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At least 127 records · Page 7

Genetic diversity, population structure and anthracnose resistance response in a novel sweet sorghum diversity panel

Sweet sorghum is an attractive feedstock for the production of renewable chemicals and fuels due to the readily available fermentable sugars that can be extracted from the juice, and the additional stream of fermentable sugars that can be obtained from the cell wall polysaccharides in the bagasse. An important selection criterion for new sweet sorghum germplasm is resistance to anthracnose, a disease caused by the fungal pathogen Colletotrichum sublineolum. The identification of novel anthracnose-resistance sources present in sweet sorghum germplasm offers a fast track towards the development of new resistant sweet sorghum germplasm. We established a sweet sorghum diversity panel (SWDP) of 272 accessions from the USDA-ARS National Plant Germplasm (NPGS) collection that includes landraces from 22 countries and advanced breeding material, and that represents ~15% of the NPGS sweet sorghum collection. Genomic characterization of the SWDP identified 171,954 single nucleotide polymorphisms (SNPs) with an average of one SNP per 4,071 kb. Population structure analysis revealed that the SWDP could be stratified into four populations and one admixed group, and that this population structure could be aligned to sorghum’s racial classification. Results from a two-year replicated trial of the SWDP for anthracnose resistance response in Texas, Georgia, Florida, and Puerto Rico showed 27 accessions to be resistant across locations, while 145 accessions showed variable resistance response against local pathotypes. A genome-wide association study identified 16 novel genomic regions associated with anthracnose resistance. Four resistance loci on chromosomes 3, 6, 8 and 9 were identified against pathotypes from Puerto Rico, and two resistance loci on chromosomes 3 and 8 against pathotypes from Texas. In Georgia and Florida, three resistance loci were detected on chromosomes 4, 5, 6 and four on chromosomes 4, 5 (two loci) and 7, respectively. One resistance locus on chromosome 2 was effective against pathotypes from Texas and Puerto Rico and a genomic region of 41.6 kb at the tip of chromosome 8 was associated with resistance response observed in Georgia, Texas, and Puerto Rico. This publicly available SWDP and the extensive evaluation of anthracnose resistance represent a valuable genomic resource for the improvement of sorghum.

59 BASIC BIOLOGICAL SCIENCES↗

Multigene engineering in plants: Technologies, applications, and future prospects

The emerging bioeconomy presents a promising solution to both economic and environmental challenges. Within the bioeconomy, plants serve as a renewable, sustainable, and cost-effective source of foods, fuels, chemicals, and materials. However, traditional breeding and single-gene engineering approaches fall short in addressing complex traits (e.g., drought tolerance, disease resistance, yield, nutrient use efficiency) which are controlled by multiple genes. The complexity of plant biology often necessitates the use of multigene engineering (MGE), which involves simultaneous ectopic expression, up/down-regulation, or editing of multiple genes, to enhance plant traits relevant to the bioeconomy. These genes may be associated with distinct traits or function as components of specific metabolic and regulatory pathways. This review summarizes current technologies for MGE within the synthetic biology-driven Design-Build-Test-Learn (DBTL) framework, detailing its four key stages: Design – gene construct development; Build – DNA assembly and plant transformation; Test – the molecular, biochemical, and physiological characterization of engineered plants; and Learn – computational modeling to refine, multiplex and iterate the process. Despite good progress in the applications of MGE in biofortification, metabolic engineering, and stress resilience, challenges remain in construct stability, coordinated gene expression, and regulatory predictability. We identified optimization paths and future directions to accelerate MGE deployment in sustainable agriculture, with possible societal benefits including reduced production costs, increased yield, and improved food and nutritional security.

AI-aided plant engineering↗

Ornamental origins and genomic frontiers: a review of big-bracted dogwood research

The big-bracted (Benthamidia) dogwood clade consists of small- to medium-sized deciduous trees within the genus Cornus, known for their showy spring-time floral bract display. Cornus is within the family Cornaceae and order Cornales, and as Cornales is one of the earliest diverging asterids, these taxa have been important for phylogenetic research. Three species within the big-bracted clade, flowering (Cornus florida), kousa (C. kousa), and Pacific (C. nuttallii) dogwoods, are popular ornamental landscape plants in North America, with more than 130 cultivars released. Despite their commercial popularity, numerous research gaps have limited the expansion of fundamental research and dogwood breeding programs. In this present review, we aim to provide a thorough overview of our current understanding of 1) the phylogenetic and biogeographic context, 2) plant biology and major pests and pathogens impacting commercialization, 3) historical commercialization and propagation methods, and 4) genetic and genomic resources and how they have been implemented to understand these species. Research gaps and future directions to advance basic research and breeding of big-bracted ornamental dogwoods are discussed throughout.

Cornus florida↗

Camelina circRNA landscape: Implications for gene regulation and fatty acid metabolism

Abstract Circular RNAs (circRNAs) are closed‐loop RNAs forming a covalent bond between their 3′ and 5′ ends, the back splice junction (BSJ), rendering them resistant to exonucleases and thus more stable compared to linear RNAs. Identification of circRNAs and distinction from their cognate linear RNA is only possible by sequencing the BSJ that is unique to the circRNA. CircRNAs are involved in the regulation of their cognate RNAs by increasing transcription rates, RNA stability, and alternative splicing. We have identified circRNAs from C. sativa that are associated with the regulation of germination, light response, and lipid metabolism. We sequenced light‐grown and etiolated seedlings after 5 or 7 days post‐germination and identified a total of 3447 circRNAs from 2763 genes. Most circRNAs originate from a single homeolog of the three subgenomes from allohexaploid camelina and correlate with higher ratios of alternative splicing of their cognate genes. A network analysis shows the interactions of select miRNA:circRNA:mRNAs for regulation of transcript stabilities where circRNA can act as a competing endogenous RNA. Several key lipid metabolism genes can generate circRNA, and we confirmed the presence of KASII circRNA as a true circRNA. CircRNA in camelina can be a novel target for breeding and engineering efforts.

Utley, Delecia [Department of Plant and Microbial ↗

Safeguarding Commercial Breed and Burn Sodium-Cooled Fast Reactors

A new class of reactors is under development in the United States. These new reactor designs use fast neutron spectra and rely on fuel technology advancements to reach fleet-wide operating conditions where neither enrichment nor reprocessing fuel are required to sustain or grow the fleet. Achieving this level of operation requires nuclear fuel that can remain in the reactor environment for much longer than current limits. The transfer of irradiated fuel is also required as the initial fissile source for new and replacement reactors. This class of reactors is known as breed and burn reactors and can be deployed as a fleet whereby the transfer of fuel is used to power subsequent generations of reactors. The use of breed and burn reactors reduces, and potentially eliminates, the need for enrichment and reprocessing to sustain a reactor fleet. Currently, enrichment and reprocessing plants require extremely complicated safeguards implementation and offer States diversion pathways for indirect use material. By eliminating the need for these facilities, a nuclear power fleet based on the BREED AND BURN reactor concept has the potential to indirectly reduce the burden on IAEA safeguards. However, this complex dynamic system does pose new safeguards challenges that are explored further in this report.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Major impacts of widespread structural variation on sorghum

Genetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent genome analyses in plants reveal many structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent of the impact of SVs on global trait variation, as well as their utility in genome-wide selection, is not yet understood. In this study, we built an SV data set based on whole-genome resequencing of diverse sorghum lines (n = 363), validated the correlation of photoperiod sensitivity and variety type, and identified SV hotspots underlying the divergent evolution of cellulosic and sweet sorghum. In addition, we showed the complementary contribution of SVs for heritability of traits related to sorghum adaptation. Importantly, inclusion of SV polymorphisms in association studies revealed genotype–phenotype associations not observed with SNPs alone. Three-way genome-wide association studies (GWAS) based on whole-genome SNP, SV, and integrated SNP + SV data sets showed substantial associations between SVs and sorghum traits. The addition of SVs to GWAS substantially increased heritability estimates for some traits, indicating their important contribution to functional allelic variation at the genome level. Our discovery of the widespread impacts of SVs on heritable gene expression variation could render a plausible mechanism for their disproportionate impact on phenotypic variation. This study expands our knowledge of SVs and emphasizes the extensive impacts of SVs on sorghum.

59 BASIC BIOLOGICAL SCIENCES↗

Gas Exchange, Transpiration and Yield of Sweetpotato Grown in a Controlled Environment

Sweetpotato was grown to harvest maturity within NASA Johnson Space Center's Variable Pressure Growth Chamber (VPGC) to characterize crop performance for potential use in advanced life support systems as a contributor to food production, air revitalization and resource recovery. Stem cuttings of breeding clone "TU-82-155" were grown hydroponically at a density of 17 plants m(sup -2) using a modified pressure-plate growing system (Patent No. 4860-490, Tuskegee University). Lighting was provided by HPS lamps at a photoperiod of 12h light: 12h dark. The photosynthetic photon flux was maintained at 500, 750 and 1000 micro mol m(sup -2) s(sub -1) during days 1-15, 16-28, 29-119, respectively. Canopy temperatures were maintained at 28 C: light: 22 C:dark. During the light period, relative humidity and carbon dioxide were maintained at 70% and 1200 micro liters l(sup -1), respectively. Nutrient solution was manually adjusted 2 to 4 times per week by addition of 10X concentrated modified half-strength Hoagland nutrient salts and NaOH to return the electrical conductivity and pH to 1.2 mS cm(sup -1) and 6.0, respectively. At 17 weeks (119 days) from transplanting, a total of 56.5 kilograms fresh mass of storage roots (84.1% moisture) were harvested from the 11.2 m(sup 2) chamber, resulting in a yield 5.0 kilograms m(sup -2). Harvest index, based on fresh mass, was 38.6%. Rates of net photosynthesis, dark respiration, transpiration, and ethylene production will be reported.

Barta, Daniel J.↗

Longitudinal genome-wide association study reveals early QTL that predict biomass accumulation under cold stress in sorghum

Sorghum bicolor is a promising cellulosic feedstock crop for bioenergy due to its high biomass yields. However, early growth phases of sorghum are sensitive to cold stress, limiting its planting in temperate environments. Cold adaptability is crucial for cultivating bioenergy and grain sorghum at higher latitudes and elevations, or for extending the growing season. Identifying genes and alleles that enhance biomass accumulation under early cold stress can lead to improved sorghum varieties through breeding or genetic engineering. We conducted image-based phenotyping on 369 accessions from the sorghum Bioenergy Association Panel (BAP) in a controlled environment with early cold treatment. The BAP includes diverse accessions with dense genotyping and varied racial, geographical, and phenotypic backgrounds. Daily, non-destructive imaging allowed temporal analysis of growth-related traits and water use efficiency (WUE). A genome-wide association study (GWAS) was performed to identify genomic intervals and genes associated with cold stress response. The GWAS identified transient quantitative trait loci (QTL) strongly associated with growth-related traits, enabling an exploration of the genetic basis of cold stress response at different developmental stages. This analysis of daily growth traits, rather than endpoint traits, revealed early transient QTL predictive of final phenotypes. The study identified both known and novel candidate genes associated with growth-related traits and temporal responses to cold stress. The identified QTL and candidate genes contribute to understanding the genetic mechanisms underlying sorghum's response to cold stress. These findings can inform breeding and genetic engineering strategies to develop sorghum varieties with improved biomass yields and resilience to cold, facilitating earlier planting, extended growing seasons, and cultivation at higher latitudes and elevations.

59 BASIC BIOLOGICAL SCIENCES↗

A best-practice guide to predicting plant traits from leaf-level hyperspectral data using partial least squares regression

Partial least squares regression (PLSR) modelling is a statistical technique for correlating datasets, and involves the fitting of a linear regression between two matrices. One application of PLSR enables leaf traits to be estimated from hyperspectral optical reflectance data, facilitating rapid, high-throughput, non-destructive plant phenotyping. This technique is of interest and importance in a wide range of contexts including crop breeding and ecosystem monitoring. The lack of a consensus in the literature on how to perform PLSR means that interpreting model results can be challenging, applying existing models to novel datasets can be impossible, and unknown or undisclosed assumptions can lead to incorrect or spurious predictions. We address this lack of consensus by proposing best practices for using PLSR to predict plant traits from leaf-level hyperspectral data, including a discussion of when PLSR is applicable, and recommendations for data collection. Further, we provide a tutorial to demonstrate how to develop a PLSR model, in the form of an R script accompanying this manuscript. This practical guide will assist all those interpreting and using PLSR models to predict leaf traits from spectral data, and advocates for a unified approach to using PLSR for predicting traits from spectra in the plant sciences.

54 ENVIRONMENTAL SCIENCES↗

Exploring drought-responsive crucial genes in Sorghum

Drought severely affects global food production. Sorghum is a typical drought-resistant model crop. Based on RNA-seq data for Sorghum with multiple time points and the gray correlation coefficient, this paper firstly selects candidate genes via mean variance test and constructs weighted gene differential co-expression networks (WGDCNs); then, based on guilt-by-rewiring principle, the WGDCNs and the hidden Markov random field model, drought-responsive crucial genes are identified for five developmental stages respectively. Enrichment and sequence alignment analysis reveal that the screened genes may play critical functional roles in drought responsiveness. A multilayer differential co-expression network for the screened genes reveals that Sorghum is very sensitive to pre-flowering drought. Furthermore, a crucial gene regulatory module is established, which regulates drought responsiveness via plant hormone signal transduction, MAPK cascades, and transcriptional regulations. The proposed method can well excavate crucial genes through RNA-seq data, which have implications in breeding of new varieties with improved drought tolerance.

60 APPLIED LIFE SCIENCES↗

Direct internal recycling fractions approaching unity

Direct internal recycling (DIR) refers to the process of recovering pure hydrogen isotopes (D/T) from helium and other impurities in the fusion plasma exhaust and directing them back to the fuel injection system. Increasing the exhaust fraction purified through DIR significantly reduces the size and cost of the tritium plant and provides additional benefits including reduced requirements for both the tritium startup inventory and tritium breeding ratio. Metal foil pumps (MFPs) are the dominant technology for this separation, relying on the concept of superpermeation. We recently demonstrated that PdCu foils operated at low temperature provide both exceptional flux and resilience to helium absorption as the DIR fraction is increased. Herein we design and demonstrate continuous and semi-batch DIR processes using PdCu MFPs. Under continuous processing, stable performance was observed for DIR fractions up to 92 %. In addition, we demonstrate a semi-batch process capable of extending the DIR fraction to unity (> 99.8 %). Under the experimental conditions described within a PdCu MFP area of ~22 m 2 would be sufficient to process the fusion exhaust with 92 % DIR fraction at expected flowrates of 100 Pa·m 3 ·s -1 for a future fusion power plant.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

High-throughput detection of T-DNA insertion sites for multiple transgenes in complex genomes

Abstract Background Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency. Results We have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T 1 generation of any crop transformed via Agrobacterium . We present an example using the allohexaploid oil-seed plant Camelina sativa to determine insertion site location of two transgenes. Conclusion This new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations.

59 BASIC BIOLOGICAL SCIENCES↗

Elemental profiling and genome-wide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

The ionome represents elemental composition in plant tissues and can be an indicator of nutrient status as well as overall plant performance. Thus, identifying genetic determinants governing elemental uptake and storage is an important goal for breeding and engineering biomass feedstocks with improved performance. In this study, we coupled high-throughput ionome characterization of leaf tissues with high-resolution genome-wide association studies (GWAS) to uncover genetic loci that modulate ionomic composition in leaves of poplar ( Populus trichocarpa ). Significant agreement was observed across the three ionomic profiling platforms tested: inductively coupled plasma-mass spectrometry (ICP-MS), neutron activation analysis (NAA) and laser-induced breakdown spectroscopy (LIBS). Relative quantification of 20 elements using ICP-MS across a population of 584 genotypes, revealed larger variation in micro-nutrients and trace elements content than for macro-nutrients across genotypes. The GWAS performed using a set of high-density (>8.2 million) single nucleotide polymorphisms, identified over 600 loci significantly associated with variations in these mineral elements, pointing to numerous uncharacterized candidate genes. A significant enrichment for genes related to ion homeostasis and transport was observed, including several members of the cation-proton antiporters (CPA) family and MATE efflux transporters, previously reported to be critical for plant growth and fitness in other species. Our results also included a polymorphic copy of the high-affinity molybdenum transporter MOT1 found directly associated to molybdenum content. For the first time in a perennial plant, our results provide evidence of genetic control of mineral content in a model tree species.

59 BASIC BIOLOGICAL SCIENCES↗

Enzymes as parts in need of replacement - and how to extend their working life

Enzymes catalyze reactions in vivo at different rates and each enzyme molecule has a lifetime limit before it is degraded and replaced to enable catalysis to continue. Considering these rates together as a unitless ratio of catalytic cycles until replacement (CCR) provides a new quantitative tool to assess the replacement schedule of and energy investment into enzymes as they relate to function. Here, we outline the challenges of determining CCRs and new approaches to overcome them and then assess the CCRs of selected enzymes in bacteria and plants to reveal a range of seven orders of magnitude for this ratio. Modifying CCRs in plants holds promise to lower cellular costs, to tailor enzymes for particular environments, and to breed enzyme improvements for crop productivity.

Catalytic rate↗

Adaptive gene loss in the common bean pan-genome during range expansion and domestication

The common bean ( Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗

Nested Pebble Bed Blanket (NesPeB)

Recent advances in magnetic confinement fusion technology have attracted billions of dollars of investments in startups from venture capitals and corporations, resulting in the development of devices aiming to demonstrate net energy gain in a self-heated burning plasma, such as SPARC (under construction) and others. However, future fusion power plants must operate in regimes that will require technologies far beyond current experience. According to a National Academies of Science, Engineering, and Medicine report, to have nuclear fusion power plants contributing in a timely manner to the planned reduction of atmospheric carbon dioxide, a pilot plant should be built by 2035, and it should demonstrate fusion power production and the performance of the tritium fuel system (requiring a high enough tritium breeding) by 2040. A recognized key technology gap by [26] is the fusion first wall and blanket since no current blanket concept is considered satisfactory or has been built and proven. The first wall and blanket in magnetic fusion reactors form a vital and complex system, as it must satisfy different functions such as power extraction, tritium breeding, plasma containment, radiation shielding, and safety. The list of design requirements is even longer: high enough tritium production for fusion self-sufficiency, low material activation, decay heat and shutdown dose rates, high thermal efficiency, high-capacity factor, high magnets-divertor-vacuum vessel-first wall life, low corrosion, low cost, and intrinsically safe (requiring minimal licensing). Despite fifty-plus years of research, the first wall and blanket concepts proposed suffer from fundamental technical problems and immaturity (TRL=2-3) that jeopardize the timely delivery of a commercial fusion power plant. A fusion first-wall blanket has never been built nor tested, and a "winning", practical functioning design requires enough engineering margins (high enough tritium breeding considering the uncertainty, etc.), manufacturing simplicity, ease of continuous operation, maintenance, and low cost. A new, groundbreaking blanket concept called "Nested Pebble Bed Blanket" (NesPeB) was developed at ORNL under the successful ARPA-E GAMOW FERMI project (patent application allowed by the USPTO). The NesPeB blanket concept addresses current blanket concepts' shortcomings and technical immaturity, paving the way for accelerated delivery of fusion power plants. NesPeB is based on nested pebbles, which are binary-sized lithium-ceramic pebbles enclosed in "Beryllide" perforated and coated spherical shells, which are also binary-sized, stacked on top of each other, forming a "bed" and cooled by Nitrogen gas also "sweeping" the Helium and Tritium generated by the neutron irradiation of Lithium; the vacuum vessel plasma facing material is Molybdenum-96 and -97 with the first wall cooled by Helium while the divertor armor is made of Tungsten. The simulations of the NesPeB blanket using Fusion Reactors Models Integrator (FERMI) are encouraging as they estimate a tritium breeding ratio (TBR) greater than 1.2 using natural Lithium, acceptable pressure drop, and excellent heat transfer properties. Furthermore, the NesPeB blanket is not limited by magneto-hydro-dynamics (MHD) effects, is designed for online refueling, relies on existing tritium extraction technologies, has a simple construction, and limits the corrosion and chemical reactivity problems. NesPeB has the potential to be transformational and disruptive since it can solve all the main, challenging technical problems of fusion device blankets and accelerate a pilot plant delivery for 10 or more years.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Detection of the Metabolic Response to Drought Stress Using Hyperspectral Reflectance

Drought is the most important limitation on crop yield. Understanding and detecting drought stress in crops is vital for improving water use efficiency through effective breeding and management. Leaf reflectance spectroscopy offers a rapid, non-destructive alternative to traditional techniques for measuring plant traits involved in a drought response. We measured drought stress in six glasshouse-grown agronomic species using physiological, biochemical and spectral data. In contrast to physiological traits, leaf metabolite concentrations revealed drought stress before it was visible to the naked eye. We used full-spectrum leaf reflectance data to predict metabolite concentrations using partial least-squares regression, with validation R2 values of 0.49 to 0.87. We show for the first time that spectroscopy may be used for the quantitative estimation of proline and abscisic acid, demonstrating the first use of hyperspectral data to detect a phytohormone. We used linear discriminant analysis and partial least squares discriminant analysis to differentiate between droughted and watered plants based on measured traits (accuracy: 71%) and raw spectral data (66%). Finally, we validated our glasshouse-developed models in an independent field trial. We demonstrate that spectroscopy can detect drought stress via underlying biochemical changes, before visual differences occur, representing a powerful advance for measuring limitations on yield.

54 ENVIRONMENTAL SCIENCES↗

Integral analysis of the effect of material dimension and composition on tokamak neutronics *

Abstract The neutronics performance of a tokamak has been identified as an important factor in designing a fusion power plant. The design of the tokamak should not only meet operational parameters such as sufficient tritium breeding, but also safety parameters such as low structural material activation. This paper investigates the impacts of the neutronics metrics for the ARC-class tokamak, a compact tokamak with an immersion blanket, by perturbing the first five layers of structural material—first wall, inner vacuum vessel, coolant salt channel, neutron multiplier, and outer vacuum vessel. The goal of this work is to provide insight into shaping and scaling the flux on each layer to obtain optimized operational and safety metrics through quantification of the responses from each perturbation. Results show that increased first wall thickness can increase the tritium breeding ratio (TBR) in specific configurations with high 6 Li enrichments and that vacuum vessels decrease TBR for low- 6 Li enrichment configurations. It was also found that the neutron multiplier can either increase or decrease TBR depending on the configuration. The response of metrics to the change in layer thickness and enrichment also varies depending on the vacuum vessel material. The integral impacts of 6 Li enrichment, layer thicknesses, and vacuum vessel material choice are investigated and presented in this paper.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗