Root system markup language: toward an unified root architecture description language

The number of image analysis tools supporting the extraction of architectural features of root systems has increased over the last years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tool is able to extract in an efficient way growing array of static and dynamic features for different types of images and species. We describe the Root System Markup Language (RSML) that has been designed to overcome two major challenges: (i) to enable portability of root architecture data between different software tools in an easy and interoperable manner allowing seamless collaborative work, and (ii) to provide a standard format upon which to base central repositories which will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store 2D or 3D image metadata, plant and root properties and geometries, continuous functions along individual root paths and a suite of annotations at the image, plant or root scales, at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An xml-schema describes the features and constraints of RSML and open-source packages have been developed in several languages (R, Excel, Java, Python, C#) to enable researchers to integrate RSML files into popular research workflow

Paving the way towards future-proofing our crops

To meet the increasing global demand for food, feed, fibre and other plant-derived products, a steep increase in crop productivity is a scientifically and technically challenging imperative. The CropBooster-P project, a response to the H2020 call ‘Future proofing our plants’, is developing a roadmap for plant research to improve crops critical for the future of European agriculture by increasing crop yield, nutritional quality, value for non-food applications and sustainability. However, if we want to efficiently improve crop production in Europe and prioritize methods for crop trait improvement in the coming years, we need to take into account future socio-economic, technological and global developments, including numerous policy and socio-economic challenges and constraints. Based on a wide range of possible global trends and key uncertainties, we developed four extreme future learning scenarios that depict complementary future developments. Here, we elaborate on how the scenarios could inform and direct future plant research, and we aim to highlight the crop improvement approaches that could be the most promising or appropriate within each of these four future world scenarios. Moreover, we discuss some key plant technology options that would need to be developed further to meet the needs of multiple future learning scenarios, such as improving methods for breeding and genetic engineering. In addition, other diverse platforms of food production may offer unrealized potential, such as underutilized terrestrial and aquatic species as alternative sources of nutrition and biomass production. We demonstrate that although several methods or traits could facilitate a more efficient crop production system in some of the scenarios, others may offer great potential in all four of the future learning scenarios. Altogether, this indicates that depending on which future we are heading toward, distinct plant research fields should be given priority if we are to meet our food, feed and non-food biomass production needs in the coming decades

Improving crop yield potential: Underlying biological processes and future prospects

The growing world population and global increases in the standard of living both result in an increasing demand for food, feed and other plant‐derived products. In the coming years, plant‐based research will be among the major drivers ensuring food security and the expansion of the bio‐based economy. Crop productivity is determined by several factors, including the available physical and agricultural resources, crop management, and the resource use efficiency, quality and intrinsic yield potential of the chosen crop. This review focuses on intrinsic yield potential, since understanding its determinants and their biological basis will allow to maximize the plant's potential in food and energy production. Yield potential is determined by a variety of complex traits that integrate strictly regulated processes and their underlying gene regulatory networks. Due to this inherent complexity, numerous potential targets have been identified that could be exploited to increase crop yield. These encompass diverse metabolic and physical processes at the cellular, organ and canopy level. We present an overview of some of the distinct biological processes considered to be crucial for yield determination that could further be exploited to improve future crop productivity

Prospects to improve the nutritional quality of crops

A growing world population as well as the need to enhance sustainability and health create challenges for crop breeding. To address these challenges, not only quantitative but also qualitative improvements are needed, especially regarding the macro- and micronutrient composition and content. In this review, we describe different examples of how the nutritional quality of crops and the bioavailability of individual nutrients can be optimised. We focus on increasing protein content, the use of alternative protein crops and improving protein functionality. Furthermore, approaches to enhance the content of vitamins and minerals as well as healthy specialised metabolites and long-chain polyunsaturated fatty acids are considered. In addition, methods to reduce antinutrients and toxins are presented. These approaches could help to decrease the ‘hidden hunger’ caused by micronutrient deficiencies. Furthermore, a more diverse crop range with improved nutritional profile could help to shift to healthier and more sustainable plant-based diets

Prospects to improve the nutritional quality of crops

A growing world population as well as the need to enhance sustainability and health create challenges for crop breeding. To address these challenges, not only quantitative but also qualitative improvements are needed, especially regarding the macro- and micronutrient composition and content. In this review, we describe different examples of how the nutritional quality of crops and the bioavailability of individual nutrients can be optimised. We focus on increasing protein content, the use of alternative protein crops and improving protein functionality. Furthermore, approaches to enhance the content of vitamins and minerals as well as healthy specialised metabolites and long-chain polyunsaturated fatty acids are considered. In addition, methods to reduce antinutrients and toxins are presented. These approaches could help to decrease the ‘hidden hunger’ caused by micronutrient deficiencies. Furthermore, a more diverse crop range with improved nutritional profile could help to shift to healthier and more sustainable plant-based diets

Nitrogen sensing and the adaptive responses of the Arabidopsis root system to nitrogen limitation

National audienc

Analyse du développement racinaire adaptatif d'Arabidopsis thaliana en réponse à la disponibilité en nitrate

Mes travaux de recherche, au travers de 3 approches distinctes, se focalisent sur l'analyse du développement d'Arabidopsis thaliana. Ainsi, ma thèse a porté sur la caractérisation génétique, physiologique, cytologique et moléculaire d'une classe de mutants de développement d'Arabidopsis thaliana : les mutants " tonneau " et a permis de montrer que les gènes TON, impliqués dans l'ancrage du cytosquelette cortical à la membrane jouaient un rôle majeur dans le développement de la plantule. Au cours de mon stage post doctoral j'ai étudié le rôle de la protéine KNOLLE dans le trafic vésiculaire et plus précisément dans la formation du phragmoplaste et de son impact sur la division cellulaire et la formation de l'embryon d'Arabidopsis. Depuis mon recrutement à l'INRA, je me suis plus particulièrement intéressé au développement racinaire adaptatif tout d'abord en réponse à une carence en phosphore puis en réponse à l'apport de nitrate. Au travers d'approches combinées de génétique, transcriptomique, physiologie, biologie cellulaire et moléculaire, j'ai pu caractériser les réponses adaptatives et identifier plusieurs gènes clés. L'évolution récente de mon activité de recherche m'a conduit à aborder un des aspects majeurs de la nutrition minérale que constituent les mécanismes de détection et de signalisation d'un élément nutritif. Nous avons ainsi pu identifier que le transporteur de nitrate NRT1-1 jouait un rôle de senseur de nitrate et activait une voie de signalisation impliquant l'auxine conduisant à une modification de l'architecture du système racinaire. Le programme de recherche que je vais développer dans les prochaines années concerne la caractérisation des bases moléculaires impliquées dans les signalisations nitrate NRT1-1-dépendantes

Nitrate sensing and signaling in Arabidopis thaliana.

Nitrate sensing and signaling in Arabidopis thaliana. . 24th International Conference on Arabidopsis Researc