to be complemented by additional studies in a wide variety of plants using systems integration, combining genetic, molecular and immunolocalization approaches. Altogether, we discuss here how sugar is a systemic regulator of shoot branching, acting both as an energy-rich molecule and a signaling entity in the establishment of the bud sink strength.

Agriculture is particularly impacted by global changes, drought being a main limiting factor of crop production. Here, we focus on pea (Pisum sativum), a model legume cultivated for its seed nutritional value. A water deficit (WD) was applied during its early reproductive phase, harvesting plant organs at two key developmental stages, either at the embryonic or the seed‐filling stages. We combined phenotypic, physiological and transcriptome analyses to better understand the adaptive response to drought. First, we showed that apical growth arrest is a major phenotypic indicator of water stress. Sugar content was also greatly impacted, especially leaf fructose and starch contents. Our RNA‐seq analysis identified 2001 genes regulated by WD in leaf, 3684 genes in root and 2273 genes in embryonic seed, while only 80 genes were regulated during seed‐filling. Hence, a large transcriptional reprogramming occurred in response to WD in seeds during early embryonic stage, but no longer during the later stage of nutritional filling. Biological processes involved in transcriptional regulation, carbon transport and metabolism were greatly regulated by WD in both source and sink organs, as illustrated by the expression of genes encoding transcription factors, sugar transporters and enzymes of the starch synthesis pathway. We then looked at the transcriptomic changes during seed development, highlighting a transition from monosaccharide utilization at the embryonic stage to sucrose transport feeding the starch synthesis pathway at the seed‐filling stage. Altogether, our study presents an integrative picture of sugar transport and metabolism in response to drought and during seed development at a genome‐wide level.

Grain legumes are major food crops cultivated worldwide for their seeds with high nutritional content. To answer the growing concern about food safety and protein autonomy, legume cultivation must increase in the coming years. In parallel, current agricultural practices are facing environmental challenges, including global temperature increase and more frequent and severe episodes of drought stress. Crop yield directly relies on carbon allocation and is particularly affected by these global changes. We review the current knowledge on source‐sink relationships and carbon resource allocation at all developmental stages, from germination to vegetative growth and seed production in grain legumes, focusing on pea (Pisum sativum). We also discuss how these source‐sink relationships and carbon fluxes are influenced by biotic and abiotic factors. Major agronomic traits, including seed yield and quality, are particularly impacted by drought, temperatures, salinity, waterlogging, or pathogens and can be improved through the promotion of beneficial soil microorganisms or through optimized plant carbon resource allocation. Altogether, our review highlights the need for a better understanding of the cellular and molecular mechanisms regulating carbon fluxes from source leaves to sink organs, roots, and seeds. These advancements will further improve our understanding of yield stability and stress tolerance and contribute to the selection of climate‐resilient crops.

Invertases are key enzymes for carbon metabolism, cleaving sucrose into energy‐rich and signaling metabolites, glucose and fructose. Invertases play pivotal roles in development and stress response, determining yield and quality of seed production. In this context, the repertoire of invertase gene families is critically scarce in legumes. Here, we performed a systematic search for invertase families in 16 Fabaceae genomes. For instance, we identified 19 invertase genes in the model plant Medicago and 17 accessions in the agronomic crop Pisum sativum. Our comprehensive phylogenetic analysis sets a milestone for the scientific community as we propose a new nomenclature to correctly name plant invertases. Thus, neutral invertases were classified into four clades of cytosolic invertase (CINV). Acid invertases were classified into two cell wall invertase clades (CWINV) and two vacuolar invertase clades (VINV). Then, we explored transcriptional regulation of the pea invertase family, focusing on seed development and water stress. Invertase expression decreased sharply from embryogenesis to seed‐filling stages, consistent with higher sucrose and lower monosaccharide contents. The vacuolar invertase PsVINV1.1 clearly marked the transition between both developmental stages. We hypothesize that the predominantly expressed cell wall invertase, PsCWINV1.2, may drive sucrose unloading towards developing seeds. The same candidates, PsVINV1.1 and PsCWINV1.2, were also regulated by water deficit during embryonic stage. We suggest that PsVINV1.1 along with vacuolar sugar transporters maintain cellular osmotic pressure and PsCWINV1.2 control hexose provision, thereby ensuring embryo survival in drought conditions. Altogether, our findings provide novel insights into the regulation of plant carbon metabolism in a challenging environment.