Scholarly Works, School of Plant and Environmental Sciences

Permanent URI for this collection

https://hdl.handle.net/10919/97229

Browse

Now showing 1 - 20 of 1225

A Comparative Analysis of Transfected and Integrated Auxin Reporter Systems Reveals Sensitivity Advantages in Protoplast Transient Expression Assays
Taylor, Joseph S.; Villaseñor, Eric A.; Rashkovsky, James; Simson, Jaime; Wright, R. Clay; Bargmann, Bastiaan O. R. (2025-02-28)
Reporter-gene activation studies using transient transformation of protoplasts are a powerful tool for the investigation of transcriptional regulation in plants. Here, we perform a comparative analysis of reporter-gene activation sensitivity using an integrated versus a co-transfected reporter-gene construct in Arabidopsis seedling mesophyll protoplasts. The DR5 synthetic auxin-responsive promoter was used to assay the response to auxin treatment and over-expression of activator Auxin Response Factors. We show that sensitivity, as measured by the fold-change in fluorescent-protein reporter-gene expression, is significantly increased by using a co-transfected reporter-gene construct.
Automated Flow-Cytometric Readout of Reporter-Gene Activation in Transiently Transformed Protoplasts
Chisholm, Samuel; Taylor, Joseph S.; Wright, R. Clay; Bargmann, Bastiaan O. R. (Springer Nature, 2026-04-01)
Reporter-gene activation studies are essential for dissecting gene regulatory mechanisms, yet traditional whole-plant assays are often low-throughput and difficult to quantify. This chapter presents a streamlined method for analyzing reporter-gene activity using transiently transformed Arabidopsis thaliana mesophyll protoplasts. We describe the use of the pBeaconRFP vector for positive-fluorescent selection, enabling the isolation of successfully transformed cells via flow cytometry and fluorescence-activated cell sorting. Additionally, we introduce the pEvTV Gateway-compatible vector for flexible reporter-gene construct delivery and an automated pipeline for reproducible flow-cytometric data analysis. These methods facilitate rapid, robust, and scalable quantification of transcriptional responses, exemplified by the activation of the DR5 auxin-responsive reporter by gain-of-function Auxin Response Factor expression. The protocols are adaptable to other tissues and species, offering a versatile platform for high-throughput functional genomics.
Evaluating Environmental and Crop Factors Affecting Drone-Mounted GPR Performance in Agricultural Fields
Vahidi, Milad; Shafian, Sanaz (MDPI, 2026-03-16)
Drone-mounted ground-penetrating radar (GPR) systems offer new opportunities for integrating subsurface characterization into remote sensing workflows. However, the interaction between flight parameters, surface conditions, and vegetation characteristics remains poorly understood. This study investigates the impact of flight altitude, surface topography, crop presence, and canopy water content on the stability and interpretability of GPR signals collected using a drone. Field experiments were conducted under controlled conditions using agricultural plots with variable canopy cover and soil moisture regimes. Radargrams were processed to evaluate signal amplitude, reflection continuity, and attenuation patterns in relation to terrain slope and vegetation structure derived from co-registered RGB drone imagery. The results reveal that lower flight altitudes and smoother surfaces yield higher signal coherence and greater subsurface penetration, while increased canopy water content and biomass reduce signal strength and clarity. Integrating drone-based GPR observations with surface spectral and thermal data improved discrimination between soil and vegetation-induced signal distortions. The findings highlight the potential of drone–GPR systems as a complementary layer in a multi-sensor remote sensing framework for precision agriculture, environmental monitoring, and 3D soil mapping.
Whole-Genome Sequencing Reveals Breed-Specific SNPs, Indels, and Signatures of Selection in Royal White and White Dorper Sheep
Liao, Mingsi; Kravitz, Amanda; Haak, David C.; Sriranganathan, Nammalwar; Cockrum, Rebecca R. (MDPI, 2026-03-05)
Whole-genome sequencing (WGS) is a powerful tool for uncovering genome-wide variation, identifying selection signatures, and guiding genetic improvement in livestock. Royal White (RW) and White Dorper (WD) sheep are economically important meat-type hair breeds in the U.S., yet their genomic architecture remains poorly characterized. In this study, WGS was performed on 20 ewes (n = 11 RW, n = 9 WD) to identify and annotate SNPs and small insertions and deletions (indels). Functional annotation, gene enrichment, population structure, and selective sweep analysis were also performed. Selective sweep analysis was conducted by integrating the fixation index (F_ST), nucleotide diversity (π), and Tajima’s D to identify candidate regions under putative recent positive selection. A total of 21,957,139 SNPs and 2,866,600 indels were identified in RW sheep, whereas 18,641,789 SNPs and 2,397,368 indels were identified in WD sheep. In RW sheep, candidate genes under selection were associated with health and parasite resistance (NRXN1, HERC6, TGFB2) and growth traits (JADE2). In WD sheep, selective sweep regions included genes linked to immune response and parasite resistance (TRIM14), body weight (PLXDC2), and reproduction (STPG3). These findings were supported by sheep-specific quantitative trait loci (QTL) annotations and previously reported SNP–trait associations. This study provides the first WGS-based genomic comparison between RW and WD sheep, establishing a foundation for future genetic improvement, including targeted selection for enhanced immune function, disease resistance, and other economically important traits in these breeds.
A previously unrecognized class of fungal ice-nucleating proteins with bacterial ancestry
Eufemio, Rosemary J.; Rojas, Mariah; Shaw, Kaden; de Almeida Ribeiro, Ingrid; Guo, Hao-Bo; Renzer, Galit; Belay, Kassaye; Liu, Haijie; Suseendran, Parkesh; Wang, Xiaofeng; Fröhlich-Nowoisky, Janine; Pöschl, Ulrich; Bonn, Mischa; Berry, Rajiv J.; Molinero, Valeria; Vinatzer, Boris A.; Meister, Konrad (American Association for the Advancement of Science, 2026-03-13)
Ice-nucleating proteins (INpros) catalyze ice formation at high subzero temperatures, with major biological and environmental implications. While bacterial INpros have been structurally characterized, their counterparts in other organisms have remained largely unknown. Here, we identify membrane-independent proteins in fungi of theMortierellaceae family that promote ice formation with high efficiency. These proteins are predicted to adopt β-solenoid folds and multimerize to form extended ice-binding surfaces, exhibiting mechanistic parallels with bacterial INpros. Structural modeling, phylogenetic analysis, and heterologous gene expression leading to ice nucleation in Escherichia coli and Saccharomyces cerevisiae show that the fungal INpros are encoded by orthologs of the bacterial InaZ gene, which was likely acquired by a fungal ancestor through horizontal gene transfer. The discovery of cell-free fungal INpros provides tools for innovative freezing applications and reveals biophysical constraints on ice nucleation across life.
Faba Bean: Unlocking nutritional potential and agricultural sustainability
Singh, Madhvi; Balota, Maria; Huang, Haibo; O'Keefe, Sean; Carneiro, Renata (Elsevier, 2025-07)
Faba bean (Vicia faba L.) has been identified as a versatile specialty crop for North America due to its rich nutritional profile, ability to thrive in diverse climates, and economic potential. Although friendly to most diets, faba bean consumption is challenged by the presence of vicine and convicine—antinutritional compounds that trigger favism in individuals with glucose-6-phosphate dehydrogenase deficiency. This review delves into the genetic, molecular, and biochemical dimensions of vicine and convicine accumulation in faba beans, pinpointing knowledge gaps and unearthing historical and lesser-known insights about these compounds. This comprehensive review synthesizes and discusses recent efforts and challenges in enhancing nutrition of faba beans to promote its production and consumption in North America. We spotlight the strides made in breeding low-vicine and low-convicine varieties and critically assess attempts aimed at mitigating these favism-inducing factors. The development of low-vicine and low-convicine faba bean lines represents a significant advancement in crop breeding, addressing safety concerns for individuals with G6PD deficiency. By utilizing marker-assisted breeding techniques, researchers are effectively reducing vicine and convicine levels, even as the complete biosynthetic pathways of these compounds remain unresolved. Current research efforts are steadily progressing toward cultivars with minimal or no vicine and convicine, enhancing the safety and nutritional profile of faba beans. These breakthroughs hold the potential to transform faba beans into a more sustainable, inclusive, and widely consumed food source, expanding their utility in both human diets and agricultural systems.
Pivotal role of municipal wastewater resource recovery facilities in urban agriculture: A review
Wang, Jiefu; Sun, Yuepeng; Xia, Kang; Deines, Allison; Cooper, Ross; Pallansch, Karen; Wang, Zhiwu (Wiley, 2022-05-18)
Urban agriculture provides a promising, comprehensive solution to water, energy, and food scarcity challenges resulting from the population growth, urbanization, and the accelerating effects of anthropogenic climate change. Their close access to consumers, profitable business models, and important roles in educational, social, and physical entertainment benefit both developing and developed nations. In this sense, Urban Water Resource Reclamation Facilities (WRRFs) can play a pivotal role in the sustainable implementation of urban agriculture. Reclaimed water as a recovered resource has less supply variability and in certain cases can be of higher quality than other water sources used in agriculture. Another recovered resource, namely, biosolids, as byproduct from wastewater treatment can be put to beneficial use as fertilizers, soil amendments, and construction material additives. The renewable electricity, heat, CO₂, and bioplastics produced from WRRFs can also serve as essential resources in support of urban agriculture operation with enhanced sustainability. In short, this review exhibits a holistic picture of the state of-the-art of urban agriculture in which WRRFs can potentially play a pivotal role.
Virginia Horticulture Production Trends: 2017-2022
Stallknecht, Eric J.; South, Kaylee (Virginia Cooperative Extension, 2025-08-15)
Effect of maturity at harvest of small grain grasses on the nutritional composition of forage and ration formulation
Ferreira, Gonzalo; Teets, C. L.; Galyon, Hailey; Cappellina, Anna; Schultz, Milton; Payne, Kathryn; Stewart, Shamar; Thomason, Wade E. (2025-02-09)
We hypothesized that, relative to harvesting small-grain grasses at the soft dough stage (SFT) of maturity, harvesting small-grain grasses at the boot stage (BT) of maturity would result in less expensive dairy rations when commodity prices are high but not when commodity prices are low. Small plots of small-grain grasses were planted during the fall of 2020 and 2021 in Blacksburg, Blackstone, and Orange, Virginia. In each year and location, 2 varieties of barley, 2 varieties of rye, and 4 varieties of triticale were planted in plots replicated 6 times, yielding 288 plots. Within each year and location, we harvested half of the plots at BT and the other half at SFT. For each of the 6 small-grain grasses, we formulated 8 rations according to 8 different scenarios using the least-cost optimizer. The scenarios included high and low commodity prices, high and low dietary forage (60% and 40% forage, respectively), and the inclusion of small-grain grasses harvested at BT or SFT. Harvesting at SFT yielded 107% to 205% more DM than harvesting at BT. Relative to BT, small-grain grasses harvested at SFT had greater concentrations of OM, NDF, ADF, ADL, and starch but lower concentrations of CP. Relative to BT, small-grain grasses harvested at SFT also had a greater concentration of undegraded NDF (NDF basis). Species had minimal influence on the nutritional quality of small-grain grasses for silage. Under a low-price scenario, the ration formulation system ignored all 6 small-grain grass silages and included corn silage as the only forage source when we did not limit its inclusion. Under a high-price scenario, the ration formulation system included all 6 small-grain grass silages when formulating low-forage diets with unlimited corn silage. However, a preference between BT and SFT stages did not exist, with the optimizer not consistently selecting a specific maturity stage. After evaluating the yields, the chemical composition, and the effects on ration formulation in this study, future studies should aim to evaluate the influence of maturity at harvest of small-grain grasses on cow performance and environmental impacts.
Comparing in-home and bottled drinking water quality: regulated and emerging contaminants in rural Central Appalachia
Albi, Kate; Krometis, Leigh-Anne H.; Ling, Erin; Cohen, Alasdair; Xia, Kang; Gray, Austin D.; Dudzinski, Emerald; Ellis, Kimberly P. (IWA Publishing, 2025-09)
An increasing number of Americans rely on bottled water for household use, citing perceptions of poor in-home water quality and/or distrust of public water utilities. We analyzed in-home (n = 23), roadside spring (n = 4), and bottled drinking water (n = 36) in Central Appalachia. All samples were analyzed for regulated (bacteria, inorganic ions) and emerging (PFAS, microplastics) contaminants. Study survey results indicated the majority (83%) of participants viewed their in-home water quality as satisfactory or poor due to negative organoleptic perceptions. Coliform bacteria and sodium levels exceeding recommended levels were detected in 52% of home water samples, though detections varied by source, i.e., high sodium was more often observed in municipal water, while bacteria were more often observed in private system water. Bottled water samples did not exceed any regulations, though median microplastic concentrations were statistically higher (p = 0.001, Wilcoxon rank-sum test) than those recovered from in-home samples. PFAS compounds were detected in some in-home and bottled water samples at very low levels. While in general bottled water appears to be a safe drinking water source in these areas, the associated costs in time and money for lower-income households are considerable, and were estimated by participants as $68–400/month.
Broadcasting cover crops at corn harvest can maximize biomass and reduce nitrogen leaching
Lipford Zahed, Mary Michael; Haymaker, Joseph; Mott, Joshua; Abaye, Azenegashe Ozzie ; Reiter, Mark S. (Elsevier, 2026-07-01)
Mitigating nitrogen (N) leaching from agricultural fields is critical for improving water quality in the Chesapeake Bay Watershed. Because N mineralization continues after corn (Zea mays L.) uptake ceases, losses may occur between harvest and cover crop (CC) establishment. The objectives of this study were to identify effective establishment methods and CC species for N uptake and biomass production; determine whether planting at harvest enhances N scavenging compared to delayed planting; and assess impacts on corn yield. Four seeding methods were evaluated: (1) broadcasting with incorporation at corn harvest, (2) broadcasting without incorporation at corn harvest, (3) broadcasting with incorporation four weeks post-harvest, and (4) drilling four weeks post-harvest, using cereal rye (Secale cereale L.), hairy vetch (Vicia villosa Roth), rapeseed (Brassica napus L.), and a three-species mix. In Year 2, fall soil nitrate concentrations at 0–15 cm depth in post-harvest treatments (11.4–11.8 mg kg−1) were more than double that of at-harvest treatments (5.2 mg kg−1), with at-harvest incorporated rye showing the lowest winter nitrate (1.7 mg kg−1). At-harvest mix and hairy vetch accumulated the most N in aboveground biomass (181–208 kg ha−1). Year 1 corn yield increased following at-harvest hairy vetch (11,022–11,384 kg ha−1) and incorporated mix (11,587 kg ha−1) compared to the control (8895 kg ha−1), though not in Year 2. Incorporation did not significantly affect outcomes compared to non-incorporated treatments. Planting CCs at corn harvest maximized N accumulation, biomass, and nitrate reduction, offering a practical strategy to mitigate N leaching.
Evaluation of selected foliar insectcides against stink bugs in edamame, 2022
Bradley, Sierra E.; Sutton, Kemper L.; Doughty, Helene; Zhang, Bo; McIntyre, Kelly; Kuhar, Thomas P. (Oxford University Press, 2023-01-01)
'Candidatus Pseudomonas auctus' sp. nov. JDE115 isolated from nodules on soybean (Glycines max)
Ali, Md Sahadat; Mony, Fatima Tuz Zohora; Evans, Michael; Rideout, Steven L.; Haak, David C.; Vieira, Paulo; Eisenback, Jonathan D. (Public Library of Science, 2025-09-11)
A Gram-negative, facultative anaerobic, rod-shaped, motile with peritrichous flagella, fluorescent bacterium, designated ‘Candidatus Pseudomonas auctus’ sp. nov. JDE115, was isolated from soybean root nodules in Virginia and characterized using a comprehensive integrative methodology. Growth of JDE115 occurred with 0–5.0% (w/v) NaCl (optimum 1%), at pH 6.0–10.0 (optimum pH 7.0), and at 10–40°C (optimum 28°C) in LB broth. Phylogenetic analyses based on the 16S rRNA gene placed the isolate as a member of a novel species within the genus Pseudomonas. Phylogenetic analyses based on whole-genome sequences, 16S rRNA, showed JDE115 having the highest similarity to Pseudomonas glycinae MS586. Average Nucleotide Identity (ANI) analysis also revealed the highest similarity of JDE115 to Pseudomonas glycinae MS586 (94.59%), which is below the 95% threshold for species delineation. Genome-to-genome distance analysis (GGDC, Formula 2) showed a maximum value of 57.10% with the same strain, far below the 70% cutoff. The primary isoprenoid quinone detected in JDE115 was ubiquinone-9 (Q-9) and the DNA G + C content was 60.68 mol%. The whole-cell fatty acid profile was dominated by C16:0, C17:0 cyclo, and the summed features 3 (C16:1ω7c and/or C16:1ω6c) and 8 (C18:1ω7c and/or C18:1ω6c). Additional fatty acids detected included 12:0, 14:0, and 18:0. Based on these phenotypic, chemotaxonomic, and phylogenetic data, strain JDE115 is proposed to represent a new species in the genus Pseudomonas, for which the name ‘Candidatus Pseudomonas auctus’ sp. nov. is proposed.
Morphological Ambiguity between Chambersiella Cobb, 1920, and Geraldius Sanwal, 1971: A Taxonomic Dilemma Solved through a Note from N. A. Cobb
Eisenback, Jonathan D.; Vieira, Paulo (Society of Nematologists, 2025-02-01)
The genera Chambersiella and Geraldius (Nematoda) are nearly morphologically identical, differing primarily in female ovary number: Chambersiella was described as monodelphic, while Geraldius was diagnosed as didelphic. This note reevaluates the validity of that distinction, incorporating original descriptions and a previously overlooked archival note from N. A. Cobb. Field observations failed to recover monodelphic specimens, even in type localities. We propose synonymizing Geraldius with Chambersiella, supported by Cobb's archived observations and consistent morphological evidence.
Production performance, nutrient digestibility, and milk fatty acid profile of lactating dairy cows fed diets containing triticale silage of different maturities and different dietary forage levels
Schultz, M. E.; Corl, Benjamin A.; Payne, Kathryn M.; Stewart, Shamar L.; Thomason, Wade E.; Ferreira, Gonzalo (Elsevier, 2025-09)
This study aimed to evaluate the production performance, the milk fatty acid profile, and the nutrient digestibility of high-producing dairy cows fed high-forage (HF) or low-forage (LF) diets containing triticale silages harvested at either the boot stage (BT) or the soft-dough stage (SFT) of maturity. A 10-ha field was seeded with 105 kg/ha of triticale. Half of the field was harvested at BT and the other half at SFT. The harvested forage was ensiled in separate concrete-walled bunker silos for at least 60 d. The BT silage had 97.0% OM, 9.6% CP, 61.0% NDF, 42.0% ADF, 8.9% ADL, and 1.6% starch, whereas the SFT silage had 97.3% OM, 8.3% CP, 63.0% NDF, 44.0% ADF, 10.2% ADL, and 3.7% starch. The similar nutritional compositions of the 2 silages might be related to splitting the field in 2 halves that reflected differences in growing conditions of the crop. The animal study involved 8 primiparous (584 ± 21 kg BW and 105 ± 11 DIM) and 16 multiparous (710 ± 57 kg BW and 105 ± 18 DIM) Holstein cows. The experiment was a replicated 4 × 4 Latin square design with 21-d periods, with a 2 × 2 factorial arrangement of treatments. The HF diets were formulated to contain 55% dietary forage, and the LF diets were formulated to contain 38% dietary forage. Cows were housed in a freestall barn and fed once daily. Cows fed BT and SFT diets had similar DMI, but cows fed LF diets had higher DMI than cows fed HF diets. Feeding BT diets resulted in more milk production (43.5 vs. 42.4 kg/d) and higher milk protein (1.30 vs. 1.23 kg/d) and lactose yields (2.13 vs. 2.04 kg/d) compared with feeding SFT diets. Energy-corrected milk yield did not differ between BT and SFT diets. Cows fed HF diets produced less milk (41.1 vs. 43.0 kg/d) but tended to increase milk fat concentration (4.56% vs. 4.37%) compared with cows fed LF diets. Milk protein concentration was similar between cows fed HF and LF diets, but cows fed HF diets increased lactose concentration (5.02% vs. 4.80%). Triticale maturity did not affect NDF digestibility, but LF diets improved NDF digestibility (45.2 vs. 41.7%). No difference existed in de novo fatty acids between cows fed the BT and SFT diets despite the higher concentrations of CLA trans-10, cis-12 fatty acid and slightly higher concentrations of C18:1 trans-10 fatty acid. Under the conditions of this study, production performance did not appear to be sensitive to diets with triticale silage harvested at different maturity stages, and this occurred with both HF and LF diets.
UAVs in Agriculture: A Review of Challenges, Limitations, Stakeholder Perspectives, and Data Privacy
Rathore, Jitender; Walsh, Olga S.; Gardezi, Maaz; Mehla, Mukesh Kumar; Vardhan, Kirti (Wiley, 2026)
The agriculture sector continuously attracts a wide range of technologies, making it one of the oldest yet most rapidly evolving Industries. While technological integration has brought significant advancements in agriculture. Among these, remote sensing has emerged as a powerful tool due to its ability to monitor and manage crops over large areas across different spatial, spectral, and temporal resolutions. However, its adoption is often hindered by issues related to cost, complexity, and contextual adaptability. Many tools still face limitations and unique challenges when applied in agricultural contexts. Unmanned Aerial Vehicles (UAVs), a prominent example of modern remote sensing technologies, have enabled the collection of very-high-resolution data at the field level, offering new insights into crop health, yield forecasting, and precision management. Despite their potential, UAVs face several operational challenges, including limited flight time, weather dependency, regulatory constraints, data storage limitations, and the need for skilled personnel for both operation and analysis. This review article critically examines the current challenges associated with UAV-based remote sensing in agriculture, drawing upon recent peer-reviewed literature. It provides a consolidated understanding of the technological, operational, and institutional barriers.
Registration of 'Avalon' winter malt barley
Brooks, Wynse; Griffey, Carl; Sabadin, Felipe; Vaughn, Mark; Liu, Limei; Seago, John; Thomason, Wade E.; Light, Jon; Rucker, Elizabeth; Browning, Phillip; McMaster, Niki; Schmale, David G. III; Saville, Brooks; Hardiman, Thomas; Custis, J. Tommy; Jones, Karl; Jones, Ned; Lillard, Gregory; Marshall, David; Fountain, Myron; Tuong, Tan; Lee, Michelle; Oakes, Joseph; Mott, Joshua; Martens, Christopher; Walling, Jason; Bettenhausen, Harmonie; Macleod, Aaron; Santantonio, Nicholas (Wiley, 2024-12-25)
‘Avalon’ (Reg. no. CV-383, PI 700308) is the first two-row, winter malt barley (Hordeum vulgare L.) cultivar developed by the Virginia Agricultural Experimental Station. Avalon was released in May 2020. Prior to being named, Avalon was tested under the experimental designation VA16M-81. Avalon was evaluated from 2018 to 2023 in the Eastern Malt Barley Trials (EMBT) at one to three locations in three states and in the Winter Malt Barley Trial (WMBT) from 2020 to 2023 in six to 15 states. In the EMBT in Virginia, mean grain yield (5604 kg ha⁻¹) of Avalon was higher to cultivar ‘Violetta’, but lower than those of ‘Flavia’, ‘Calypso’, and ‘Thoroughbred’. Average grain volume weight of Avalon (64.9 kg hL⁻¹) was significantly (P ≤ 0.05) higher than the check cultivars, except Violetta. Head emergence of Avalon was 3 days earlier than Flavia and Calypso and 1 to 2 days later than Violetta and Thoroughbred, respectively. Avalon was developed primarily as a malt barley cultivar. On the basis of malting evaluations, Avalon has acceptable quality profiles with specific quality traits including high extract, low protein content, and low beta-glucan for the years tested. Avalon provides malt barley producers and end users in the eastern United States with excellent malt quality and a unique and distinct flavor profile having good to moderate resistance to all diseases prevalent in the eastern United States. It is moderately susceptible to Fusarium head blight but has moderately low deoxynivalenol accumulation in the grain.
Wheat mineral nutrient uptake, harvest indices, and grain density from a regional perspective
Adams, Curtis B.; Rogers, Christopher W.; Marshall, Juliet M.; Walsh, Olga S.; Thurgood, Garrett; Dari, Biswanath; Loomis, Grant (Wiley, 2025-05)
Research is lacking on wheat (Triticum aestivum L.) mineral nutrient uptake at broad scales, accounting for environmental variation, which is needed to effectively manage and model nutrient dynamics of wheat cropping systems. Therefore, our primary research objectives were to (1) provide analysis and estimation tools characterizing wheat nutrient (N, P, K, Mg, Ca, S, Mn, Fe, Zn, Cu) uptake in grain and the whole crop at farm and regional scales and (2) evaluate nutrient harvest indices (NutHIs)—nutrients deposited in grain relative to total aboveground uptake—as an indicator of crop nutrient relations/economies. There were clear linear relationships between grain yield and nutrient uptakes in grain and the whole crop. Functions describing the nature and error of these relationships are presented, along with more flexible estimation approaches. Median NutHIs approximated averages synthesized from recent studies and generally exceeded those from older studies, consistent with evidence that NutHIs have increased with wheat improvement. The NutHIs, except ZnHI, were generally positively associated with grain harvest index and not related to yield. Given that grain mineral density, an indicator of nutritional value, has declined over time, making ongoing progress in simultaneously improving grain yield and mineral density may depend on selection for increased crop nutrient uptake and partitioning to grain. This study also provided corroborative evidence that the modern wheat classes do not differ in grain mineral density. In summary, this research provides valuable data and tools useful for sustainable nutrient management and provides insights into the nutrient economy and nutritional value of modern wheat.
Deep fusion approach: Combining hyperspectral imaging and ground penetrating radar for accurate cornfield soil moisture mapping
Vahidi, Milad; Shafian, Sanaz; Frame, W. Hunter (Elsevier, 2025-08-01)
Precise estimation of soil moisture is critical for refining irrigation strategies, improving crop production, and ensuring efficient management of water supplies. This study employs a time-series L-pika hyperspectral sensor, covering the spectral range of 400–1100 nm, and an air-launched Zond Aero 500 GPR sensor, capturing data across various corn growth stages. The research focuses on assessing soil moisture at different soil depths, with an emphasis on accuracy of 10 cm and 30 cm of the root zone. While GPR provides reliable measurements at near-surface depths, its effectiveness decreases at lower levels. In contrast, the canopy spectrum relates closely to root zone water content, aiding in the estimation of soil moisture through a model informed by canopy spectra. Integrating these datasets aims to address the limitations of each method and enhance the accuracy of soil moisture measurements throughout the crop's lifecycle. To analyze the spectral signals from the canopy and the amplitude signals from the GPR, two separate one-dimensional convolutional neural network (1D-CNN) networks were developed. The features extracted by these networks were then utilized in Gradient Boosting Machine (GBM) and Artificial Neural Network (ANN) models to estimate soil moisture. The 1DCNN-ANN model demonstrated superior performance, particularly at soil depths of 10 cm and 30 cm. At 10 cm, it achieved an impressively low RMSE of 1.7 % and a high R^2 of 0.82, indicating precise predictive accuracy. The model also minimized bias to nearly zero, effectively balancing overestimations and underestimations across the datasets. At the deeper layer of 30 cm, the ANN outperformed the XGBoost model, showing robust performance with an RMSE of 2.9 % and an R^2 of 0.79. Moreover, the improvement in Lin's Concordance Correlation from 0.84 to 0.90 for the integrated approach between the models suggests that the ANN more accurately reflects the variability in the true data, enhancing the reliability of the predictions. These outcomes highlight the effectiveness of the 1DCNN-ANN in handling complex datasets and its consistent success in refining model accuracy and reliability.
Multi-depth soil moisture estimation via 1D convolutional neural networks from drone-mounted ground penetrating Radar data
Vahidi, Milad; Shafian, Sanaz; Frame, W. Hunter (Elsevier, 2025-05)
Accurate soil moisture estimation is pivotal for sustainable agricultural practices, directly influencing irrigation management, crop yield optimization, and water conservation. Precise moisture assessment ensures the efficient use of water resources, which is critical in the context of climate variability and the increasing scarcity of freshwater. However, a significant challenge in soil moisture estimation has been the limited capability of conventional remote sensing techniques to penetrate biomass and provide accurate moisture data at multiple soil depths. These methods often struggle to differentiate between surface moisture and the moisture profile across the soil column, especially under dense vegetation cover. This study introduces an advanced methodology using a 1D Convolutional Neural Network Artificial Neural Network (1D-CNN-ANN) to process raw Ground Penetrating Radar (GPR) amplitude data for enhanced soil moisture estimation. The 1D-CNN-ANN model is designed to tackle the multi-depth moisture estimation challenge and penetrate through biomass to yield accurate soil moisture readings. Our approach is validated by comparing the 1D-CNN-ANN model's performance with two other established machine learning algorithms: Gradient Boosting Machine (GBM), and Support Vector Machine (SVM). The results demonstrate the 1D-CNN-ANN model's superiority, reflected in higher R2 values and lower error metrics (RMSE) across different soil depths compared to the other machine learning models. At a depth of 10 cm, the 1D-CNN-ANN model achieved an R2 value of 0.84, outperforming the GBM, and SVM models with R2 values of 0.77 and 0.79, respectively. At 20 cm and 30 cm depths, the model also showed superior accuracy with R2 values of 0.82 and 0.74, respectively. Notably, the 1D-CNN-ANN model maintained its robust performance even at the challenging depth of 40 cm, with an R2 of 0.64, where traditional sensors typically falter due to biomass interference. Conceptually, the study reveals the model's capacity to discern the complex patterns of soil moisture across a range of conditions, offering valuable insights for irrigation scheduling and water resource management in both irrigated and non-irrigated agricultural settings..

Browse

Recent Submissions