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229 records · Page 13

High precision control and deep learning-based corn stand counting algorithms for agricultural robot

This paper presents high precision control and deep learning-based corn stand counting algorithms for a low-cost, ultra-compact 3D printed and autonomous field robot for agricultural operations. Currently, plant traits, such as emergence rate, biomass, vigor, and stand counting, are measured manually. This is highly labor-intensive and prone to errors. The robot, termed TerraSentia, is designed to automate the measurement of plant traits for efficient phenotyping as an alternative to manual measurements. In this paper, we formulate a Nonlinear Moving Horizon Estimator that identifies key terrain parameters using onboard robot sensors and a learning-based Nonlinear Model Predictive Control that ensures high precision path tracking in the presence of unknown wheel-terrain interaction. Moreover, we develop a machine vision algorithm designed to enable an ultra-compact ground robot to count corn stands by driving through the fields autonomously. The algorithm leverages a deep network to detect corn plants in images, and a visual tracking model to re-identify detected objects at different time steps. We collected data from 53 corn plots in various fields for corn plants around 14 days after emergence (stage V3 - V4). The robot predictions have agreed well with the ground truth with C robot =1.02×C human -0.86 and a correlation coefficient R=0.96. The mean relative error given by the algorithm is -3.78%, and the standard deviation is 6.76%. These results indicate a first and significant step towards autonomous robot-based real-time phenotyping using low-cost, ultra-compact ground robots for corn and potentially other crops.

97 MATHEMATICS AND COMPUTING↗

Gene and genome duplications have contrasting impacts on biosynthetic and flower developmental pathways in California poppy

Benzylisoquinoline alkaloids (BIAs) represent a vast group of specialized plant metabolites with diverse pharmaceutical applications, synthesized by a variety of gene families. Among the multiple plant lineages that produce BIAs, the most notable is the poppy family (Papaveraceae), with California poppy (Eschscholzia californica) emerging as a model organism. Here, we report a haplotype-resolved genome assembly, in combination with a high-density expression atlas, for California poppy. Genome analyses reveal recent diversification of BIA biosynthesis genes in poppy through localized duplications. Furthermore, we demonstrate that the degree of phylogenetic relatedness among paralogs within BIA biosynthesis-associated gene families correlates with similarities in gene expression. In contrast, gene families involved in carotenoid biosynthesis, which contributes to the intense orange petal pigmentation, are not phylogenetically clustered, and floral developmental regulators exhibit a high degree of retention of gene duplicates associated with ancient polyploidy events. These findings illustrate alternative roles for gene and genome duplications as drivers of trait evolution. Given the position of California poppy in the angiosperm phylogeny, the high-quality genomic resources generated for this work constitute a valuable resource for comparative genomic and transcriptomic analyses for poppies and flowering plants more generally.

Rössner, Le-Han [Justus-Liebig University, Giessen↗

Shifting agricultural practices to produce sustainable, low carbon intensity feedstocks for biofuel production

The carbon intensity (CI) of biofuel's well-to-pump life cycle is calculated by life cycle analysis (LCA) to account for the energy/material inputs of the feedstock production and fuel conversion stages and the associated greenhouse gas (GHG) emissions during these stages. The LCA is used by the California Air Resources Board's Low Carbon Fuel Standard (LCFS) program to calculate CI and monetary credits are issued based on the difference between a given fuel's CI and a reference fuel's CI. Through the Tier 2 certification program under which individual fuel production facilities can submit their own CIs with their facility input data, the LCFS has driven innovative technologies to biofuel conversion facilities, resulting in substantial reductions in GHG emissions as compared to the baseline gasoline or diesel. A similar approach can be taken to allow feedstock petition in the LCFS so that lower-CI feedstock can be rewarded. Here we examined the potential for various agronomic practices to improve the GHG profiles of corn ethanol by performing feedstock-level CI analysis for the Midwestern United States. Our system boundary covers GHG emissions from the cradle-to-farm-gate activities (i.e. farm input manufacturing and feedstock production), along with the potential impacts of soil organic carbon change during feedstock production. We conducted scenario-based CI analysis of ethanol, coupled with regionalized inventory data, for various farming practices to manage corn fields, and identified key parameters affecting cradle-to-farm-gate GHG emissions. The results demonstrate large spatial variations in CI of ethanol due to farm input use and land management practices. In particular, adopting conservation tillage, reducing nitrogen fertilizer use, and implementing cover crops has the potential to reduce GHG emissions per unit corn produced when compared to a baseline scenario of corn–soybean rotation. This work shows a large potential emission offset opportunity by allowing feedstock producers a path to Tier 2 petitions that reward low-CI feedstocks and further reduce biofuels' CI. The prevalence of significant acreage that has not been optimized for CI suggests that policy changes that incentivize optimization of this parameter could provide significant additionality over current trends in farm efficiency and adoption of conservation practice.

09 BIOMASS FUELS↗

Multi-Trait Regressor Stacking Increased Genomic Prediction Accuracy of Sorghum Grain Composition

Genomic prediction has enabled plant breeders to estimate breeding values of unobserved genotypes and environments. The use of genomic prediction will be extremely valuable for compositional traits for which phenotyping is labor-intensive and destructive for most accurate results. We studied the potential of Bayesian multi-output regressor stacking (BMORS) model in improving prediction performance over single trait single environment (STSE) models using a grain sorghum diversity panel (GSDP) and a biparental recombinant inbred lines (RILs) population. A total of five highly correlated grain composition traits—amylose, fat, gross energy, protein and starch, with genomic heritability ranging from 0.24 to 0.59 in the GSDP and 0.69 to 0.83 in the RILs were studied. Average prediction accuracies from the STSE model were within a range of 0.4 to 0.6 for all traits across both populations except amylose (0.25) in the GSDP. Prediction accuracy for BMORS increased by 41% and 32% on average over STSE in the GSDP and RILs, respectively. Prediction of whole environments by training with remaining environments in BMORS resulted in moderate to high prediction accuracy. Our results show regression stacking methods such as BMORS have potential to accurately predict unobserved individuals and environments, and implementation of such models can accelerate genetic gain.

54 ENVIRONMENTAL SCIENCES↗

Assessing Nutrient and Carbon Responses to Agricultural Conservation Practices in Two Midwest Watersheds

The United States is undertaking efforts to transition to a low-carbon economy in response to the heightened impacts of climate change, which are largely attributed to decades of carbon-intensive development. A concerted effort by the energy sector to achieve net-zero carbon emissions is aimed at strategically reducing the carbon footprint of the energy supply chain, particularly in the production of feedstocks for biofuels. The production of biofuels relies heavily on land use and management practices in biomass cultivation. Among other factors, soil organic carbon (SOC) plays a crucial role in the biofuel carbon cycle, impacting land productivity, greenhouse gas emissions, and water quality. The process of carbon drawdown during plant growth and storage helps to mitigate the release of carbon dioxide (CO 2 ) into the atmosphere. Another key parameter is the release of nitrous oxide (N 2 O) — a potent greenhouse gas with a global warming potential 273 times that of CO 2 — from soil. While prioritizing low-carbon production, sustainable bioenergy also necessitates improved water quality and ecosystem services. Agricultural conservation practices can contribute to enhanced soil health and reduce nutrient and sediment loss into streams. However, studies that explore the broader impact of these practices on soil carbon storage and N 2 O emissions at a watershed scale are limited. Specifically, our understanding of how low-carbon feedstock production and management affect nutrient cycle dynamics is incomplete. This study assesses watershed responses to land management practices in two agriculturally dominant watersheds: the Raccoon River watershed and the Southfork of Iowa River watershed. The study focuses on carbon and nutrient dynamics, characterizing spatial and temporal variations in SOC, N 2 O, and nutrient loadings to examine the relationship between nutrient and carbon responses and agricultural conservation practices. The study employs the newly developed Soil Water Analysis Tool for Carbon (SWAT-C) model, calibrated using 20 years’ of climate and water monitoring data, to simulate and evaluate two agricultural conservation practices: no-till and crop residue harvest with cover crop planting. We compared the calibrated SWAT-C model with a historical baseline model, which allowed us to analyze various aspects of the watershed, including stream flow, suspended sediments, nitrogen, phosphorus, organic carbon, SOC at different depths, and N 2 O emissions from topsoil. Our SWAT-C modeling results indicate that, compared with results from the historical baseline model, no-till practices are positively correlated with SOC accumulation, reduced N 2 O emissions, and decreased soil loss. We also observed no change or slightly increased nitrogen and phosphorus loss to water bodies in the watersheds compared with the baseline. Conversely, crop residue harvest with cover crop planting improved water quality by reducing nutrient and soil losses but also increased N 2 O emissions. This SWAT-C modeling study establishes the groundwork for further smaller-scale and/or sub-basin-level assessments of nitrogen, phosphorus, and carbon cycles. It provides valuable science-based insights to inform policy decisions — particularly in the context of transitioning to biofuel feedstock production in these watersheds — by addressing concerns about nutrient exports to local water bodies and, ultimately, the Mississippi River.

54 ENVIRONMENTAL SCIENCES↗

BSMV-mediated genome editing exhibits host-specific heritability: germline transmission in barley and somatic edits in Nicotiana benthamiana

Plant RNA virus–mediated guide RNA (gRNA) delivery represents a transformative advance in genome editing technologies. Unlike conventional transformation methods that rely on labor-intensive tissue culture and regeneration for each individual gRNA delivery, viral vectors can rapidly and systemically transmit gRNAs into pre-established Cas-expressing plants, providing an accelerated route for functional genomics and trait discovery directly in planta . However, key design parameters, including subgenomic promoter choice, transcript architecture, and their effects on viral fitness and editing outcomes, remain to be elucidated for most viral platforms. We developed five Barley stripe mosaic virus (BSMV) vectors, each with distinct subgenomic promoter elements to drive single gRNA expression. These were initially evaluated in Cas9-expressing transgenic Nicotiana benthamiana plants targeting the Phytoene desaturase ( PDS ) gene to compare their editing efficiencies. Single gRNAs expressed under the duplicated γb subgenomic promoter or when fused directly to the γb genome achieved the highest mutation frequencies (up to 90% at 60 days post-inoculation), whereas β1- and β2-driven sgRNAs produced delayed and reduced editing. Thus, promoter selection critically determines gRNA accumulation and the efficacy of BSMV-mediated genome editing. The top-performing design was then applied to Cas9-expressing barley ( Hordeum vulgare ) targeting HvCMF7 (conferring green-white variegation) and HvGW2.1 (impacts grain width and weight). BSMV spread systemically throughout barley, inducing somatic and heritable mutations at frequencies up to 100%, with virus-free edited progeny. In contrast, despite robust somatic editing in N. benthamiana, no heritable mutations were detected indicating species-dependent limitations in germline transmission. Our systematic comparison of subgenomic promoter architectures establishes clear design principles for optimizing viral vector–mediated delivery. Promoter choice and transcript structure critically shape editing efficiency and viral stability. The host-specific boundary for germline editing, defined by efficient heritable editing in barley but not N. benthamiana , highlights where BSMV offers advantages and where alternative vectors or hybrid strategies are required, guiding rational platform selection for diverse crop species and applications. Collectively, these findings establish BSMV as a promising next-generation vector for rapid, tissue culture–free, and transformation-independent genome editing in cereals and other recalcitrant monocots.

barley↗

Object-oriented analysis as a foundation for building climate storylines of compounding short-term drought and crop heat stress

Introduction: Crops are vulnerable to precipitation and heat extremes during late spring through summer. Methods: We analyzed for a north-central U.S. region short-term drought and agricultural heat stress during April-May-June-July. We used the 4-km Parameter Elevation Regression on Independent Slopes Model (PRISM) for observations, aggregated to a 25-km grid, and two 25-km Regional Climate Model version 4 (RegCM4) simulns used either GFDL- or MPI-GCM boundary conditions. We chose 1981-2000 as our contemporary time period, and 2041- 2060 as our scenario time period, which used the Representative Concentration Pathway 8.5 emissions scenario. We used object-oriented analysis to identify events of interest in observations and simulations by identifying objects in a space-time domain that meet specified criteria, such as exceeding a heat-stress temperature threshold. The event diagnosis allowed analysis of compound events, occurring when temperature and drought objects overlap. Results: Identified objects yielded events that can undermine agricultural productivity and which are thus relevant to decision makers, making them building blocks for possible climate storylines. The observations and simulations showed similar spatial distributions of event frequencies across the analysis region. However, the simulations attained this distribution by having fewer events that tend to cover larger areas compared to observed events, suggesting that the effective resolution of the simulations was coarser than their 25-km grids. Short-term drought frequency increased and heat-stress frequency decreased in transitioning to the scenario climate. When compounding occurred heat-stress events generally preceded the short-term drought events. The overlapping, compound events tended to be more extreme compared to non-overlapping events of either type. Discussion: The information yielded projected changes in these agriculturally motivated events. One prominent conditional behavior emerging from the work was that a heat-stress event should be a warning to watch for potential drought, as both could compound each other to more intense levels.

54 ENVIRONMENTAL SCIENCES↗

Measuring environmental and cost benefits of riparian buffers for drinking water production in a Midwest watershed

Here, this study focuses on the economic value and carbon benefits of riparian buffers in urban drinking water production. The impact of riparian buffers on the waterworks operation in the Raccoon River watershed was quantified using the following metrics: nitrate concentration, days of nitrate removal operation, material and energy cost (based on 17 years of historical records with a watershed model), regression, and cost analysis. The findings indicate that the presence of riparian buffers in agricultural land can substantially decrease nitrate concentration in the water intake of the waterworks during the crop-growing season: 19% in April, 9% in May, and 11% in June. These reductions mean less nitrate treatment of the plant intake flow: 23% in April, 12% in May, and 3% in June. These changes lead to significant resource savings: 425 metric tons of sodium chloride (NaCl), 147 810 kWh of electricity, 253 metric tons of powdered activated carbon, and 20.8 million liters of fresh water. The buffers would also reduce greenhouse gas emissions by 86.9 metric tons (CO 2 equivalent) in 17 years. The total cost saving was estimated at $\$$327 326, with the highest potential savings in May ($\$$215 100), followed by April ($\$$65 465), and June ($\$$46 761). When factoring in buffer installation, cropland loss, nitrate removal, and cost associated with buffer harvest for biofuel in an established biomass market, the benefit to the entire watershed community would be $\$$2.63 million annually. The results underscore the significant cost benefits and environmental benefits associated with cropland riparian buffers in a watershed community. The approach employed in this study holds promise for assessing riparian buffer benefits in other watersheds, contributes to an understanding of sustainable water management practices, and provides a basis for decision making in a wide range of agricultural regions.

54 ENVIRONMENTAL SCIENCES↗

Data for "Enhancing Lipid Production in Plant Cells through Automated High-Throughput Genome Engineering and Phenotyping"

Plant bioengineering is a time-consuming and labor-intensive process with no guarantee of achieving desired traits. Here, we present a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB) in maize (Zea mays) and Nicotiana benthamiana. FAST-PB enables genome editing and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single-cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrated that FAST-PB could streamline Golden Gate cloning, with the capacity to construct 96 vectors in parallel. Using FAST-PB in protoplasts, we found that PEG2050 increased transfection efficiency by over 45%. For proof-of-concept, we established a reporter-gene-free method for CRISPR editing and phenotyping via mutation of high chlorophyll fluorescence 136. We show that diverse lipids were enhanced up to 6-fold using CRISPR activation of lipid controlling genes. In callus cells, an automated transformation platform was employed to regenerate plants with enhanced lipid traits through introducing multigene cassettes. Lastly, FAST-PB enabled high-throughput single-cell lipid profiling by integrating MALDI-MS with the biofoundry, protoplast, and callus cells, differentiating engineered and unengineered cells using single-cell lipidomics. These innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering and change what is possible using single-cell metabolomics in plants.

AI/ML↗

Aboveground woody biomass estimation of young bioenergy plantations of Populus and its hybrids using mobile (backpack) LiDAR remote sensing

Woody aboveground biomass (AGB) including short-rotation Populus is used as a feedstock for renewable and carbon-neutral bioenergy. While woody AGB can be estimated with allometric equations requiring labor-intensive field data, remote sensing technologies like mobile terrestrial light detection and ranging (LiDAR) can estimate woody AGB quickly and accurately. Therefore, the goals of this study were to develop a model to predict woody AGB of 2-year-old Populus spp. from three taxa (P. deltoides, P. deltoides × P. maximowiczii and P. deltoides × P. trichocarpa) using allometric (height and diameter at breast height (DBH)) or LiDAR-derived metrics from a mobile terrestrial (backpack) system. Likewise, we sought to compare LiDAR-estimated tree height and DBH with field-measured values. We found that a taxa-specific model containing LiDAR-measured tree height, crown volume, and taxa interactions with the height of the 10 th percentile, and the density of the lowest interval (density metric 0) explained 84 % of the variation in woody AGB with a root mean square error (RMSE) of 28.7 % and performed slightly better than the allometric model. The best model excluding taxa had a slightly higher RMSE but lower bias than the allometric model. LiDAR-derived tree heights were highly correlated with field-measured heights, but DBH could not be estimated accurately. Therefore, terrestrial mobile LiDAR systems can accurately estimate woody AGB and tree height of Populus in short rotation systems to aid in the fast and efficient quantification of woody bioenergy production and renewable energy resources.

AGB↗

Data for A Role for Differential Rubisco Activase Isoform Expression in C4 Bioenergy Grasses at High Temperature

Rubisco activase (Rca) facilitates the release of sugar-phosphate inhibitors at Rubisco catalytic sites during CO2 fixation. Most plant species express two Rca isoforms, the larger Rca-α and the shorter Rca-β, either by alternative splicing from a single gene or expression from separate genes. The mechanism of Rubisco activation by Rca isoforms has been intensively studied in C3 plants. However, the functional role of Rca in C4 plants where Rubisco and Rca are located in a much higher [CO2] compartment is less clear. In this study, we selected four C4 bioenergy grasses and the model C4 grass setaria ( Setaria viridis ) to investigate the role of Rca in C4 photosynthesis. All five C4 grass species contained two Rca genes, one encoding Rca-α and the other Rca-β, which were positioned closely together in the genomes. A variety of abiotic stress-related motifs were identified in the Rca-α promoter of each grass, and while the Rca-β gene was constantly highly expressed at ambient temperature, Rca-α isoforms were expressed only at high temperature but never surpassed 30% of Rca-β content. The pattern of Rca-α induction on transition to high temperature and reduction on return to ambient temperature was the same in all five C4 grasses. In sorghum ( Sorghum bicolor ), sugarcane ( Saccharum officinarum ), and setaria, the induction rate of Rca-α was similar to the recovery rate of photosynthesis and Rubisco activation at high temperature. This association between Rca-α isoform expression and maintenance of Rubisco activation at high temperature suggests that Rca-α has a functional thermo-protective role in carbon fixation in C4 grasses by sustaining Rubisco activation at high temperature.

Genomics↗

Herbicide, fertilization, and planting density effects on intensively managed loblolly pine early stand development

Production forestry in the southeast US has been partially transitioned to intensively managed short rotations (~10 years), in which multiple silvicultural interventions are performed during forest development. Understanding the responses to silvicultural practices and continued refinement of site-specific recommendations is critical to sustainably maximize forest production. We evaluated the effects of silvicultural practices (herbicide, fertilization, and planting density) on growth, stand homogeneity, and above- and belowground biomass accumulation and partitioning of loblolly pine (Pinus taeda) throughout early stand development (age 5 years) in the southeastern US. Five treatments with eight replications each were tested: no herbicide and no fertilization (C); herbicide only (H); herbicide and half-reduced fertilization rate (R); herbicide and full fertilization (F); and increased stand density (60+ %; 1346 vs. 2152 trees per hectare) with herbicide and full fertilization rate (D). Allometric equations generated from destructive harvests were applied to annual diameter measurements to estimate plot-level biomass and allocation. Herbicide was crucial to promote stand uniformity and increase yield (~600+ % stem biomass compared with C at age 5). Aboveground biomass was similar in R and F treatments, which was ~25% higher than in H at age 5. Increasing planting density along with multiple herbicide and fertilizer applications yielded higher biomass without compromising individual tree size (diameter and height). There was little effect of silviculture practices on allocation patterns. Our results parallel what was found for fertilization with herbicide from a number of loblolly stands under similar conditions and indicate a ~28% volume gain with fertilization during early stand development. Similarly, our results were consistent with other studies implementing similar differences in planting density and suggest a ~26% volume gain through early stand development with an initial 60% increase in planting density. Furthermore, our study helps to understand complex relationships between production and silvicultural practices during early stand development and demonstrates that silvicultural prescriptions can be optimized to increase sustainability of production forestry

59 BASIC BIOLOGICAL SCIENCES↗

Climate adaptation and sustainability in switchgrass: exploring plant-microbe-soil interactions across continental scale environmental gradients

Less carbon-intensive energy sources are needed to reduce greenhouse gas emissions and their predicted role in climate change. There is growing interest in the potential of biofuels for meeting this need. A critical question is whether large-scale biofuel production can be sustainable over the time scales needed to mitigate our carbon debt from fossil fuel consumption. The carbon balance and ultimately the sustainability of biofuel feedstock production is the result of complex climate-coupled interactions between carbon fixation, sequestration, and release through combustion. Similarly, the long-term productivity of biofuels depends on the environmental factors limiting plant growth. These factors are often related to soil resources which involve complex interactions at the plant-microbe-soil interface impacting their availability and cycling. Our collaborative project addressed sustainable switchgrass (Panicum virgatum) production by exploring Plant Systems, Plant-Microbiome Interactions, and Ecosystem Processes through the integrating lens of Multi-Scale Modeling. Our research was based on detailed characterization of genetically diverse switchgrass genotypes planted in common gardens across a continental latitudinal gradient. The underlying theme of our Plant Systems research was the use of locally adapted plant material to explore plant function, to understand the mechanistic basis of environmental interactions, and to discover the plant genes important for adaptation and sustainability in the face of climate change. Our Plant-Microbiome Interaction project characterized the microbial communities associated with switchgrass using genomic tools. Our Ecosystem Processes research focused on carbon cycle responses at the ecosystem level using stand level plantings. Finally, our Multi-Scale Modeling helped to define conditions of a sustainable biofuel system and identify key tradeoffs between genetic diversity, productivity, and ecosystem services. Genome-wide association analyses were used to identify alleles that contribute to successful establishment and biomass production across North America. Together, our work provided a baseline analyses of the potential of switchgrass as a biofuel feedstock. Our project resulted in a number of successful outcomes. First, we were successful in collecting switchgrass germplasm across the species range, propagating the material, and establishing common garden experiments across the species range. In collaboration with DOE JGI, we successfully assembled the first tetraploid switchgrass genome and published this resource with an analyses of the genetic basis local adaptation from our gardens (Lowry et al. 2019, Lovell et al. 2021). The gardens were used to characterize the genetic architecture for a number of important plant phenotypes. Our project also conducted extensive sampling and sequencing to characterize the bacterial and fungal associates of switchgrass roots and leaves. We showed that host genotype, location, and harvesting practices can play a role in microbiome assembly (Singer et al. 2019 & 2022, Van Wallendael et al. 2020 & 2022, Edwards et al. 2023). Our ecosystem processes work created baseline dataset of carbon and nutrient cycling in realistic stand plantings of switchgrass. Data from this experiment provided new insight into the role of plant traits, phenology, and local environments in ecosystem processes like soil respiration, net-ecosystem exchange, and dynamics of soil and plant nutrients (Ricketts et al. 2023). Finally, our crop modelling experiments help to characterize the sensitivity of common modeling frameworks to parameters, identify key limiters of productivity across large geographic scales, and leverage patterns of local adaptation in prediction. Ultimately, these studies help to identify critical plant-microbe-soil traits that may be manipulated, through breeding or agronomic management, to improve the sustainability of biofuel feedstocks.

09 BIOMASS FUELS↗