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At least 217 records · Page 12

Tracking precipitation features and associated large-scale environments over southeastern Texas

Abstract. Deep convection initiated under different large-scale environmental conditions exhibits different precipitation features and interacts with local meteorology and surface properties in distinct ways. Here, we analyze the characteristics and spatiotemporal patterns of different types of convective systems over southeastern Texas using 13 years of high-resolution observations and reanalysis data. We find that mesoscale convective systems (MCSs) contribute significantly to both mean and extreme precipitation in all seasons, while isolated deep convection (IDC) plays a role in intense precipitation during summer and fall. Using self-organizing maps (SOMs), we found that convection can occur under unfavorable conditions without large-scale lifting or moisture convergence. In spring, fall, and winter, front-related large-scale meteorological patterns (LSMPs) characterized by low-level moisture convergence act as primary triggers for convection, while the remaining storms are associated with an anticyclonic pattern and orographic lifting. In summer, IDC events are mainly associated with front-related and anticyclonic LSMPs, while MCSs occur more in front-related LSMPs. We further tracked the life cycle of MCS and IDC events using the Flexible Object Tracker algorithm over southeastern Texas. MCSs frequently initiate west of Houston, traveling eastward for around 8 h to southeastern Texas, while IDC events initiate locally. The average duration of MCSs in southeastern Texas is 6.1 h, approximately 4.1 times the duration of IDC events. Diurnally, the initiation of convection associated with favorable LSMPs peaks at 11:00 UTC, 3 h earlier than that associated with anticyclones.

54 ENVIRONMENTAL SCIENCES↗

Effect of Ice Number Concentration on the Evolution of Boundary Layer Clouds During Arctic Marine Cold‐Air Outbreaks

Abstract Marine cold‐air outbreaks (MCAOs) are crucial for Arctic Ocean heat loss, featuring convective cloud rolls that transition into convection cells downstream. Understanding factors controlling this transformation is the key for improving MCAO cloud representation in climate models. This study employs large‐eddy simulations to investigate how cloud ice number concentrations () affect cloud evolution using a case from the Cold‐Air Outbreaks in the Marine Boundary Layer Experiment (COMBLE) campaign. The simulations, performed in a Lagrangian framework following an air mass trajectory, are driven by ERA5 reanalysis data. Initially, all simulations produce similar cloud patterns, but higher leads to earlier breakup of cloud rolls. Between 4 and 10 hr, surface precipitation rates are similar across simulations, but precipitation initiates earlier, and the cloud‐base precipitation rates are higher when is higher. The stronger precipitation evaporation leads to increased stability of the boundary layer and reduced intensity of vertical mixing between the surface and cloud layer. An increased sink of cloud layer moisture via precipitation and decreased source through diminished vertical transport result in earlier cloud breakup in higher conditions. Simulations with different sea surface temperatures (SST) indicate that this cloud breakup mechanism remains valid for MCAOs of different strengths, although the cloud organization is more sensitive to SST changes in low environments. This work highlights the importance of accurate representations of ice processes in simulating MCAO clouds and suggests the need for observational constraints of ice nucleating particles and over the mixed‐phase cloud regimes.

54 ENVIRONMENTAL SCIENCES↗

Accelerating CO2 Storage Site Characterization through a New Understanding of Favorable Formation Properties and the Impact of Core-Scale Heterogeneities

CO2 sequestration in deep geologic formations can permanently reduce atmospheric CO2 emissions and help to abate climate change. Target formations must undergo a time- and resource-intensive site evaluation process, assessing storage capacity, environmental safety, and suitability for CO2 trapping via reactive transport models based on data from a limited number of core samples. As such, simulations are often simplified and omit heterogeneities in formation properties that may be significant but are not well understood. To facilitate more rapid site assessment, this work first defines the aquifer properties of favorable storage formations through the analysis of promising and active storage sites. Data show quartz is the most prevalent formation mineral with carbonate minerals, highly reactive with injected CO2, present in over 75% of formations. Porosity and permeability data are highly clustered at 10–30% and 10–1000 mD. Field-scale reactive transport simulations are then constructed and used to analyze CO2 trapping efficiency. The models consider porosity and carbonate mineral heterogeneity as well as the impacts of typical temperature gradients. Simulated sequestration efficiencies are compared to results from a comparable homogenous model to understand the implications of aquifer non-uniformities. The results show a lower sequestration efficiency in the homogeneous model during the injection phase. During the post-injection phase, the homogenization of porosity and carbonate mineralogy results in a higher sequestration efficiency. Incorporating the temperature gradient also increases the sequestration efficiency. Importantly, the maximum deviation between the homogeneous and heterogeneous simulations at the end of the 50-year study period is only ~10%. Larger impacts may be incurred for properties outside the defined, promising ranges suggested here.

Environmental Sciences & Ecology↗

Litter Production and Foliar Nutrient Resorption in Pioneer and Non-Pioneer Species in a Selective Logging Experiment in the Central Amazon, BIONTE, ZF-2, Manaus, 2022-23

This dataset was collected near the city of Manaus, Brazil, at the Experimental Station of Tropical Forestry (EEST, aka “ZF2”), inside the BIONTE (BIOmass and NuTrient Experiment). The experiment included three levels of increasing selective logging intensity, along with control, with 1-hectare permanent plots (12 total) located at the center of 4-hectare treatment plots. The vegetation has a high floristic diversity, the soils of the region are poor in nutrients, and the topography is characterized by plateaus (where BIONTE is located), and also valley bottoms and slopes. Three treatments of differing logging intensities were applied in the BIONTE experiment (T1, T2 and T3). The study was conducted in Treatment 3 (Block I – permanent plot), which represents the most intensive logging treatment, with 69% of the basal area (m²∙ha⁻¹) removed in 1988. The present dataset spans the period from May 1, 2022, to May 1, 2023. The data package includes leaf_nutrient_data, litterfall_total_data, leaf_litterfall_species_specific_data, and species_info, all provided in .csv format. These formats allow users to process and analyze the data in various software applications and programming languages, such as Python and R. This dataset was collected to advance knowledge on nutrient cycling in Amazonian forests, specifically distinguishing between species with two distinct functional traits: fast-growing and slow-growing. It also aims to improve Earth System Models, such as the E3SM Functionally Assembled Terrestrial Ecosystem Simulator (FATES). Additionally, it was used in a paper currently in preparation (Carvalho et al., in prep.), which aims to quantify seasonal litter production and foliar nutrient resorption in pioneer (fast-growing) and non-pioneer (slow-growing) tree species in the central Amazon. Specifically, it seeks to answer two key questions: 1) Is there a difference in leaf litter production, leaf nutrient flux and leaf nutrient concentration between pioneers and non-pioneers species? Is there a difference in the efficiency of foliar nutrient resorption between pioneers and non-pioneers species?

54 ENVIRONMENTAL SCIENCES↗

Estimates of Lake Nitrogen, Phosphorus, and Chlorophyll‐ a Concentrations to Characterize Harmful Algal Bloom Risk Across the United States

Abstract Excess nutrient pollution contributes to the formation of harmful algal blooms (HABs) that compromise fisheries and recreation and that can directly endanger human and animal health via cyanotoxins. Efforts to quantify the occurrence, drivers, and severity of HABs across large areas is difficult due to the resource intensive nature of field monitoring of lake nutrient and chlorophyll‐aconcentrations. To better characterize how nutrients interact with other environmental factors to produce algal blooms in freshwater systems, we used spatially explicit and temporally matched climate, landscape, in‐lake characteristic, and nutrient inventory data sets to predict nutrients and chlorophyll‐aacross the conterminous US (CONUS). Using a nested modeling approach, three random forest (RF) models were trained to explain the spatiotemporal variation in total nitrogen (TN), total phosphorus (TP), and chlorophyll‐aconcentrations across US EPA's National Lakes Assessment (n = 2,062). Concentrations of TN and TP were the most important predictors and, with other variables, the RF model accounted for 68% of variation in chlorophyll‐a. We then used these RF models to extrapolate lake TN and TP predictions to lakes without nutrient observations and predict chlorophyll‐afor ∼112,000 lakes across the CONUS. Risk for high chlorophyll‐aconcentrations is highest in the agriculturally dominated Midwest, but other areas of risk emerge in nutrient pollution hot spots across the country. These catchment and lake‐specific results can help managers identify potential nutrient pollution and chlorophyll‐ahot spots that may fuel blooms, prioritize at‐risk lakes for additional monitoring, and optimize management to protect human health and other environmental end goals.

Environmental Sciences & Ecology↗

JWST Observations of Starbursts: Dust Processing in the M82 Superwind

We present JWST MIRI and NIRCam imaging of the inner ∼5 kpc of the M82 superwind at ~ $0''_{.}05 - 0''_{.}375$(∼0.9–6.5 pc) resolution. Targeted filters probe emission from polycyclic aromatic hydrocarbons (PAHs; F335M, F360M, F770W, F1130W) and continuum (F250M, F360M) The images reveal a network of cool wind filaments traced by PAHs. PAH surface brightness declines with the inverse square of distance to the midplane, suggesting that the incident radiation field from the starburst drives the observed PAH intensity out to ±2.5 kpc. The 3.3/11.3 and 3.3/7.7 μm band ratios show uniformity with distance from the starburst, though comparisons with mid-IR dust emission models indicate a modest shift toward larger PAHs. Outside the disk, 11.3/7.7 μm increases moderately, reflecting that PAHs become more neutral with distance from the starburst as they are exposed to a declining radiation field and ionization parameter. Overall, PAHs in the wind are consistent with standard-to-large sizes and standard-to-high ionization states. Including Spitzer and Herschel data, PAH abundance (q PAH ) is set at ∼1% in the starburst and remains unchanging out to ±5 kpc off the disk. This flat q PAH profile suggests that PAHs are shielded from the hot wind, perhaps residing in the surface layers of cool clouds, with possible replenishment from cloud interiors and enrichment of the halo from previous bursts. In this picture, clouds are not dense enough to promote PAH growth, and they likely undergo radiative cooling and mixing with the hot phase to survive the gauntlet for at least ∼20 Myr.

Cronin, Serena A. [University of Maryland, College↗

Eddy covariance towers as sentinels of abnormal radioactive material releases

Ensuring accurate detection and attribution of abnormal releases of radioactive material is critical for protecting human health and safety. Most commonly, such detection is accomplished via active monitoring approaches involving the collection of physical samples. Further, this is labor intensive and limits the temporal and spatial resolution of any detected events to a relatively coarse level. As an alternative first step towards passive monitoring, we developed an approach using eddy flux tower data records to identify signals from a known abnormal release and quantify the extent to which that signal also occurs at other times in the data record. Through two case studies, one of which targeted the Fukushima nuclear disaster and the other targeting an abnormal release event at a radioisotope production facility in Fleurus, Belgium, we tested our approach and identified several potential heretofore unidentified abnormal events that were consistent with atmospheric circulation patterns and/or wind direction from known release sites. Because our approach is relatively simple and is resistant to systematic errors in the observational record, it has broad applicability beyond specific constituents and ecosystem types to identify a wide variety of limited-duration anomalies in flux tower data to ensure human health and industrial safety.

54 ENVIRONMENTAL SCIENCES↗

Benchmark of the Fe xvv 𝓡 ratio in photoionized plasma during eclipse of Centaurus X-3 with XRISM/Resolve

The $\mathcal {R}$ ratio is a useful diagnostic of the X-ray emitting astrophysical plasmas and is defined as the intensity ratio of the forbidden over the inter-combination lines in the K$\alpha$ line complex of He-like ions. The value is altered by excitation processes (electron impact or UV photoexcitation) from the metastable upper level of the forbidden line, thereby constraining the electron density or UV field intensity. The diagnostic has been applied mostly in electron density constraints in collisionally ionized plasmas using low-Z elements, as was originally proposed for the Sun (Gabriel & Jordan, 1969a, MNRAS, 145, 241), but it can also be used in photoionized plasmas. To make use of this diagnostic, we need to know its value in the limit of no excitation of metastables ($\mathcal {R}_{0}$), which depends on the element, how the plasmas are formed, how the lines are propagated, and the spectral resolution affecting line blending principally with satellite lines from Li-like ions. We benchmark $\mathcal {R}_0$ for photoionized plasmas by comparing calculations using radiative transfer codes and observation data taken with the Resolve X-ray microcalorimeter onboard XRISM. We use the Fe xxv He$\alpha$ line complex of the photo-ionized plasma in Centaurus X-3 observed during eclipse, in which the plasma is expected to be in the limit of no metastable excitation. The measured $\mathcal {R} = 0.65 \pm 0.08$ is consistent with the value calculated using xstar for the plasma parameters derived from other line ratios of the spectrum. We conclude that the $\mathcal {R}$ ratio diagnostic can be used for high-Z elements such as Fe in photoionized plasmas, which has wide applications in plasmas around compact objects at various scales.

X-rays: binaries↗

Self-supervised physics-informed generative networks for phase retrieval from a single X-ray hologram

X-ray phase contrast imaging significantly improves the visualization of structures with weak or uniform absorption, broadening its applications across a wide range of scientific disciplines. Propagation-based phase contrast is particularly suitable for time- or dose-critical in vivo/in situ/operando (tomography) experiments because it requires only a single intensity measurement. However, the phase information of the wave field is lost during the measurement and must be recovered. Conventional algebraic and iterative methods often rely on specific approximations or boundary conditions that may not be met by many samples or experimental setups. In addition, they require manual tuning of reconstruction parameters by experts, making them less adaptable for complex or variable conditions. Here we present a self-learning approach for solving the inverse problem of phase retrieval in the near-field regime of Fresnel theory using a single intensity measurement (hologram). A physics-informed generative adversarial network is employed to reconstruct both the phase and absorbance of the unpropagated wave field in the sample plane from a single hologram. Unlike most state-of-the-art deep learning approaches for phase retrieval, our approach does not require paired, unpaired, or simulated training data. This significantly broadens the applicability of our approach, as acquiring or generating suitable training data remains a major challenge due to the wide variability in sample types and experimental configurations. The algorithm demonstrates robust and consistent performance across diverse imaging conditions and sample types, delivering quantitative, high-quality reconstructions for both simulated data and experimental datasets acquired at beamline P05 at PETRA III (DESY, Hamburg), operated by Helmholtz-Zentrum Hereon. Furthermore, it enables the simultaneous retrieval of both phase and absorption information.

36 MATERIALS SCIENCE↗

An accelerated framework for predicting creep rupture lifetimes in engineering alloys

Confidently predicting high-temperature deformation, including creep and creep rupture, is paramount for the design and commercialization of candidate materials for advanced nuclear energy systems. To accelerate creep quantification, we introduce a framework that enables rapid, cost-effective, and reliable prediction of creep rupture lifetimes, minimizing reliance on time-intensive bulk creep testing. Unlike conventional creep analysis, which requires extensive time and resources, our method leverages a maximum of four short-term bulk creep tests as training data for prediction. This framework combines high-throughput nanoindentation up to 700 °C with these targeted bulk tests to inform our creep rupture model in order to predict rupture lifetimes. The strong agreement between our predictions and conventional experimental data demonstrates the effectiveness of our approach for accelerated creep analysis and lifetime prediction of structural components in high-temperature applications. Our multi-pronged approach motivates further integration of computational tools and advanced instrumentation to establish a universal framework for understanding high-temperature material responses.

36 MATERIALS SCIENCE↗

An Integral Activity-Based Protein Profiling Method for Higher Throughput Determination of Protein Target Sensitivity to Small Molecules

Activity-based protein profiling (ABPP) is a chemoproteomic technique that uses small molecule probes to label active enzymes selectively and covalently in complex proteomes. Competitive ABPP, which involves treatment of the active proteome with an analyte of interest, is especially powerful for profiling how small molecules impact specific protein activities. Advances in higher throughput workflows have made it possible to generate extensive competitive ABPP data across diverse biological samples, making this approach highly appealing for characterizing shared and unique proteins affected by perturbations such as drug or chemical exposures. To use the competitive ABPP approach effectively to understand potential adverse effects of chemicals of concern (CoC), a wide range of concentrations may be needed, particularly for chemicals that lack potency or toxicity data. In this work, we present an integral competitive ABPP method that enables target sensitivity determination for different organophosphate (OP) pesticides as model toxicants. Using previously developed OP-ABPs, we optimized conditions for tandem mass tag (TMT) multiplexing of ABPP samples and compared conventional competitive ABPP involving samples at discrete paraoxon concentrations to pooled samples across that same concentration range. We then expanded our approach to compare protein target sensitivities toward two additional OP pesticides, chlorpyrifos oxon and malaoxon. The results showed that differences in integral intensities for the pooled competition sample can be used to evaluate the relative sensitivity of specific proteins without increasing the overall number of samples. For 8 CoC concentrations of interest, this strategy reduced the number of TMT plexes and the corresponding number of LC–MS/MS analyses 3-fold. In conclusion, we envision the integral ABPP (IABPP) method will provide a means to screen diverse chemicals more rapidly to identify both high and low sensitivity protein targets.

activity-based probes↗

Incorporating Diurnal and Meter-Scale Variations of Ambient CO 2 Concentrations in Development of Direct Air Capture Technologies

To be implemented on climate-relevant scales, direct air capture of CO 2 (DAC) will require large capital-intensive facilities and careful attention to cost minimization. In making decisions among potential sites for DAC facilities, all of the factors that will impact process cost and efficiency should be considered. In this paper we focus on a factor that has previously received little attention in the DAC community, namely variations in atmospheric conditions on hourly time scales and length scales of meters. We present data curated from extensive previous studies of biosphere-atmosphere fluxes with observations of CO 2 concentration, temperature, and relative humidity (RH) with hourly resolution from many sites in North America. These include locations where typical diurnal variations in CO 2 concentration during summer months exceeds 150 ppm. These variations are larger than the seasonal variations that exist between averaged CO 2 concentrations in winter and summer, and they are highly correlated with diurnal variations in temperature and RH. Diurnal variations are dependent on the height above ground at which CO 2 concentrations are measured, with smaller variations existing at heights of 10 m or more than at ground level. We illustrate the potential implications of these short-term variations for the operation and optimization of a DAC process with process-level calculations for a specific adsorption-based process using amine-rich adsorbents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Angular Correlations of Gamma Rays from Fission Product Solution

Fission products from photon-induced fission are routinely used at Idaho National Laboratory as part of nuclear forensics activities. Typically, the focus is on fission products with relatively large fission yields (Ba-140, Mo-99, etc.). The nuclear data associated with the well-known isotopes have small uncertainties, and many have well-known angular correlations between emitted gamma-rays, if applicable. However, for isotopes with smaller fission yields or less intense gamma-ray emission intensities, the nuclear decay schemes and gamma-ray emission intensities may be less well-known. The Germanium Rotational Measurements for Angular Correlation (GeRMAC) system was designed to use two high-purity germanium (HPGe) detectors in a coincidence counting set-up but allows one of the HPGe detectors to rotate at a constant distance from a radioactive source, changing the relative angle between the two HPGe detectors. Angular correlations can then be determined from the relative photopeak areas between two gamma-rays emitted as part of the same nuclear decay. By recording the HPGe spectra in list mode, the angular correlations of gamma-rays emitted from complex sources, consisting of multiple isotopes, can be measured simultaneously and the individual isotope emissions can be isolated. Using the GeRMAC system, a multi-isotope fission product source, produced with photon-induced fission of U-238, was measured using a single rotational arc (180 degrees) to obtain the angular correlation between gamma-rays emitted by the large number of fission products contained in the solution with an angular accuracy of 1 degree. In particular, La-140 (38 gamma rays) and Nd-147 (26 gamma rays) are of interest to the nuclear forensics community.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗

Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library

Current approaches to analyzing metabolomic data often rely on matching MS/MS fragmentation data to sparse libraries or databases. This approach results in limited identification of features, often with less than 10% of the dataset being annotated. A complementary approach is to assign molecular formula to features based on accurate mass measurements, but the platforms commonly used for metabolomics do not have the needed accuracy or resolving power to do this robustly, particularly for larger molecules. Using our newly modified analysis tool, CoreMS, we generated a library of molecular formula from pooled samples analyzed with LC-21T FT-ICR MS. This library successfully annotated approximately 53.2% of features identified from the exometabolome of marine diatom Phaeodactylum tricornutum – a nearly ten-fold increase over the 5.9% annotation rate achieved using a conventional MS/MS library matching approach. Using this FT-ICR MS library approach, we were able to differentiate differences in the exometabolome of P. tricornutum in iron replete and iron limited conditions, with 668 metabolites being differentially expressed (p < 0.05, 2 x intensity difference) under these conditions. The traditional MS/MS fragmentation-based annotation approach only annotated 61 of these metabolites, while our novel pipeline annotated 450 metabolites and revealed 12 metabolites that were significantly more abundant under low iron conditions. Our results demonstrate the utility of ultrahigh resolution mass spectrometry for generating more comprehensive and confident molecular annotations.

21T-FTICR-MS, CoreMS↗

Strategies for the in-orbit gain tracking using the modulated X-ray sources for the Resolve microcalorimeter spectrometer on the X-ray Imaging and Spectroscopy Mission

Accurate and precise correction of the gain drift is the key to achieve the required energy resolution of the Resolve microcalorimeter spectrometer on the X-ray Imaging and Spectroscopy Mission (XRISM). Therefore, Resolve is equipped with highly configurable X-ray sources called the modulated X-ray source (MXS). The pulsed nature allows us to separate calibration and astrophysical X-rays by time interval selections. However, undesirable characteristics of the MXS, such as the afterglow X-rays, restrict the allowed configuration range. Moreover, the nonlinear and discontinuous behaviors of the calibration line count rate make the determination of the optimal setting highly complex. The MXS count rate model has been established using measurements in the spacecraft thermal vacuum test with the flight detector and MXS. A trade-off study using the model enables us to choose a few settings for the continuous use of the MXS optimized for different ranges of target gain tracking intervals. An alternative approach, where the MXS is used only intermittently, has also been developed and implemented. This new mode enables us to reconstruct the drift without having most of the undesirable effects in science data. This also forms the basis of the gain tracking under the current Resolve configuration with the closed gate valve.

Astronomy and AstroPhysics↗

Hybrid data-driven cement-stabilized soil design: An integration of machine learning, multi-objective optimization, and life cycle assessment

Soil stabilization is crucial in geotechnical engineering, yet conventional methods are often time-consuming, resource-intensive, and environmentally unsustainable. Despite growing interest in Machine Learning (ML) and optimization tools for mix design, few studies integrate these methods with decision-making techniques and environmental assessment to support practical implementation. This study proposes a hybrid data-driven framework for predicting strength, optimizing mix compositions, and evaluating environmental impacts via life cycle assessment of cement-stabilized soft soils. Six ML models were evaluated, and the top-performing eXtreme Gradient Boosting (XGB) model was further improved using the Grey Wolf Optimizer (GWO). The optimized XGB-GWO model, integrated with a polynomial cost function, served as the objective function in a multi-objective optimization problem solved via the Non-Dominated Sorting Genetic Algorithm II (NSGA-II), with final mix selection guided by the entropy-weighted TOPSIS method. Validation through a case study produced mix designs offering superior strength-cost trade-offs, with the optimal mix achieving 2243.2 kPa unconfined compressive strength and a 16.07 % reduction in carbon emissions compared to the highest-cost design. In conclusion, this study offers a sustainable, scalable approach to soil stabilization and supports informed decision-making in construction.

Life cycle assessment↗

Stability of the fcc phase in shocked nickel up to 332 GPa

Despite making up 5-20 wt.% of Earth’s predominantly iron core, the melting properties of elemental nickel at core conditions remain poorly understood, due largely to a dearth of experimental data. We present here an in situ X-ray diffraction study performed on laser shock-compressed samples of bulk nickel, reaching pressures up to ~ 500 GPa. Hugoniot states of nickel were targeted using a flat-top laser drive, with in situ X-ray diffraction data collected using the Linac Coherent Light Source. Rietveld methods were used to determine the densities of the shocked states from the measured diffraction data, while peak pressures were determined using a combination of measured particle velocities, shock transit times, hydrodynamic simulations, and laser intensity calibrations. We observed solid compressed face-centered cubic (fcc) Ni up to at least 332 ± 30 GPa along the Hugoniot—significantly higher than expected from the majority of melt lines that have been proposed for nickel. We also bracket the partial melting onset to between 377 ± 38 GPa and 486 ± 35 GPa.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Data for Comparison of Genotyping Assays for Detection of Targeted CRISPR/Cas Mutagenesis in Highly Polyploid Sugarcane

Sugarcane ( Saccharum spp.) is an important biofuel feedstock and a leading source of global table sugar. Saccharum hybrid cultivars are highly polyploid (2n = 100–130), containing large numbers of functionally redundant hom(e)ologs in their genomes. Genome editing with sequence-specific nucleases holds tremendous promise for sugarcane breeding. However, identification of plants with the desired level of co-editing within a pool of primary transformants can be difficult. While DNA sequencing provides direct evidence of targeted mutagenesis, it is cost-prohibitive as a primary screening method in sugarcane and most other methods of identifying mutant lines have not been optimized for use in highly polyploid species. In this study, non-sequencing methods of mutant screening, including capillary electrophoresis (CE), Cas9 RNP assay, and high-resolution melt analysis (HRMA), were compared to assess their potential for CRISPR/Cas9-mediated mutant screening in sugarcane. These assays were used to analyze sugarcane lines containing mutations at one or more of six sgRNA target sites. All three methods distinguished edited lines from wild type, with co-mutation frequencies ranging from 2% to 100%. Cas9 RNP assays were able to identify mutant sugarcane lines with as low as 3.2% co-mutation frequency, and samples could be scored based on undigested band intensity. CE was highlighted as the most comprehensive assay, delivering precise information on both mutagenesis frequency and indel size to a 1 bp resolution across all six targets. This represents an economical and comprehensive alternative to sequencing-based genotyping methods which could be applied in other polyploid species.

Genomics↗