Biology subjects

Jones, D. H.

Publications and source records attributed to Jones, D. H..

7 recordsLinked to original sources

bioRxiv2026

Root phenotypic plasticity improves yield stability when directed toward an adaptive integrated phenotype

Root phenotypic plasticity is often proposed to improve crop performance under stress, yet it remains unclear how much plasticity is beneficial and whether adaptive responses require changes across many traits or adjustments in few specific traits. Using public data of 6,500 field-grown maize and barley plants, this study examined the extent and distribution of root plasticity, and when it is associated with yield stability. We quantified root plasticity across nine anatomical and architectural traits using complementary statistical models and applied a feature-discovery framework to identify the drought-associated optimal integrated phenotypes and determine whether plasticity toward these phenotypes improved yield stability. More plasticity did not mean greater yield stability. Neither the number of plastic traits nor the magnitude of plastic responses predicted yield stability. Rather, we identified species-specific high-yielding, stable integrated phenotypes defined by distinct trait configurations. Critically, genotypes whose plastic responses moved their root phenotype toward these targets achieved greater yield stability, whereas movement away from them was associated with lower stability. Root plasticity is adaptive when it shifts root phenotypes towards an optimal integrated phenotype. These findings show that the value of plasticity depends on the trajectory of phenotypic change rather than its magnitude alone.

plant biology↗

bioRxiv2026

A thermal time framework drives coordinated below- and above-ground development in temperate cereal crops

O_LICereal architecture is underpinned by the coordinated development of modular phytomer units. While above-ground phenology is well characterized by metrics such as the phyllochron, an equivalent framework for root system development is lacking. Because each phytomer node initiates both leaves and adventitious roots, root and shoot development are inherently linked. C_LIO_LIHere, we quantified this coordination in wheat, barley, and rye across contrasting temperature regimes and validated the results under field conditions. We introduce the rhizochron, defined as the thermal time (growing degree-days, {degrees}C d) period between the emergence of nodal roots on successive stem nodes, and the root appearance interval, describing the emergence rate of individual root axes. Root development followed a highly conserved thermal sequence synchronized with shoot phenology. C_LIO_LIAcross species and environments, the rhizochron averaged 146.1{degrees}C d, closely matching the phyllochron (126.6{degrees}C d). We also identified a consistent thermal offset, with nodal roots emerging approximately 185.3{degrees}C d after the corresponding leaf on the same phytomer node. The root appearance interval averaged 45.3{degrees}C d, reflecting continuous root deployment across active nodes. C_LIO_LIBy integrating root phenology into a node-based framework, the rhizochron provides a predictive tool for crop modeling, trait-based breeding, and more target phenotyping aimed at improving resource acquisition and climate resilience. C_LI

plant biology↗

bioRxiv2025

Root anatomical gradients and cultivar differences underlie variation in root hydraulic properties in German winter wheat

Root hydraulic properties affect water uptake in wheat (Triticum aestivum L.) and are strongly influenced by root anatomy, yet how they vary along root axes and interact with cultivar differences remains underexplored. We investigated crown roots of six German winter wheat cultivars spanning one century of release, sampled from a field experiment. Roots were imaged at different positions along their axis using a high-throughput system (Rapid Anatomics Tool), and the resulting anatomical traits were coupled to GRANAR-MECHA to model radial (Kr) and axial conductance (kx). Longitudinal anatomical gradients were pronounced: tissue dimensions, metaxylem number, and apoplastic barriers decreased from the base onwards, resulting in Kr increasing and kx decreasing with distance from the base. Cultivar differences were also apparent: modern cultivars had smaller tissues and fewer metaxylem vessels, reducing both axial and radial conductance and lowering whole-root water uptake capacity ([~]20-30%). By integrating field sampling with high-throughput image analysis and mechanistic modeling, this study establishes an integrated phenotyping approach that links root anatomy to water uptake and uncovers anatomical traits relevant to hydraulic function. The results show that longitudinal gradients and cultivar-associated anatomical differences contribute to variation in hydraulic properties and persist along fully mature root segments. HighlightHigh-throughput imaging-modeling shows that longitudinal gradients and cultivar-associated anatomical differences along crown roots shape radial and axial conductance, leading to reduced whole-root water uptake capacity in modern winter wheat

plant biology↗

bioRxiv2025

The Rapid Anatomics Tool (RAT): A low-cost root anatomical phenotyping pipeline reveals changes in root anatomy along the root axis

Root anatomical phenotyping has become a demonstrably essential part of investigating root physiology and in acquiring a holistic understanding of plant development. However, accessible high throughput methods for root anatomical analysis are still lacking. Here, we present the Rapid Anatomics Tool (RAT), a novel, low-cost system for high throughput root anatomical imaging with a shallow learning curve for obtaining high quality images suitable for comparative analysis across a number of plant species. Its efficiency comes from combining blockface-like imaging and stain-free imaging using near-ultraviolet (nUV) autofluorescence utilising a combination of low-cost commercial equipment, readily available mechanical components, and custom designed and 3D printed tools. Using this system, we investigated the anatomy of mature tissue along the axis of wheat crown roots, revealing a tendency of reduction in vascular complexity (expressed through a reduction in metaxylem number, area, and mean area per metaxylem file) from the basal to the distal region of the root. This study highlights the importance of thorough sampling strategies for investigating root anatomy in relation to organ function and introduces an accessible, relatively high-throughput method to support such research.

plant biology↗

bioRxiv2024

Inhibition of acid ceramidase as a therapeutic strategy for Niemann-Pick C disease

Lysosomal storage disorders (LSDs) are a group of individually rare diseases that as a group constitute the most common forms of childhood neurodegeneration. These life limiting and life shortening diseases have the largest economic burden per patient of any rare disease with the majority being orphan diseases with no disease modifying therapy. Whilst there is significant development in the area of gene therapies for LSDs, these can only be used to treat individual diseases, are expensive, and in recent times many companies have abandoned their gene therapy pipelines. Small molecules on the other hand can be developed to target common mechanisms of pathogenesis or common central disease phenotypes providing therapies that can treat multiple diseases. In this study we report acid ceramidase as a novel therapeutic target for treating Niemann-Pick type C (NPC) disease. Using siRNA, and the literature tool compound carmofur, we observed a reduction in lysosomal area and reduced accumulation of the lipids cholesterol and LBPA in an NPC cellular model. These lipids are known to accumulate as secondary storage molecules across many lysosomal diseases, particularly primary sphingolipid storage disorders where lyso-sphingolipids are known to accumulate via the action of acid ceramidase. As acid ceramidase has also been shown to be a therapeutic target for Krabbe disease, our findings indicate that this is a novel target for the potential treatment of multiple LSDs with primary or secondary storage of sphingolipids.

cell biology↗

bioRxiv2024

Root metaxylem area influences drought tolerance and transpiration in pearl millet in a soil texture dependent manner

O_LIPearl 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. C_LIO_LIWe 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. C_LIO_LIIn 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. C_LIO_LIWe 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. C_LI

physiology↗

bioRxiv2022

Duckweed roots are dispensable and are on a trajectory toward vestigiality

Duckweeds are morphologically simplified, free floating aquatic monocots comprising both rooted and rootless genera. This has led to the idea that roots in these species may be vestigial, but empirical evidence supporting this is lacking. Here we show that duckweed roots are no longer required for their ancestral role of nutrient uptake. Comparative analyses of nearly all rooted duckweed species revealed a highly reduced anatomy, with greater simplification in the more recently diverged genus Lemna. A series of root excision experiments demonstrated that roots are dispensable for normal growth in Spirodela polyrhiza and Lemna minor. Furthermore, ionomic analyses of fronds in these two species showed little difference in the elemental composition of plants in rooted versus root-excised samples. In comparison, another free-floating member of the Araceae, Pistia stratiotes, which colonized the aquatic environment independently of duckweeds, has retained a more complex root anatomy. Whilst Pistia roots were not absolutely required for growth, their removal inhibited plant growth and resulted in a broad change in the mineral profile of aerial tissues. Collectively, these observations suggest that duckweeds and Pistia may be different stages along a trajectory towards root vestigialization Given this, along with the striking diversity of root phenotypes, culminating in total loss in the most derived species, we propose that duckweed roots are a powerful system with which to understand organ loss and vestigiality. One sentence summaryThrough their adaption to the aquatic environment, duckweed roots have progressively become structurally reduced making them an ideal plant model with which to study vestigiality.

evolutionary biology↗