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Pour aider les populations à prévoir les aléas climatiques et réfléchir à la meilleure façon de s'adapter, les données relatives au climat et à l'agriculture n'ont jamais été aussi importantes. L'essor de nouvelles technologies a permis de multiplier les façons de les collecter. Mais par un triste paradoxe, alors que ces données n'ont jamais été aussi nombreuses et importantes, en Afrique de l'Ouest elles sont aussi de moins en moins accessibles, du fait d'aléas diplomatiques, sécuritaires, mais aussi d'une privatisation grandissante de la data.

This data article presents a high-resolution map of available water content (AWC) for Senegal, derived from the iSDA Africa dataset and the USDA Rosetta3 model, as well as the method used for its production. The map covers the entire country at a resolution of 30 m and provides a valuable resource for hydrological studies and spatialized crop model simulations in the region where water is a limiting factor for crop production. The dataset is based on existing soil properties data and leverages pedotransfer functions (PTFs) to estimate water retention capabilities from soil properties. This AWC map derived from datasets with enhanced accuracy offers a more precise estimate of soil water retention capacity, which can be instrumental in informing water and agricultural management, policy decisions and investments. The dataset, including intermediate variables, is available in geotiff format at Cirad Dataverse under the DOI 10.18167/DVN1/SGNSII and complies with FAIR data principles, allowing its broad reuse. The code used to produce this dataset is also made available under the DOI 10.5281/zenodo.10078399, so that AWC maps can be produced for any territory covered by the iSDA Africa product.

Background: Roots play an important role during plant growth and development, ensuring water and nutrient uptake. Understanding the mechanisms regulating their initiation and development opens doors towards root system architecture engineering. Results: Here, we investigated by RNA-seq analysis the changes in gene expression in the barley stem base of 1 day-after-germination (DAG) and 10DAG seedlings when crown roots are formed. We identified 2,333 genes whose expression was lower in the stem base of 10DAG seedlings compared to 1DAG seedlings. Those genes were mostly related to basal cellular activity such as cell cycle organization, protein biosynthesis, chromatin organization, cytoskeleton organization or nucleotide metabolism. In opposite, 2,932 genes showed up-regulation in the stem base of 10DAG seedlings compared to 1DAG seedlings, and their function was related to phytohormone action, solute transport, redox homeostasis, protein modification, secondary metabolism. Our results highlighted genes that are likely involved in the different steps of crown root formation from initiation to primordia differentiation and emergence, and revealed the activation of different hormonal pathways during this process. Conclusions: This whole transcriptomic study is the first study aiming at understanding the molecular mechanisms controlling crown root development in barley. The results shed light on crown root emergence that is likely associated with a strong cell wall modification, death of the cells covering the crown root primordium, and the production of defense molecules that might prevent pathogen infection at the site of root emergence.

Soil water availability is crucial for ecosystem services, particularly in Sub-Saharan Africa where agriculture depends heavily on rainfed systems, directly impacting food security. The key to estimating water available for crops lies in the Available Water Content (AWC) – a metric indicating the water that soil can retain and provide to plants. AWC plays a vital role in crop and ecological models and is particularly integral to spatial crop simulation models. Despite many digital soil mapping endeavors, the production of AWC maps remains limited. This study illustrates the initial phase in crafting a high-resolution AWC map for Burkina Faso, utilizing iSDA Africa's 30m soil properties maps and the USDA Rosetta pedotransfer model. It also frames a research question for a student project proposed during the IDIL graduate program launch event (Montpellier University, sept. 6, 2023), aimed at refining the AWC map development method, focusing on identifying and overcoming barriers to generalize the method for global application and to enhance the usability of AWC data in crop models.

In cereals, the root system is mainly composed of post-embryonic shoot-borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or an LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and an LBD-box in their promoter show that CRL1 binds preferentially to the LBD-box in these promoter contexts. CRISPR/Cas9-targeted mutation of these two CRL1-regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix–loop–helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.

Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by functional genomics approaches. Nevertheless, these approaches are impaired by functional redundancy and mutant lethality. To overcome these limitations, organ targeted transcriptome analysis can help to identify genes involved in crown root formation and early development. In this study, we generated an atlas of genes expressed in developing crown root primordia in comparison with adjacent stem cortical tissue at three different developmental stages before emergence, using laser capture microdissection. We identified 3975 genes differentially expressed in crown root primordia. About 30% of them were expressed at the three developmental stages, whereas 10.5%, 19.5% and 12.8% were specifically expressed at the early, intermediate and late stages, respectively. Sorting them by functional ontology highlighted an active transcriptional switch during the process of crown root primordia formation. Crossanalysis with other rice root development-related datasets revealed genes encoding transcription factors, chromatin remodeling factors, peptide growth factors, and cell wall remodeling enzymes that are likely to play a key role during crown root primordia formation. This atlas constitutes an open primary data resource for further studies on the regulation of crown root initiation and development.

Background. Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of roo