Foreign Agricultural Service

Abstract Peanut smut, caused by the fungus Thecaphora frezzii , is a significant disease of peanuts in Argentina. Infected plants have seeds replaced by a mass of dark teliospores, reducing yield and seed quality. To prevent the spread of the pathogen, several countries have limited import of raw peanuts from Argentina, a major grower and exporter. Following successful in vitro culture of the fungus in its haploid stage, we produced a chromosome-level genome assembly of the species for the first time. We compare this genome with those of 49 other species of true smut fungi, or Ustilaginomycetes, including species of medical, agricultural, and industrial importance, some of which are known as pathogens and others only as saprotrophic yeasts. At almost 39 Mb, T. frezzii has the largest genome of the smut fungi sequenced to date and the highest repetitive content. While it shares some core effectors with species of the distantly related and better studied Ustilago and related fungi, predicted effectors only found in T. frezzii or in Thecaphora suggest unique infection strategies. Comparisons among the 50 smut genomes also show that the 14 smut fungi observed only as yeasts share genomic traits such as low repeat content and generally smaller genomes. This supports the hypothesis that some smut fungi are adapted to saprotrophic growth as yeasts. The high-quality, annotated genome for T. frezzii will be a valuable resource for investigating the population dynamics and evolution of an economically important pathogen, as well as illuminating an understudied clade of smut fungi. Article summary Peanut smut is a destructive and costly disease of peanuts in Argentina. For the first time, a high quality, annotated genome is presented for the causal agent, Thecaphora frezzii . This fungus has the largest and most repetitive genome of the true smut fungi, thus prompting comparison with 49 other species of smut fungi with available genomes, including non-pathogenic ones. While it shares some likely pathogenicity factors with well-studied smuts, it has many unique genes, a trait reflective of its evolutionary distance and likely novel mechanism for infection. This important genomic resource will benefit research regarding the evolution and adaption of T. frezzii , the development of diagnostic tools that enable rapid detection of it, and the study of smut fungi broadly.

The Tadla Plain, situated in central Morocco under semi-arid climatic conditions, represents a key agricultural area at the national scale, yet it is highly exposed to climate-related constraints, particularly fluctuations in rainfall and increasing stress on irrigation water resources. Building on earlier findings that documented a 21% reduction in cultivated land between 2013 and 2023, this study examines vegetation dynamics during the subsequent period from 2023 to 2025, marked by a notable recovery in precipitation. Vegetation conditions were evaluated using the Normalized Difference Vegetation Index (NDVI) derived from Landsat 8 imagery, in conjunction with rainfall records obtained from the NASA database. Field surveys were conducted to support and validate the remote sensing analysis. The results indicate a clear improvement in vegetation status across the Tadla Plain, with high-density vegetation areas increasing from 5.9% to 11.4% of the total surface area. In parallel, zones with moderate vegetation cover expanded from 24.6% to 29.2%. These changes closely coincide with a substantial rise in annual rainfall, which increased from an average of 240.38 mm in 2023 to 402.43 mm in 2025. The findings underline the strong dependence of agricultural systems in the Tadla Plain on climatic variability and demonstrate the effectiveness of satellite-based indicators as valuable tools for supporting sustainable land and water resource management.

Modern agricultural operations increasingly rely on integrated monitoring systems that combine multiple data sources for farm optimization. Aerial drone-based animal health monitoring serves as a key component but faces limited data availability, compounded by scene-specific issues such as small, occluded, or partially visible animals. Transfer learning approaches often fail to address this limitation due to the unavailability of large datasets that reflect specific farm conditions, including variations in animal breeds, environments, and behaviors. Therefore, there is a need for developing a problem-specific, animal-focused data augmentation strategy tailored to these unique challenges. To address this gap, we propose an object-focused data augmentation framework designed explicitly for animal health monitoring in constrained data settings. Our approach segments animals from backgrounds and augments them through transformations and diffusion-based synthesis to create realistic, diverse scenes that enhance animal detection and monitoring performance. Our initial experiments demonstrate that our augmented dataset yields superior performance compared to our baseline models on the animal detection task. By generating domain-specific data, our method empowers real-time animal health monitoring solutions even in data-scarce scenarios, bridging the gap between limited data and practical applicability.

Abstract Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici, is a major disease of wheat worldwide. To find additional sources of resistance, Genome-Wide Association (GWA) was used to analyze 337 soft winter wheat genotypes from Indiana, USA, by inoculating seedlings with two isolates of Z. tritici in a complete randomized design. Necrosis and pycnidia development were assessed at 14, 18 and 22 days post inoculation, enabling the calculation of area under the disease progress curve (AUDPC) for each parameter. Adjusted necrosis and pycnidia AUDPC scores were compared with 14,341 high-quality SNPs in a GWA analysis using the FarmCPU and GAPIT CMLM models to identify markers associated with the resistance. Significant (p < 0.05) isolate × genotype interactions were identified, confirming that the phenotypic variation was caused by isolate-specific resistance genes. Overall, 9 marker-trait associations (MTAs) were identified with Z. tritici necrosis and pycnidia resistance. All mapped MTAs were isolate and necrosis/pycnidia specific. Distinct MTAs were mapped for necrosis and pycnidia on chromosome 6A, and for pycnidia on chromosomes 1A, 1D, 4A, 7A, 3B and 5B. The MTAs on chromosomes 4A, 6A, 5B and 1D likely corresponded with the known genes Stb7, Stb15, Stb1 and Stb19, respectively. Those on chromosomes 1A, 7A and 3B were not associated with previously known genes and may be novel. Candidate genes near the marker locations have been identified for further investigations. Indiana soft winter wheat germplasm segregates for novel and known Stb genes and constitutes a valuable breeding resource for Z. tritici resistance.

Effective pollination is a key challenge for indoor farming, since bees struggle to navigate without the sun. While a variety of robotic system solutions have been proposed, it remains difficult to autonomously check that a flower has been sufficiently pollinated to produce high-quality fruit, which is especially critical for self-pollinating crops such as strawberries. To this end, this work proposes a novel robotic system for indoor farming. The proposed hardware combines a 7 -degree-of-freedom (DOF) manipulator arm with a custom end-effector, comprised of an endoscope camera, a 2-DOF microscope subsystem, and a custom vibrating pollination tool; this is paired with algorithms to detect and estimate the pose of strawberry flowers, navigate to each flower, pollinate using the tool, and inspect with the microscope. The key novelty is vibrating the flower from below while simultaneously inspecting with a microscope from above. Each subsystem is validated via extensive experiments.

Tetracycline repressible (Tet-Off) male-only sexing systems have great potential for improving the efficacy of sterile insect control programs in addition to reducing rearing cost. The relationship between insects and their microbial symbionts, as well as potential physiological stress caused by tetracycline class antibiotics, pose concerns that Tet-Off strains could have reduced fitness in nature. Here, we evaluated the biological performance, midgut microbiome, and midgut transcriptomes of wild-type screwworm, Cochliomyia hominivorax, reared in diet without Tc (control), with Tc (on-Tc), or a pseudo "male-only" condition where offspring of the Tc fed line were reared without Tc (post-Tc), like Tet-Off strains previously developed for this species. Biological performance was not significantly changed by the inclusion of Tc in the diet, and in most cases the flies reared with Tc were generally more fit than lines reared without Tc. The gut microbiome and transcriptome revealed interesting and similar patterns. In both surveys, the greatest changes were between both control and post-Tc treatments and the on-Tc treatment. Very few differences were observed between control and post-Tc treatments, suggesting that there are few negative persistent effects of Tc exposure to fly colonies, and flies revert to their natural state rapidly after the removal of Tc. These results suggest there are limited negative impacts of Tet-Off regulatory systems for use by the C. hominivorax eradication program, and differences observed in Tet-Off strain performance are likely not related to Tc exposure.

Shewanella is a genus of Gram-negative marine bacteria with some species associated with human and shellfish illnesses. This study evaluated the abundance of Shewanella species in oysters and seawater from the Chesapeake and Maryland Coastal Bays at four sites between 2019 and 2021. Physicochemical parameters such as temperature, salinity, dissolved oxygen, turbidity, pH, chlorophyll-a, rainfall within the last 48 h, total dissolved solids, and atmospheric pressure were also recorded to evaluate if there was a correlation between environmental parameters and the level of Shewanella. The highest total Shewanella counts were 1.8 × 107 CFU/g in oysters and 4.0 × 102 CFU/mL in seawater. 16S rRNA sequencing was performed on 1,344 representative isolates of which 890 (713 oyster, 177 seawater) were confirmed as Shewanella within 16 species. The top four species isolated from oysters and seawater were S. khirikhana a known shrimp pathogen (49%), S. marisflavi (19%), S. loihica (11%), and S. algae (8%). Testing for alpha and beta hemolysis were performed on all confirmed Shewanella isolates. Beta hemolysis was observed in 405 (46%) of the isolates of which 313 were in oysters and 92 in seawater. In oysters, beta-hemolysis was most prevalent in S. khirikhana (233 of 344 isolates, 68%), while in seawater 64 of 92 isolates (70%) were beta-hemolytic strains. Beta-hemolysis suggests that these could be potentially pathogenic strains. Correlations were performed between physicochemical attributes of the seawater and Shewanella counts. Only seawater temperature and dissolved oxygen correlated with Shewanella counts (r = 0.45 and - 0.41), respectively. No correlations were observed between the physicochemical parameters and Shewanella abundances in oysters. Results suggest that virulent strains of Shewanella may be present in oysters and seawater from the Chesapeake and Maryland Coastal Bays, perhaps as a consequence of rising seawater temperatures.

Abstract Predicting the efficiency of managed aquifer recharge (MAR) operation requires understanding the distribution of sediment type and water content in the vadose zone. In this study we assess the use of a direct-push nuclear magnetic resonance logging technique which can rapidly image water content profiles without the need for permanent boreholes. By combining nuclear magnetic resonance logging with direct-push sediment texture logging using cone penetrometer testing, it is possible to estimate the water content in the vadose zone and relate differences in water content to sediment type. We demonstrate this approach using four co-located nuclear magnetic resonance and cone penetrometer testing logs acquired to depths of approximately fifteen meters at an active almond orchard in California’s Central Valley. The results show water contents typically greater than 25% in clay- and silt-rich sediments, and up to 10% in sand-rich sediments. The ability to rapidly assess sediment type and water content using two direct-push tools opens up many exciting opportunities to study complex groundwater systems, even active orchards and other agricultural environments.

Abstract The use of biosolids as a sustainable alternative in the management of planted Pinus taeda forests affects availability of nutrients and beneficial elements. Calcium (Ca) and Silicon (Si) play important roles in plant regulatory and protective systems; therefore, our objective was to use scanning electron microscopy combined with energy-dispersive spectroscopy (SEM-EDS) to analyze the accumulation of elements in P. taeda needles grown in soil that received 0 to 60 Mg ha-1 applications of cellulosic waste. Microanalyses of needle sections were performed using a SEM with elemental detection by EDS. Mapping mode allowed for detection and analysis of Ca, Si, and C distributions in needle sections. Calcium and Si precipitation occurred in needles, with Ca accumulating in the phloem and Si in the epidermal cells. Application of 60 Mg ha-1 changed the availability and accumulation of elements, which resulted in more Ca crystals and fewer Si crystals.

ABSTRACT As the global population of elderly women continues to grow, understanding their financial well-being has become increasingly important. Despite the growing attention on financial inclusion, limited research has focused on how it impacts the financial resilience of elderly women, a group particularly vulnerable to financial shocks. This study addresses this gap by exploring how financial inclusion contributes to elderly women’s ability to cope with unexpected financial emergencies. Using survey data from 1,664 elderly women (above 60 years), the study investigates the role of various financial inclusion indicators – such as savings and insurance products, as well as reliance on family members for saving money – in enhancing financial resilience. Our findings show that financial inclusion plays a crucial role in strengthening the financial resilience of elderly women, with significant contributions from owning savings and insurance products. These insights have important implications for policymakers, regulators, and financial institutions seeking to design more inclusive financial services for elderly populations. By fostering financial inclusion, this study contributes to broader efforts toward achieving the United Nations’ Sustainable Development Goals (SDGs), particularly those related to reducing inequality and promoting economic security for all.