Alexandre Grondin

Root anatomy plays a critical role in water and nutrients acquisition and influences plant adaptation to abiotic stresses. A better understanding of the genetic control of anatomical traits is important to improve rice production, a staple crop for half of the world’s population. In this study, we measured eleven root anatomical traits in a collection of 185 Vietnamese rice landraces, and conducted genome-wide association studies to uncover the genetic architecture underlying these traits. A total of 24 significant small nucleotide polymorphisms were identified, corresponding to 19 quantitative trait loci for traits such as root cross section area, cortex area, metaxylem area or theoretical axial conductance. Interestingly, several root anatomical traits correlated with previously characterized root architectural traits measured within the same Vietnamese rice collection, and some genetic regions associated with anatomical traits and drought-tolerance-related traits colocalized. Candidate genes potentially involved in root development and cell wall patterning were identified within these QTLs regions. In particular, the significant SNP in qRA10.1 associated with metaxylem area induces an amino-acid change in the kinase domain of a wall associated kinase (WAK) receptor-like protein kinase (OsWAK111) with an extracellular epidermal growth factor (EGT)-containing domain that bind pectin, which presumably sense perturbations in this component to influence cell elongation during plant development. This study reveal key determinants of the genetic control of root anatomy in rice, which could be exploited to enhance tolerance to abiotic stresses such as drought.

Plant-plant interactions shape community productivity and resilience, yet how genetic variation influences these interactions remains poorly understood. We conducted multi-environment field phenotyping of 200 common bean (Phaseolus vulgaris) lines grown in association with three maize (Zea mays ssp. mays) landraces to characterize the determinants of interspecific interactions. Our results reveal that maize landraces constitute distinct biotic environments, and interactions were strongly asymmetric, with maize acting as the dominant competitor. Bean responses to the identity of the maize partner involved phenology, vegetative development, productivity, and root architecture, and varied across field environments, with no evidence of bean local adaptation. We used genome-wide association to link variation across the bean genome to variation in bean and maize traits, thereby capturing both direct and indirect genetic effects, and tested for maize bean interactions. We identified six genomic regions with indirect effects: three with stable effects across maize partners and three whose effects varied with maize partner identity, including candidate genes involved in neighbor perception and facilitative interactions. Our findings demonstrate that the phenotypic effects of genetic variation extend beyond individual plants, with competitive tolerance modulated by the genetic identity of neighboring plants and the environment.

Les mouvements stomatiques sont dus à des changements importants du volume des cellules de garde. Un rôle des canaux hydriques membranaires (aquaporines) dans ces processus a été proposé mais n'a jamais été démontré. Des analyses transcriptomiques indiquent que plusieurs aquaporines de la membrane plasmique (PIPs), dont AtPIP1;2 et AtPIP2;1, sont exprimées dans la cellule de garde. Dans ce travail, nous avons étudié la fonction de ces deux aquaporines dans les mouvements stomatiques. Les stomates des mutants d'insertion pip1;2 et pip2;1 montrent une ouverture normale à la lumière et aux faibles concentrations en CO2, une fermeture normale en réponse à l'obscurité et aux fortes concentrations en CO2, mais sont quasiment insensibles à la fermeture induite par l'ABA. Le rôle d'AtPIP1;2 et d'AtPIP2;1 dans le transport d'eau a été testé en mesurant la perméabilité hydrique de protoplastes (Pf) à l'obscurité, à la lumière ou à la lumière et en présence d'ABA. Le Pf des protoplastes de cellules de garde de pip2;1 est réduit de façon significative, spécifiquement en présence d'ABA. Comme la production extracellulaire de peroxyde d'hydrogène (H2O2) est essentielle pour la signalisation intracellulaire de l'ABA, nous avons également étudié la possibilité qu'AtPIP1;2 et AtPIP2;1 facilitent la diffusion de l'H2O2 à l'intérieur des cellules de garde en réponse à l'ABA. La cinétique d'accumulation d'espèces réactives de l'oxygène est abolie dans les cellules de garde chez pip2;1, mais pas chez pip1;2. Par ailleurs, dans d'autres types d'approches, nous avons étudié la régulation de ces deux aquaporines après production en levure Pichia pastoris et reconstitution fonctionnelle en protéoliposomes. Une analyse structure fonction a été réalisée avec succès pour AtPIP2;1. Elle montre que le résidu His199 est impliqué dans l'inhibition de l'activité de cette isoforme par les protons et les cations divalents. A l'inverse, le résidu Arg124 rend AtPIP2;1 complètement insensible au calcium, mais n'altère pas sa sensibilité aux protons. La surexpression de formes dérégulées d'AtPIP1;2 et d'AtPIP2;1 dans, respectivement, les mutants pip1;2 et pip2;1, indique que les régulations de l'activité intrinsèque de ces isoformes sont importantes pour leurs fonctions stomatiques. L'ensemble des résultats suggère qu'AtPIP1;2 et AtPIP2;1 ont des fonctions majeures et distinctes dans le transport d'eau et d'H2O2 lors de la fermeture stomatique induite par l'ABA chez Arabidopsis thaliana.

Root water transport has been viewed as primarily limited by the radial component, with the axial pathway considered highly conductive and non-limiting. This is supported by theoretical estimates of axial conductance using the Hagen–Poiseuille equation. However, increasing evidence indicates that actual axial conductance is often nearly an order of magnitude lower than predicted, challenging assumptions that it does not limit water uptake. In this review, we discuss how recent model inversion approaches, guided by root hydraulic conductance measurements, have revealed that water transport can be co-limited by radial and axial conductance. We explore possible explanations for this co-limitation, with particular attention to root topology. Finally, we highlight how drought-induced adjustments in xylem vessel traits can reduce axial conductance, contributing to water conservation and cavitation resistance, thereby supporting drought adaptation strategies. Leveraging this overlooked limitation opens new avenues for breeding crops with improved water-use efficiency and resilience to drought .

Phenotypic plasticity can contribute to crop adaptation to challenging environments. Plasticity indices are potentially useful to identify the genetic basis of crop phenotypic plasticity. Numerous methods exist to measure phenotypic plasticity, but their ability to capture quantitative trait loci with environmental effects remains elusive. Here, we analysed a published multi-trial maize phenotyping dataset that examined the water stress response of leaf area, shoot biomass, and water use efficiency, calculating phenotypic plasticity for these traits using seven different plasticity indices. A comprehensive genetic analysis of phenotypic plasticity for these traits was further performed and the ability of methods to detect genetic regions capturing variance due to genotype-by-environment interaction was evaluated. Our results suggest that not all plasticity indices are amenable to identifying genomic regions associated with phenotypic plasticity. We observed that plasticity indices based on calculation of a ratio between environments or the slope of the Finlay–Wilkinson model were particularly useful in uncovering the genetic architecture underlying phenotypic plasticity when studying responses to treatments within and across trials. Ultimately, a deeper understanding of phenotypic plasticity should provide opportunities for breeding plants better able to adapt to climate uncertainty.

Rice (Oryza sativa L.) is a staple food for half of the world’s population, and its biofortification is a key factor in fighting micronutrient malnutrition. However, harmful heavy metals tend to accumulate in rice grains due to soil and water contamination. Therefore, it is important to improve beneficial micronutrient contents and reduce the accumulation of undesirable metals in rice grain. To better characterize the genetic control of mineral accumulation in rice, we conducted association genetics on the ion contents of white and brown grains using a collection of 184 Vietnamese rice landraces. In total, 27 significant associations were identified and delimited into quantitative trait loci associated with macronutrients such as phosphorus, potassium or calcium; micronutrients such as iron or zinc; or toxic heavy metals such as arsenic and cadmium. Several genes related to ion homeostasis or ion transport were identified in the different quantitative trait loci. LOC_Os10g30610, present in qRAs10-1 associated with arsenic content in brown rice, encodes an ABC transporter (OsABCG25), which is involved in the silicon-induced formation of the Casparian strip in the rice exodermis and could act as a barrier restricting As diffusion within the root cortex. LOC_Os05g04330, present in qRP5-1 and associated with phosphorus content in brown rice, encodes a CHH methylation maintenance protein, and its expression is downregulated in roots in the presence of the phosphorus uptake 1 (Pup1), suggesting a role for epigenetics in the regulation of phosphorus uptake and accumulation in grain. These findings reveal novel quantitative trait loci associated with grain ion content and candidate genes that are potentially valuable for breeding programs aimed at rice grain biofortification and reducing toxic metal accumulation.

Summary: Pearl millet is a key cereal for food security in drylands but its yield is strongly impacted by drought. We investigated how root anatomical traits contribute to mitigating the effects of vegetative drought stress in pearl millet. We examined associations between root anatomical traits and agronomical performance in a pearl millet diversity panel under irrigated and vegetative drought stress treatments in field trials. The impact of associated anatomical traits on transpiration was assessed using subpanels grown in different soil within a greenhouse. In the field, total metaxylem area was positively correlated with grain weight and its maintenance under drought. In the greenhouse, genotypes with larger metaxylem area grown in sandy soil exhibited a consumerist water use strategy under irrigation, which shifted to a conservative strategy under drought. Water savings was mediated by transpiration restriction under high evaporative demand. This mechanism was dependent on soil hydraulics as it was not observed in peat soil with higher hydraulic conductivity upon soil drying. We propose that water savings under drought, mediated by large metaxylem area and its interaction with soil hydraulics, help mitigate vegetative drought stress. Our findings highlight the role of soil hydraulic properties in shaping plant hydraulics and drought tolerance.

Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet’s early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Sahelian climate. Using crop modeling, we demonstrate that early drought stress is an important constraint in agrosystems in the Sahel where pearl millet was domesticated. Furthermore, we show that increased pearl millet primary root growth is correlated with increased early water stress tolerance in field conditions. Genetics including genome-wide association study and quantitative trait loci (QTL) approaches identify genomic regions controlling this key root trait. Combining gene expression data, re-sequencing and re-annotation of one of these genomic regions identified a glutaredoxin-encoding gene PgGRXC9 as the candidate stress resilience root growth regulator. Functional characterization of its closest Arabidopsis homolog AtROXY19 revealed a novel role for this glutaredoxin (GRX) gene clade in regulating cell elongation. In summary, our study suggests a conserved function for GRX genes in conferring root cell elongation and enhancing resilience of pearl millet to its Sahelian environment.

Drought is a major threat to food security worldwide. Recently, the root–soil interface has emerged as a major site of hydraulic resistance during water stress. Here, we review the impact of soil drying on whole-plant hydraulics and discuss mechanisms by which plants can adapt by modifying the properties of the rhizosphere either directly or through interactions with the soil microbiome.

Water scarcity is already set to be one of the main issues of the 21st century, because of competing needs between civil, industrial, and agricultural use. Agriculture is currently the largest user of water, but its share is bound to decrease as societies develop and clearly it needs to become more water efficient. Improving water use efficiency (WUE) at the plant level is important, but translating this at the farm/landscape level presents considerable challenges. As we move up from the scale of cells, organs, and plants to more integrated scales such as plots, fields, farm systems, and landscapes, other factors such as trade-offs need to be considered to try to improve WUE. These include choices of crop variety/species, farm management practices, landscape design, infrastructure development, and ecosystem functions, where human decisions matter. This review is a cross-disciplinary attempt to analyse approaches to addressing WUE at these different scales, including definitions of the metrics of analysis and consideration of trade-offs. The equations we present in this perspectives paper use similar metrics across scales to make them easier to connect and are developed to highlight which levers, at different scales, can improve WUE. We also refer to models operating at these different scales to assess WUE. While our entry point is plants and crops, we scale up the analysis of WUE to farm systems and landscapes.