Biology subjects

Sparks, E. E.

Publications and source records attributed to Sparks, E. E..

13 recordsLinked to original sources

bioRxiv2026

An open field phenomics resource for multimodal maize yield prediction across divergent environments

Temporal drone phenotyping captures crop development, but irregular flight schedules complicate comparisons across environments. We release curated imagery from 356 flights across 19 Genomes to Fields environments containing 1,180 maize (Zea mays L.) hybrids. To evaluate its utility, we integrated functional principal components of vegetation index and weather trajectories with genomic information. Combinined genomic and phenomic kernels improved yield prediction, reaching correlations up to r = 0.501 for held-out hybrids in environments represented in training and 0.408 when environments were also withheld. Accumulated growing degree days offered no consistent predictive advantage over days after planting, and weather contributed modest, task-dependent gains. A transformer neural process learned directly from irregular observations, serving as a novel application of neural process models in agriculture. Mapping vegetation index functional principal components identified recurrent quantitative trait loci on chromosomes 3 and 7. This resource and its reproducible analyses guide the use of temporal spectral data for crop prediction and genetic discovery.

plant biology↗

bioRxiv2026

Maize root system stiffness is determined by the size and distribution of the below-ground root system

Root system stiffness is a measurement associated with root lodging resistance in maize. This measurement combines contributions of root architecture, individual root-level mechanics, and root-soil interactions. In this study, we deconvolve the contribution of each of these factors to root system stiffness. Collectively, larger above- and below-ground root systems and stiffer individual brace roots contribute to a higher root system stiffness. When considering all traits in predictive models, the below-ground root architecture drives the prediction of root system stiffness categories. These below-ground traits describe the size and distribution of the root system. Analysis of a roothairless3 mutant revealed a reduction in root system stiffness primarily driven by a reduction in root size, with limited evidence for a contribution from root hairs. Together these results link root system stiffness to the size and distribution of the below-ground root system and highlight the importance of this measurement for both root lodging resistance and root phenotyping.

plant biology↗

bioRxiv2025

Vascular anatomy changes in tomato stems grown under simulated microgravity

Plants grown in spaceflight exhibit differences in physiology and morphology compared to those grown on Earth. While changes in gravity are a major environmental change, other space-related stressors make it difficult to identify the microgravity-specific responses. These knowledge gaps can be filled by ground-based microgravity simulators that randomize the perceived gravity vector, but these approaches have primarily been limited to smaller plants and seedlings. This study reports a set of meter-scale 2D clinostats that support the growth of plants beyond the seedling stage. Tomato plants were grown in five sequential trials under upright rotating control and clinorotated "simulated microgravity" conditions. We found that simulated microgravity impacted plant growth in each trial, but the response varied by trial. Analysis of environmental co-variates across trials revealed that temperature significantly contributed to variation in plant growth. Further, our results show that moderate heat stress can promote plant growth under simulated microgravity. Thus, this work demonstrates the potential of meter-scale clinostats to uncover interactions between the environmental and simulated microgravity, which alter plant growth.

plant biology↗

bioRxiv2025

Lead, a toxic metal, alters auxin-mediated root growth and gravitropic responses in maize and Arabidopsis

Toxic metal contamination in the environment is pervasive and of significant concern due to its high abundance in agricultural lands across the globe. Future engineering of plants tolerant to toxic metals requires a detailed understanding of plant responses to these toxins, which are currently poorly understood. We discovered that, among four toxic metals, lead (Pb) targets conserved cellular and developmental processes in evolutionary diverse plant systems - the model plant Arabidopsis thaliana and crop plant Zea mays. This study shows that Pb increases the phytohormone auxin, which in turn inhibits cell cycle progression to inhibit root growth and alters root gravitropic responses. Both root growth and gravitropic responses are critical for soil exploration, which is required for plants to live and thrive in harsh environments.

plant biology↗

bioRxiv2025

A biphasic trajectory for maize stalk mechanics shaped by internal and external factors

Stalk mechanical properties impact plant stability and interactions with pathogenic microorganisms. The evaluation of stalk mechanics has focused primarily on the end-of-season outcomes and defined differences among inbred and hybrid maize genotypes. However, there is a gap in understanding how these different end-of-season outcomes are achieved. This study measured stalk flexural stiffness in maize inbred genotypes across multiple environments and in maize commercial hybrid genotypes under different disease states. Under all conditions, stalk flexural stiffness followed a biphasic trajectory, characterized by a linear increase phase and a sustained phase. Within a genotype, the environment or disease state altered the rate of increase in the linear phase but did not impact the timing of transition to the sustained phase. Whereas between genotypes, the timing of transition between phases varied. Destructive 3-point bend tests of inbred stalks showed that the trajectory of stalk mechanics is defined by the bending modulus, not the geometry. Together, these results define a biphasic trajectory of maize stalk mechanics that can be modulated by internal and external factors. This work provides a foundation for breeding programs to make informed decisions when selecting for optimized stalk mechanical trajectories, which is necessary for enhancing resilience to environmental stresses. HIGHLIGHTSO_LIA common trajectory of stalk mechanics was found across genotypes and conditions. C_LIO_LITransition between phases of stalk mechanics is inherent to genotype. C_LIO_LIThe rate of linear increase phase is modulated within a genotype by environmental or biotic factors. C_LIO_LIMaterial properties determine the trajectory of stalk mechanics. C_LI

plant biology↗

bioRxiv2024

AraRoot - A Comprehensive Genome-Scale Metabolic Model for the Arabidopsis Root System.

Being the first plant to have its genome sequenced, Arabidopsis thaliana (Arabidopsis) is a well-established genetic model plant system. Studies on Arabidopsis have provided major insights into plants physiological and biochemical nature. Methods that allow us to computationally study the metabolism of organisms include the use of genome-scale metabolic models (GEMs). Despite its popularity, currently no GEM maps the metabolic activity in the roots of Arabidopsis, which is the organ that faces and responds to stress conditions in the soil. Weve developed a comprehensive GEM of the Arabidopsis root system - AraRoot. The final model includes 2,682 reactions, 2,748 metabolites, and 1,310 genes. Analyzing the metabolic pathways in the model identified 158 possible bottleneck genes that impact biomass production, most of which were found to be related to phosphorous-containing- and energy-related pathways. Further insights into tissue-specific metabolic reprogramming conclude that the cortex layer in the roots is likely responsible for root growth under prolonged exposure to high salt conditions, while the endodermis and epidermis are responsible for producing metabolites responsible for increased cell wall biosynthesis. The epidermis was found to have a very poor ability to regulate its metabolism during exposure to high salt concentrations. Overall, AraRoot is the first GEM that accurately captures the comprehensive biomass formation and stress responses of the tissues in the Arabidopsis root system.

systems biology↗

bioRxiv2024

Graft incompatibility between pepper and tomato can be attributed to genetic incompatibility between diverged immune systems

O_LIGraft compatibility is the capacity of two plants to form cohesive vascular connections. Tomato and pepper are incompatible graft partners; however, the underlying cause of graft rejection between these two species remains unknown. C_LIO_LIWe diagnosed graft incompatibility between tomato and diverse pepper varieties based on weakened biophysical stability, decreased growth, and persistent cell death using trypan blue and TUNEL assays. Transcriptomic analysis of cell death in the junction was performed using RNA-sequencing, and molecular signatures for incompatible graft response were characterized based on meta-transcriptomic comparisons with other biotic processes. C_LIO_LIWe show that tomato is broadly incompatible with diverse pepper cultivars. These incompatible graft partners activate prolonged transcriptional changes that are highly enriched for defense processes. Amongst these processes was broad NLR upregulation and hypersensitive response. Using transcriptomic datasets for a variety of biotic stress treatments, we identified a significant overlap in the genetic profile of incompatible grafting and plant parasitism. In addition, we found over 1000 genes that are uniquely upregulated in incompatible grafts. C_LIO_LIBased on NLR overactivity, DNA damage, and prolonged cell death we have determined that tomato and pepper graft incompatibility is likely caused by a form of genetic incompatibility, which triggers a hyperimmune-response. C_LI

plant biology↗

bioRxiv2022

Bigger is better: Thicker maize brace roots are advantageous for both strength and nitrogen uptake.

Plant root systems provide critical functions to enable plant survival. From anchoring the plant in the soil to finding and acquiring water and nutrients, these organs are essential for plant productivity. Despite a variety of root functions, research typically focuses on defining only one function. In this study, we explore a trade-off hypothesis, that the optimization of one root function (i.e. anchorage) may negatively impact another root function (i.e. nitrogen uptake). Previous work has demonstrated that larger roots are stronger, but may also have a diminished capacity for nutrient acquisition due to a reduced surface area to volume ratio. Using maize brace roots that had entered the soil, we show here that larger roots are both stronger and take up more nitrogen. Despite this general relationship, there are subtle trade-offs between mechanics and uptake that occur when assessing individual genotypes. These trade-offs represent an opportunity to optimize one root function without compromising other root functions. Together these data demonstrate that our original trade-off hypothesis was incorrect for maize brace roots, and that larger roots are both stronger and take up more nitrogen.

plant biology↗

bioRxiv2021

Image-based assessment of plant disease progression identifies new genetic loci for resistance

A major challenge in global crop production is mitigating yield loss due to plant diseases. One of the best means of disease control is plant resistance, but the identification of genes that promote resistance has been limited by the subjective quantification of disease, which is typically scored by the human eye. We hypothesized that image-based, non-destructive quantification of disease phenotypes would enable the rapid identification of new disease resistance loci. We tested this using the interaction between tomato and Ralstonia solanacearum, a soilborne pathogen that causes bacterial wilt disease. We acquired over 40,000 time-series images of disease progression in a tomato recombinant inbred line population, and developed an image analysis pipeline providing a suite of ten traits to quantify wilt disease based on plant shape and size. Quantitative trait loci (QTL) analyses using image-based phenotyping identified QTL that were both unique and shared compared with those identified by human assessment of wilting. When shared loci were identified, image-based phenotyping could detect some QTL several days earlier than human assessment. Thus, expanding the phenotypic space of disease with image-based, non- destructive phenotyping allowed both earlier detection and identified new genetic components of resistance.

plant biology↗

bioRxiv2021

Brace root phenotypes predict root lodging susceptibility and the contribution to anchorage in maize

Plant mechanical failure (lodging) causes global yield losses of 7-66% in cereal crops. We have previously shown that the above-ground nodal roots (brace roots) in maize are critical for anchorage. However, it is unknown how brace root phenotypes vary across genotypes and the functional consequence of this variation. This study quantifies the contribution of brace roots to anchorage, brace root traits, plant height, and root lodging susceptibility in 52 maize inbred lines. We show that the contribution of brace roots to anchorage and root lodging susceptibility varies among genotypes and this contribution can be explained by plant architectural variation. Additionally, supervised machine learning models were developed and show that multiple plant architectural phenotypes can predict the contribution of brace roots to anchorage and root lodging susceptibility. Together these data define the plant architectures that are important in lodging resistance and show that the contribution of brace roots to anchorage is a good proxy for root lodging susceptibility.

plant biology↗

bioRxiv2020

Maize brace roots provide stalk anchorage

Mechanical failure, known as lodging, negatively impacts yield and grain quality in crops. Limiting crop loss from lodging requires an understanding of the plant traits that contribute to lodging-resistance. In maize, specialized aerial brace roots are reported to reduce root lodging. However, their direct contribution to plant biomechanics has not been measured. In this manuscript, we find that brace roots establish a rigid base (i.e. stalk anchorage) to limit plant deflection in maize. The more brace root whorls that contact the soil, the greater the contribution of brace roots to anchorage. Previous studies have linked the number of brace root whorls to flowering time in maize. To determine if flowering time selection alters the brace root contribution to anchorage, a subset of the Hallauers Tuson tropical population was analyzed. Despite a significant change in flowering time, selection neither altered the number of brace root whorls in the soil nor the overall contribution of brace roots to anchorage. These results demonstrate that brace roots provide a rigid base in maize, but the contribution to anchorage is not linearly related to flowering time.

plant biology↗

bioRxiv2019

Comparative biomechanical characterization of maize brace roots within andbetween plants

Root lodging is responsible for significant crop losses world-wide. During root lodging, roots fail by breaking, buckling, or pulling out of the ground. In maize, above-ground roots, called brace roots, have been shown to reduce root lodging susceptibility. However, the underlying structural-functional properties of brace roots that prevent root lodging are poorly defined. In this study, we quantified structural mechanical properties, geometry, and bending moduli for brace roots from different whorls, genotypes, and reproductive stages. Using 3-point bend tests, we show that brace root mechanics are variable by whorl, genotype, and reproductive stage. Generally, we find that within each genotype and reproductive stage, the brace roots from the whorl closest to the ground had higher structural mechanical properties and a lower bending modulus than brace roots from the second whorl. There was additional variation between genotypes and reproductive stages. Specifically, genotypes with higher structural mechanical properties also had a higher bending modulus, and senesced brace roots had lower structural mechanical properties than hydrated brace roots. Collectively these results highlight the importance of considering whorl-of-origin, genotype, and reproductive stage for quantification of brace root mechanics, which is important for mitigating crop loss due to root mechanical failure.

plant biology↗

bioRxiv2017

Minimum requirements for reprogramming and maintaining cell fate in the Arabidopsis root

Changes in gene regulation during differentiation are governed by networks of transcription factors. To identify the minimal network for endodermal differentiation in the Arabidopsis root, we asked what transcription factors are sufficient to program a non-native cell-type into endodermis. Our results show the transcription factors SHORTROOT and MYB36 have limited ability to reprogram a non-native cell-type (the epidermis) and that this reprogramming is reversible in the absence of additional cues. The stele-derived signaling peptide CIF2 stabilizes SHORTROOT-induced reprogramming. The outcome is a partially impermeable barrier deposited in the sub-epidermal cell layer that has a transcriptional signature similar to endodermis. The trans-differentiation mechanism depends on the expression of genes downstream in the gene regulatory network but is independent of SHORTROOT movement. These results highlight a non cell-autonomous induction mechanism for endodermis that resembles differentiation in many animal systems.\n\nOne Sentence SummarySHORTROOT and CIF2 combined can induce and stabilize an endodermis in sub-epidermal cells and do so in a non cell-autonomous manner.

developmental biology↗