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At least 109 records · Page 6

Laboratory evolution in Novosphingobium aromaticivorans enables rapid catabolism of a model lignin-derived aromatic dimer

Lignin contains a variety of interunit linkages, leading to a range of potential decomposition products that can be used as carbon and energy sources by microbes. β-O-4 linkages are the most common in native lignin, and associated catabolic pathways have been well characterized. However, the fate of the mono-aromatic intermediates that result from β-O-4 dimer cleavage has not been fully elucidated. Here, we used experimental evolution to identify mutant strains of Novosphingobium aromaticivorans with improved catabolism of a model aromatic dimer containing a β-O-4 linkage, guaiacylglycerol-β-guaiacyl ether (GGE). We identified several parallel causal mutations, including a single nucleotide polymorphism in the promoter of an uncharacterized gene that roughly doubled the growth yield with GGE. We characterized the associated enzyme and demonstrated that it oxidizes an intermediate in GGE catabolism, β-hydroxypropiovanillone, to vanilloyl acetaldehyde. Identification of this enzyme and its key role in GGE catabolism furthers our understanding of catabolic pathways for lignin-derived aromatic compounds.

59 BASIC BIOLOGICAL SCIENCES↗

Performance Validation of Endcap Timing Layer Detector Modules for CMS Phase-2 Upgrade

The High-Luminosity Large Hadron Collider (HL-LHC) will operate up to 200 simultaneous collisions per bunch crossing, which is a significant jump from the current value of about 30 collisions per bunch crossing, producing significant pileup that challenges accurate event reconstruction. To address this, the Compact Muon Solenoid (CMS) experiment is implementing the Endcap Timing Layer (ETL), a precision timing detector designed to provide timing measurements with a resolution of approximately 50 ps per hit and 35 ps per reconstructed track. This project focuses on the characterization and validation of ETL detector modules using laboratory laser test data. ETL performance is evaluated by analyzing key quantities such as Bunch Crossing Identification (BCID), Time-of-Arrival (TOA), Time-over-Threshold (TOT), Noise Stability etc. The resulting analysis provides insight into the timing performance and operational stability of ETL modules, contributing to the quality assurance process req uired before their installation in the CMS experiment and ensure that the modules can meet the long-term reliability requirements of approximately 10 years of operation without replacement.

Chipara, Munashe [Fermilab]↗

Linking Extragalactic Transients and Their Host Galaxy Properties: Transient Sample, Multiwavelength Host Identification, and Database Construction

Understanding the preferences of transient types for host galaxies with certain characteristics is key to studies of transient physics and galaxy evolution, as well as to transient identification and classification in the LSST era. Here we describe a value-added database of extragalactic transients—supernovae, tidal disruption events, gamma-ray bursts, and other rare events—and their host galaxy properties. Based on reported coordinates, redshifts, and host galaxies (if known) of events, we cross-identify their host galaxies or most likely host candidates in various value-added or survey catalogs, and compile the existing photometric, spectroscopic, and derived physical properties of the host galaxies in these catalogs. This new database covers photometric measurements from the far-ultraviolet to mid-infrared. Spectroscopic measurements and derived physical properties are also available for a smaller subset of hosts. For our 36,333 unique events, we have cross-identified 13,753 host galaxies using host names, plus 4480 using host coordinates. Besides those with known hosts, there are 18,100 transients with newly identified host candidates. This large database will allow explorations of the connections of transients to their hosts, including a path toward transient alert filtering and probabilistic classification based on host properties.

79 ASTRONOMY AND ASTROPHYSICS↗

Identification of Potent and Selective Inhibitors of Acanthamoeba : Structural Insights into Sterol 14α-Demethylase as a Key Drug Target

Acanthamoeba are free-living pathogenic protozoa that cause blinding keratitis, disseminated infection, and granulomatous amebic encephalitis, which is generally fatal. The development of efficient and safe drugs is a critical unmet need. Acanthamoeba sterol 14α-demethylase (CYP51) is an essential enzyme of the sterol biosynthetic pathway. Repurposing antifungal azoles for amoebic infections has been reported, but their inhibitory effects on Acanthamoeba CYP51 enzymatic activity have not been studied. Here, we report catalytic properties, inhibition, and structural characterization of CYP51 from Acanthamoeba castellanii. The enzyme displays a 100-fold substrate preference for obtusifoliol over lanosterol, supporting the plant-like cycloartenol-based pathway in the pathogen. The strongest inhibition was observed with voriconazole (1 h IC 50 0.45 μM), VT1598 (0.25 μM), and VT1161 (0.20 μM). The crystal structures of A. castellanii CYP51 with bound VT1161 (2.24 Å) and without an inhibitor (1.95 Å), presented here, can be used in the development of azole-based scaffolds to achieve optimal amoebicidal effectiveness.

60 APPLIED LIFE SCIENCES↗

Antifungal and Phytotoxic Activities of Isolated Compounds from Helietta parvifolia Stems

The identification of natural and environmentally friendly pesticides is a key area of interest for the agrochemical industry, with many potentially active compounds being sourced from numerous plant species. In this study, we report the bioassay-guided isolation and identification of phytotoxic and antifungal compounds from the ethyl acetate extract of Helietta parvifolia stems. We identified eight compounds, consisting of two coumarins and six alkaloids. Among these, a new alkaloid, 2-hydroxy-3,6,7-trimethoxyquinoline-4-carbaldehyde (6), was elucidated, along with seven known compounds. The phytotoxicity of purified compounds was evaluated, and chalepin (4) was active against Agrostis stolonifera at 1 mM with 50% inhibition of seed germination and it reduced Lemna pausicotata (duckweed) growth by 50% (IC50) at 168 μM. Additionally, we evaluated the antifungal activity against the fungal plant pathogen Colletotrichum fragariae using a thin-layer chromatography bioautography assay, which revealed that three isolated furoquinoline alkaloids (flindersiamine (3), kokusagenine (7), and maculine (8)) among the isolated compounds had the strongest inhibitory effects on the growth of C. fragariae at all tested concentrations. Our results indicate that these active natural compounds, i.e., (3), (4), (7), and (8), could be scaffolds for the production of more active pesticides with better physicochemical properties.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of the Entry Steps in Diterpenoid Alkaloid Biosynthesis

The diterpenoid alkaloids are a group of specialized metabolites where the terpenoid and alkaloid classes intersect, and which are found primarily within the Aconitum (Wolf’s-Bane) and Delphinium (Larkspur) genera. While there is considerable interest in these compounds for their wide range of bioactivities, their structural complexity poses a significant challenge for chemical synthesis. Biosynthesis offers an appealing alternative for production, however, little progress has been made towards elucidation of their biosynthetic pathways. Here, we employ a comparative transcriptomics approach to identify six enzymatic steps in the biosynthesis of atisinium, conserved across both Delphinium grandiflorum and Aconitum plicatum . Key to this pathway is a reductase which selectively incorporates ethanolamine over ethylamine into the diterpenoid scaffold. While the majority of diterpenoid alkaloids contain an ethylamine moiety, we demonstrate through isotope labeling in Aconitum callus cultures and a computational metabolomics approach that ethanolamine is, unintuitively, the preferred source of nitrogen for these metabolites. Identification of these enzymes and production of a key intermediate in a heterologous host paves the way for biosynthetic production of this group of metabolites with promise for medicinal applications.

biosynthesis↗

Advancing Protein Display on Bacterial Spores through an Extensive Survey of Coat Components

The profound stability of bacterial spores makes them a promising platform for biotechnological applications like biocatalysis, bioremediation, drug delivery, etc. However, though the Bacillus subtilis spore is composed of >40 types of proteins, only ∼12 have been explored as fusion carriers for protein display. Here, we assessed the suitability of 33 spore proteins (SPs) as enzyme display carriers by direct allele tagging at native genomic loci. Of the 33 SPs investigated, 26 formed functional fusions with β-glucuronidase (GUS)─a ∼272 kDa homotetramer. This almost triples the number of SPs assessed for enzyme display and doubles the number of functional fusions documented in the literature. We quantitatively assessed 1) SP promoter activation dynamics, 2) GUS activity on spores, 3) surface availability, and 4) protection from thermal and proteolytic degradation. Multicopy expression and pairwise coexpression of the most promising SP-GUS fusions highlighted the complexity of spore structure/assembly and the difficulty in predicting compatibility between different SP fusions. We also assessed the suitability of engineered spores to degrade PET (polyethylene terephthalate) films and found that surface-exposed SPs were most effective. Beyond the broad survey, a key outcome of our work was the identification of SscA (small spore coat assembly protein A) as an effective spore display carrier. SscA supported enzyme activity at least 4-fold higher than any other SP, including the well-established anchor, CotY. We attribute this to its promoter, which demonstrated early and sustained activation relative to other SPs and its small size (∼3 kDa), which likely minimally interferes with enzyme folding, oligomerization, and activity. Labeling and genetic studies, its hydrophobic nature, and low surface availability suggest that SscA assembles within the inner spore coat, which makes it stabilizing and suitable for many biocatalytic applications. Overall, this work serves as a knowledge base to advance the biotechnological utility of B. subtilis spores.

Bacillus subtilis↗

Historical Documentation of Buildings 0460 and 0463 at Technical Area 16 (Volume 1)

This report provides documentation as a standard mitigation measure to the adverse effects that occurred by the demolition of theses historic properties. To mitigate the adverse effects, LANL has followed Section 106 process contained in 36 CFR 800.6, resolution of adverse effects. In addition to these regulations and within this report, LANL has implemented the standards for documenting and reporting in accordance with the A Plan for the Management of the Cultural Heritage at Los Alamos National Laboratory, New Mexico (CRMP), LA-UR-19-21590, formerly LA-UR-15-27624. These standard reporting measures include archival-quality digital photographs of the building’s interior, exterior, outside landscape; updating LANL historic building survey forms including 11 in. x 17 in. copies (in a reduced scale) of key original and as-built drawings; identification and documentation of historically significant equipment and artifacts; a comprehensive list of LANL architectural drawings; construction-history maps of TA-16 including current Register Eligible and Ineligible Buildings; and a detailed use history of the building and technical division associated with its operation.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Signal Processing in SBND with Calibrated and Validated Electronics and Field Responses

SBND is a liquid argon time projection chamber in Fermilab’s Short-Baseline Neutrino Program, located 110 m from the neutrino source and operating in a high-rate environment with unprecedented statistics. Charged particles from neutrino interactions ionize the argon, and the resulting electrons drift to the anode wires, inducing current signals recorded as raw waveforms. These waveforms are a convolution of deposited charge with the electronics and TPC field responses, making accurate signal processing essential for recovering the true charge distribution. Signal processing forms the starting point for SBND reconstruction, directly impacting hit finding, charge calibration, clustering, and the reconstruction of tracks and showers, and therefore playing a key role in energy reconstruction and particle identification. In this poster, we present an overview of the SBND signal processing chain, including noise removal, channel-by-channel electronics correction, signal identification, and deconvolution using measured electronics and TPC field responses. We demonstrate that the two kernel functions—electronics and field responses—achieve high precision when compared to data, ensuring that the SBND signal processing chain provides a robust and accurate foundation for event reconstruction and precision physics measurements.

Singh, Prabhjot [Louisiana State U.] (ORCID:000000↗

Improving ProtoDUNE pion cross-section measurements with NuGraph Michel-electron tagging

Understanding hadron-argon interactions is essential for precise neutrino energy reconstruction and final-state interaction modeling in liquid-argon time projection chamber (LArTPC) experiments such as DUNE. In particular, pion absorption and charge-exchange processes constitute significant sources of systematic uncertainty in neutrino oscillation measurements. ProtoDUNE-SP, a large-scale LArTPC prototype operated at the CERN Neutrino Platform and exposed to charged-particle test beams in the few-GeV range, enables direct measurements of these processes. This work focuses on the measurement of differential cross sections for pion absorption and charge exchange using the 2 GeV/c pion beam data from the ProtoDUNE-SP run. A key component of this analysis is the identification of Michel electrons from $\pi \rightarrow \mu \rightarrow e$ decay chains, which helps separate different interaction topologies and improves background rejection. Michel electron identification will also assist in reliably calibrating the electromagnetic response in ProtoDUNE-SP data and for the future DUNE detectors. In this analysis, we apply NuGraph to identify Michel electrons. NuGraph is a graph neural network that models detector hits as nodes connected by spatial and temporal edges for particle and topology classification in LArTPC detectors. We first benchmark NuGraph’s Michel electron classification performance using ICEBERG data, a small-scale LArTPC prototype used for DUNE electronics and reconstruction development, and then transfer the approach to ProtoDUNE-SP. This poster presents the analysis strategy, NuGraph-based classification studies, and discusses how these developments are expected to improve the pion cross-section measurement.

Razafinime, Soamasina Herilala [Cincinnati U.] (OR↗

Integrated deep learning framework for unstable event identification and disruption prediction of tokamak plasmas

Abstract The ability to identify underlying disruption precursors is key to disruption avoidance. In this paper, we present an integrated deep learning (DL) based model that combines disruption prediction with the identification of several disruption precursors like rotating modes, locked modes, H-to-L back transitions and radiative collapses. The first part of our study demonstrates that the DL-based unstable event identifier trained on 160 manually labeled DIII-D shots can achieve, on average, 84% event identification rate of various frequent unstable events (like H-L back transition, locked mode, radiative collapse, rotating MHD mode, large sawtooth crash), and the trained identifier can be adapted to label unseen discharges, thus expanding the original manually labeled database. Based on these results, the integrated DL-based framework is developed using a combined database of manually labeled and automatically labeled DIII-D data, and it shows state-of-the-art (AUC = 0.940) disruption prediction and event identification abilities on DIII-D. Through cross-machine numerical disruption prediction studies using this new integrated model and leveraging the C-Mod, DIII-D, and EAST disruption warning databases, we demonstrate the improved cross-machine disruption prediction ability and extended warning time of the new model compared with a baseline predictor. In addition, the trained integrated model shows qualitatively good cross-machine event identification ability. Given a labeled dataset, the strategy presented in this paper, i.e. one that combines a disruption predictor with an event identifier module, can be applied to upgrade any neural network based disruption predictor. The results presented here inform possible development strategies of machine learning based disruption avoidance algorithms for future tokamaks and highlight the importance of building comprehensive databases with unstable event information on current machines.

plasma instabilities↗

A review of neutronics and thermal hydraulics–based screening methods applied to accelerated nuclear fuel qualification

This paper reviews the state-of-the-art engineering approach for using thermal hydraulic (TH) and neutronics modeling and simulation (M&S) tools to perform rapid screening studies of novel nuclear fuel concepts within the context of accelerated fuel qualification. Global research efforts have introduced nuclear fuel and material concepts that mark a significant departure from traditional reactor materials. The number of new technologies being considered for development for light water reactors and advanced reactor types has created the need for an accelerated fuel qualification procedure. A key component of this procedure is the rapid identification of the most promising fuel concepts using computational screening studies. Advanced TH and neutronic M&S tools should be leveraged to efficiently determine whether the reactor performance and safety characteristics of a given concept warrant additional studies or whether the concept requires modification or elimination. This paper reviews best practices for performing these TH and neutronics screening studies at various stages during a fuel concept's progression through the qualification procedure. The motivation behind standardizing this approach is to minimize time and resources spent on qualification activities for fuel concepts that could be quickly refined or eliminated from consideration based on their reactor physics and TH characteristics. Adoption of this screening procedure—which focuses primarily on nuclear fuels but may be applicable to other reactor materials—will also help accelerate new material qualification by generating boundary conditions crucial to fuel performance evaluations and highlighting needed areas of separate effects experimentation. This article reviews the motivation behind the introduction of novel nuclear fuel concepts, provides incentive for utilizing TH- and neutronics-based screening studies, describes the screening approach and methodology, and includes discussion on how to interpret screening results to provide recommendations for the continued development of a given concept.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis

Lignocellulosic biomass is an abundant and renewable source of carbon for chemical manufacturing, yet it is cumbersome in conventional processes. A promising, and increasingly studied, candidate for lignocellulose bioprocessing is the thermophilic anaerobe Clostridium thermocellum given its potential to produce ethanol, organic acids, and hydrogen gas from lignocellulosic biomass under high substrate loading. Possessing an atypical glycolytic pathway which substitutes GTP or pyrophosphate (PP i ) for ATP in some steps, including in the energy-investment phase, identification, and manipulation of PP i sources are key to engineering its metabolism. Previous efforts to identify the primary pyrophosphate have been unsuccessful. Here, we explore pyrophosphate metabolism through reconstructing, updating, and analyzing a new genome-scale stoichiometric model for C. thermocellum, iCTH669. Hundreds of changes to the former GEM, iCBI655, including correcting cofactor usages, addressing charge and elemental balance, standardizing biomass composition, and incorporating the latest experimental evidence led to a MEMOTE score improvement to 94%. We found agreement of iCTH669 model predictions across all available fermentation and biomass yield datasets. The feasibility of hundreds of PP i synthesis routes, newly identified and previously proposed, were assessed through the lens of the iCTH669 model including biomass synthesis, tRNA synthesis, newly identified sources, and previously proposed PP i -generating cycles. In all cases, the metabolic cost of PP i synthesis is at best equivalent to investment of one ATP suggesting no direct energetic advantage for the cofactor substitution in C. thermocellum. Even though no unique source of PP i could be gleaned by the model, by combining with gene expression data two most likely scenarios emerge. First, previously investigated PP i sources likely account for most PP i production in wild-type strains. Second, alternate metabolic routes as encoded by iCTH669 can collectively maintain PP i levels even when previously investigated synthesis cycles are disrupted. Model iCTH669 is available at github.com/maranasgroup/iCTH669.

59 BASIC BIOLOGICAL SCIENCES↗

Computational fluid dynamics analysis of char conversion in Sandia’s pressurized entrained flow reactor

Design and analysis of practical reactors utilizing solid feedstocks rely on reaction rate parameters that are typically generated in lab-scale reactors. Evaluation of the reaction rate information often relies on assumptions of uniform temperature, velocity, and species distributions in the reactor, in lieu of detailed measurements that provide local information. This assumption might be a source of substantial error, since reactor designs can impose significant inhomogeneities, leading to data misinterpretation. Spatially resolved reactor simulations help understand the key processes within the reactor and support the identification of severe variations of temperature, velocity, and species distributions. In this work, Sandia’s pressurized entrained flow reactor is modeled to identify inhomogeneities in the reaction zone. Tracer particles are tracked through the reactor to estimate the residence times and burnout ratio of introduced coal char particles in gasifying environments. The results reveal a complex mixing environment for the cool gas and particles entering the reactor along the centerline and the main high-speed hot gas reactor flow. Furthermore, the computational fluid dynamics (CFD) results show that flow asymmetries are introduced through the use of a horizontal gas pre-heating section that connects to the vertical reactor tube. Computed particle temperatures and residence times in the reactor differ substantially from the idealized plug flow conditions typically evoked in interpreting experimental measurements. Furthermore, experimental measurements and CFD analysis of heat flow through porous refractory insulation suggest that for the investigated conditions (1350 °C, <20 atm), the thermal conductivity of the insulation does not increase substantially with increasing pressure.

47 OTHER INSTRUMENTATION↗

Fire-Induced Pressure Response and Failure Characterization of PCV/SCV/3013 Containers - Phase 3

Several Department of Energy (DOE) facilities have materials stored in robust, welded, stainless - steel containers with presumed fire - induced pressure response behaviors. Lack of test data related to fire exposure requires conservative safety analysis assumptions for container response at these facilities. This conservatism can in turn result in the implementation of challenging operational restrictions with costly nuclear safety controls. To help address this issue for sites that store DOE 3013 stainless - steel containers, a series of ten tests were undertaken at Sandia National Laboratories. The goal of this test series was to obtain the response behavior for various configurations of DOE 3013 containers with various payload compositions when exposed to one of two ASTM fire conditions. Key parameters measured in the test series included identification of failure - specific characteristics such as pressure, temperature, and whether or not a vessel was breached during a test . Numerous failure - specific characteristics were identified from the ten tests. This report describes the implementation and execution of the test series performed to identify these failure - specific characteristics. Discussions on the test configurations, payload compositions, thermal insults, and experimental setups are presented. Test results in terms of pressurization and vessel breach (or no - breach) are presented along with corresponding discussions for each test.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Requirements and Recommendations for a Physical Attack Characterization Framework

This study seeks to identify existing frameworks or develop requirements and recommendations for a new framework that can consistently characterize physical attacks, analogous to MITRE ATT&CK®. MITRE ATT&CK is widely used across government, research organizations, and the cyber security community to characterize cyber attack tactics, techniques, and procedures (TTPs) in a consistent and commonly understood manner. While physical attack taxonomies, methodologies, and other tools for evaluating physical security do exist, many are sector and/or facility-type specific—and therefore not able to provide comparable scenarios across sectors—or are more focused on security assessment instead of the characterization of attacks themselves. A MITRE ATT&CK analog for physical attacks on critical infrastructure would provide a common language and structure for analysis of physical attacks. Existing attack characterization methodologies do not robustly address cyber-physical security risks. To fully understand a facility’s security needs, it is important to understand the entire vulnerability landscape from both a physical and a cyber perspective. To underscore this need, organizations such as the Cybersecurity and Infrastructure Security Agency (CISA) are calling for a coordinated approach to cyber and physical security, which they refer to as cyber and physical security convergence. A physical attack characterization framework that could be used jointly with MITRE ATT&CK would help support a more robust analysis in support of convergence, enabling the consistent characterization of attacks that utilize both cyber and physical tactics and techniques. This could provide analysts and stakeholders with a clearer understanding of how security mitigations deployed in the physical realm impact security risks in the cyber realm, and vice versa. In this study, the project team evaluates existing physical security taxonomies and methodologies to assess whether an existing method can be used to create a “physical half” of MITRE ATT&CK. This study then provides requirements and recommendations for a framework that can leverage aspects of existing methodologies. The goal of the final framework is for it to be widely adopted and referenced, regardless of critical infrastructure sector, facility type, or facility components. This study also identifies applicable use cases for when and how a framework could be applied across the various critical infrastructure sectors for a variety of attack types or motivations. Through a literature review of existing security-focused methodologies and taxonomies, engagement with relative stakeholders, evaluation of potential physical attack framework use cases, and subsequent identification of requirements, this study identified the following key findings and recommendations: There is a need for a new physical attack characterization framework; A physical attack framework should be interoperable with the MITRE ATT&CK framework; A physical attack framework should be broadly applicable, but with detailed tactics, techniques, and procedures that encompass the entire attack path; A physical attack framework should be based on observed or feasible events; A physical attack framework should adapt features from existing methodologies, frameworks, and taxonomies; A physical attack framework should be owned, overseen, and maintained by one organization.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Deer Isle and Stonington Energy Reliability Opportunities

The towns of Deer Isle and Stonington, located on the island of Deer Isle in Maine, partnered with the U.S. Department of Energy's Energy Technology Innovation Partnership Project (ETIPP) to examine options to enhance energy resilience, reduce dependence on imported fuels, and mitigate high energy costs. With technical support from the National Laboratory of the Rockies (NLR), Lawrence Berkeley National Laboratory (LBNL), and regional partner the Island Institute, the project focused on evaluation of the local electricity distribution infrastructure, examination of ongoing activities to reduce the frequency of outages, review of the applicable policy and regulatory environment, and identification of potential on-site energy solutions. Key findings revealed the island's reliance on a single distribution line, and limited hosting capacity for additional distributed energy resources. Solar photovoltaics (PV) technology, with and without battery storage, was found to be the most viable technology given economic, technical, and social considerations. While also technically feasible, wind energy faces more difficult siting and less public acceptance compared to PV. Marine energy technologies were determined to be infeasible due to technology immaturity and lengthy permitting timelines. Modeling of potential building-scale PV plus storage systems resulted in successful grant applications for installations at two local facilities. Analysis of community scale energy generation and storage options resulted the local utility, Versant, submitting a grant application for a proposed community-scale battery storage system to increase grid resilience and hosting capacity. This initiative has strengthened the communities' energy planning capabilities and laid the groundwork for future clean energy development.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Optimizing resource allocation in Miscanthus breeding via sparse testing designs for genomic prediction

Phenotyping high-biomass perennial crops is laborious and the rate of genetic gain in conventional perennial crop breeding programs is typically low. So, it is especially important to identify methods that produce efficiency gains in the breeding process. Miscanthus is a C4 perennial grass with favorable characteristics for producing biomass as a feedstock for biofuels and diverse bio-based products. Increasing biomass yield will increase profitability and environmental benefits, so it is a key target for Miscanthus breeding. In addition, the identification of well-adapted genotypes across a wide range of environmental conditions requires the establishment of multi-environment trials (METs). Sparse testing is a genomic prediction-based strategy that reduces the phenotyping costs in METs by selecting a subset of genotypes to evaluate in a subset of environments and then predicts the performance of the unobserved genotype-environment combinations. A Miscanthus sacchariflorus (MSA) population comprising 336 genotypes observed across three environments was analyzed implementing sparse testing designs. Three prediction models considering main effects (environments, genotypes, genomic) and interaction effects (genotype-by-environment; G×E interaction) were implemented for forecasting dry biomass yield (YDY), total culm (TCM), average internode length (AIL), and culm node number (CNN). Multiple calibration sets based on different compositions and sizes were considered to evaluate performance in terms of the predictive ability (PA) and the mean square error (MSE) for a fixed testing set size. The training set size ranged from 52 to 112 to predict a fixed set of 224 unobserved genotypes across all three environments. The results showed that the model accounting for G×E interaction consistently presented the highest PA and the lowest MSE: for CNN (PA: ~0.77, MSE: ~0.5) and YDY (PA: ~0.70, MSE: ~1.3) while for TCM and AIL these ranged from ~0.28 to 0.41 and ~1.3 to 4.3, respectively. Overall, varying training sets and allocation strategies did not affect PA and MSE, with 52 non-overlapping and 0 overlapping genotypes per environment as the optimal cost-effective allocation framework. This suggests that implementing sparse testing designs could significantly reduce phenotyping costs by fivefold, without compromising PA in breeding programs for perennial crops such as Miscanthus.

Miscanthus sacchariflorus (MSA)↗