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At least 19 records

Evaluation of artificial neural network performance for classification of potato plants infected with potato virus Y using spectral data on multiple varieties and genotypes

Potato virus Y (Potyviridae, PVY) is a plant virus that poses a significant threat to potato producers on a global basis. The pathogen has disrupted seed potato supplies and negatively impacted yield and quality of commercial potato crops. The potato industry currently manages PVY infection levels via insecticide applications, regional seed certification programs that rely on field scouting to visually assess individual plants for infection status, and destructive and costly tissue sampling coupled with laboratory assays. Despite these efforts, PVY continues to confound potato industry stakeholders resulting in economic harm. Remote sensing and machine learning provide for the development of new tools to more accurately detect and spatially quantify PVY-infected plants versus the current state of the art. However, there is a need to understand how the occurrence of many different potato varieties impact the dynamics of developing models to detect potato plants impacted with PVY and their potential effectiveness. This study evaluates classification modelling outcomes using spectral datasets collected in different temporal and spatial environments (greenhouse and a production field) on multiple potato varieties consisting of labelled instances of plants infected with PVY and those not infected with the virus. A modelling framework was developed to support iterative modelling runs using artificial neural network (ANN) architectures configured as binary classifiers to develop sample populations to support statistical analysis on model performance using specific spectral subsets. When using spectral data to detect PVY-infected plants, ANN models achieved the highest mean accuracy of 0.894 on a single variety. Conversely, the same ANN model architecture only achieved a mean accuracy of 0.575 on a spectral data set representing 29 potato breeding lines. Additionally, statistical analysis indicates spectral regions including the red edge, near infrared and shortwave infrared contain more important spectral features for the ANN classifier introduced in this research.

60 APPLIED LIFE SCIENCES↗

Continuous cropping of potato changed the metabolic pathway of root exudates to drive rhizosphere microflora

For potato production, continuous cropping (CC) could lead to autotoxicity buildup and microflora imbalance in the field soil, which may result in failure of crops and reduction in yield. In this study, non-targeted metabolomics (via liquid chromatography with tandem mass spectrometry (LC–MS/MS)) combined with metagenomic profiling (via high-throughput amplicon sequencing) were used to evaluate correlations between metabolomics of potato root exudates and communities of bacteria and fungi around potato plants to illustrate the impacts of CC. Potato plants were grown in soil collected from fields with various CC years (0, 1, 4, and 7 years). Metabolomic analysis showed that the contents and types of potential autotoxins in potato root exudates increased significantly in CC4 and CC7 plants (i.e., grown in soils with 4 and 7 years of CC). The differentially expressed metabolites were mainly produced via alpha-linolenic acid metabolism in plant groups CC0 and CC1 (i.e., no CC or 1 year CC). The metabolomics of the groups CC4 and CC7 became dominated by styrene degradation, biosynthesis of siderophore group non-ribosomal peptides, phenylpropanoid biosynthesis, and biosynthesis of various plant secondary metabolites. Continuous cropping beyond 4 years significantly changed the bacterial and fungal communities in the soil around the potato crops, with significant reduction of beneficial bacteria and accumulation of harmful fungi. Correlations between DEMs and microflora biomarkers were established with strong significances. These results suggested that continuous cropping of potato crops changed their metabolism as reflected in the plant root exudates and drove rhizosphere microflora to directions less favorable to plant growth, and it needs to be well managed to assure potato yield.

Xing, Yanhong↗

Multi-level impacts of climate change and supply disruption events on a potato supply chain: An agent-based modeling approach

Context: The world is experiencing frequent extreme weather events like droughts, snowstorms, and shifting of seasons due to climate change. Increased frequency and severity of these extreme weather events threaten food security because agriculture depends on climate conditions. Impacts of climate change on the agricultural system not only occur at the grower’s level, but also cascade to other levels along the supply chain. Objective: In this study, we aim to quantify a wide range of economic impacts of different extreme climate events on different stages of a food supply chain. Methods: We chose the potato supply chain in Idaho as a case study. We developed a multi-echelon supply chain simulation model using an agent-based modeling (ABM) approach with five types of agents—farmers, shippers, processors, retailers, and logistics companies. In addition to the business-as-usual (BAU) scenario, we designed two climate-related disruption events—drought and snowstorm. We quantified the heterogeneous impacts at different stages of the supply chain for both fresh and processed potatoes using key performance indicators (KPIs) including revenues, prices, lead times, traded quantities, and food waste quantity. Results and Conclusion: The impacts of the disruption events are different on different agents in the supply chain for different product categories. The price hike of fresh potatoes is far higher than processed potatoes during disruption events. This price hike makes consumers switch to processed potatoes, which require more fresh potatoes as an input that further reinforces the price hike. However, because processed potatoes have an elastic demand, once their prices go up due to higher input cost, their demand drops. Non-contracted farmers gain additional revenues from the disruption events, whereas contracted farmers incur a loss due to lock-in price and lower than usual harvest. Significance: The methodology developed in this study could be applied to other food and agricultural supply chains for understanding the vulnerabilities at agent levels due to climate change disruption events. Furthermore, the findings would help develop mitigation strategies or policies to improve the well-being of the overall supply chain.

54 ENVIRONMENTAL SCIENCES↗

Copper ions suppress abscisic acid biosynthesis to enhance defence against Phytophthora infestans in potato

Abstract Copper‐based antimicrobial compounds are widely and historically used to control plant diseases, such as late blight caused by Phytophthora infestans , which seriously affects the yield and quality of potato. We previously identified that copper ion (Cu 2+ ) acts as an extremely sensitive elicitor to induce ethylene (ET)‐dependent immunity in Arabidopsis . Here, we found that Cu 2+ induces the defence response to P. infestans in potato. Cu 2+ suppresses the transcription of the abscisic acid (ABA) biosynthetic genes StABA1 and StNCED1 , resulting in decreased ABA content. Treatment with ABA or inhibitor fluridone made potato more susceptible or resistance to late blight, respectively. In addition, potato with knockdown of StABA1 or StNCED1 showed greater resistance to late blight, suggesting that ABA negatively regulates potato resistance to P. infestans . Cu 2+ also promotes the rapid biosynthesis of ET. Potato plants treated with 1‐aminocyclopropane‐1‐carboxylate showed enhanced resistance to late blight. Repressed expression of StEIN2 or StEIN3 resulted in enhanced transcription of StABA1 and StNCED1 , accumulation of ABA and susceptibility to P. infestans . Consistently, StEIN3 directly binds to the promoter regions of StABA1 and StNCED1 . Overall, we concluded that Cu 2+ triggers the defence response to potato late blight by activating ET biosynthesis to inhibit the biosynthesis of ABA.

Liu, Hai‐Feng↗

Limited potential of irrigation to prevent potato yield losses in Germany under climate change

Climate models project higher temperatures and a substantial net water deficit during the summer months over Germany until the end of the 21st century. The agricultural sector is particularly vulnerable to changing weather and climate conditions. In this study, we examine the role of irrigation for potato yields as a climate change adaptation measure in Northeast Lower Saxony (Germany). The region represents the largest irrigated area in Germany and is one of the main growing areas of potatoes. We develop a statistical multivariate regression model to investigate whether regional climate and irrigation data at the monthly and county level are suitable to describe potato yield variability from 1978 to 2018. Irrigation is estimated based on the climatic water balance and crop water demand. These estimates are calibrated against irrigation data from local agencies to account for realistic monthly water withdrawals. We analyze future yield changes based on climate model projections for the 21st century and different irrigation scenarios. We find that the potato yield will decrease significantly by 18% on average until 2050 with climate projection uncertainty of ±6.4% under the high emission scenario RCP 8.5 and without irrigation. Irrigation at current levels could compensate for about 54% of these yield losses. Doubling the amount of irrigation minimizes yield losses by as much as 80%. Under the low (middle) emission scenario RCP 2.6 (RCP 4.5), potato yield are projected to decrease moderately by 4.5% ± 3.4% (5.4% ± 2.8%) with irrigation at current levels. We show that the yield losses mainly originate from higher temperatures during the summer. Our analysis indicates that the capacity of irrigation to minimize yield losses is limited. Strengthening climate change mitigation efforts may be more effective in preventing yield losses. However, the effect of elevated CO 2 might buffer the high yield losses, especially in RCP 8.5. The studies supports farmers and decision makers in assessing future risks in potato yields. It can guide policymakers in allocating economic resources to cope with climate change.

60 APPLIED LIFE SCIENCES↗

Effects of different pretreatment methods on the drying characteristics and quality of potatoes

Abstract The effects of different pretreatments on the vitamin C content of peeled fresh potato, the drying characteristics, and several quality attributes of dehydrated potatoes were investigated. Citric acid pretreatment (0.1%–0.3%, 10–30 min), steam blanching (100ºC, 1–2 min), and water blanching (95°C, 1–2 min) were found to have no obvious effect on the drying rate of potatoes, whereas temperature was the main influencing factor. In terms of quality of dehydrated diced potato, 20 min of citric acid pretreatment resulted in the highest vitamin C retention and better color. Furthermore, dehydrated potato pretreated with citric acid all showed similar dynamic moisture adsorption curves, namely type II sorption isotherm. The moisture adsorption curves can be well fitted using the Guggenheim–Anderson–deBoer model with R 2 higher than .97.

Sun, Xiangfeng↗

POTATO: A Unified Assessment System for HL-LHC Outer Tracker Module Productions

The CMS detector s silicon tracker will be replaced in preparation for the upcoming High-Luminosity LHC (HL LHC) upgrade. The inner tracker will include a new pixel detector while the outer tracker (OT) will feature 5,592 pixel strip (PS) and 7,608 strip strip (2S) sensor modules with production distributed across 7 sites worldwide, requiring standardized grading and testing. One testing apparatus the burn-in box replicates the temperature cycling conditions that successful modules must withstand. The Phase-II Outer Tracker Analyzer of Test Outputs (POTATO) standardizes module evaluation and grading among testing sites. Given burn-in box test output, POTATO analyzes the results and assigns a letter grade to a module and its sub-components. POTATO's grading process must adapt to evolving standards for module evaluation; hence, we detail work on POTATO's database and grading functionality that will facilitate the unified assessment of Phase-II OT module assembly and testing worldwide. Once completed, POTATO will allow technicians to interact with a database of all graded modules and efficiently assess the global module assembly effort.

Clark, Olivia J. [U. Tennessee, Knoxville]↗

Multi-Level Impacts of Extreme Climate-Related Events on Food Supply Chain: Idaho Potato's Case Study

Background: The world is experiencing frequent extreme weather events like droughts, floods, snowstorms, and shifting of seasons due to climate change. Increasing frequencies and severity of these extreme weather events threaten food security because agriculture is extremely vulnerable to climate change. Higher temperature reduces overall yields of the desirable crops but proliferates weeds and harmful pests. Current data shows that every year U.S. farmers spend more than 11 billion USD to fight weeds and this number is expected to rise in the coming years due to climate change. Due to droughts, the water required for irrigation is becoming scarcer. Since many areas are becoming climatically unusable for crop production, the amount of farmland area is shrinking rapidly. In addition, changes in precipitation patterns are causing crop failures and negatively impacting expected yields. In this study, we investigated how different extreme climate events impact different stages of a food supply chain. Approach: As a case study, we chose Idaho’s potato supply chain (SC). Idaho is the top potato producing state in the U.S. and contributes around 30% of the nation’s potato production. Using the agent-based modeling (ABM) approach, we developed a multi-echelon potato supply chain computer simulation model with six types of agents – seed producers, farmers, shippers, processors, retailers, and logistics companies. In addition to the baseline scenario, we developed two additional climate-related disruption events – drought and snowstorm. We investigated how each of these disruption events impacts different stakeholders across the supply chain in terms of revenue and some other key performance metrics such as lead time, food waste, number of delayed orders, and order fulfillment rate. Results: Extreme climate events not only impact the growers but there is also cascading ripple effects downstream of the supply chain. The methodology developed in this study could be applied to other food and agricultural SC to understand the vulnerabilities of the different links. The findings would potentially help to adopt new policies for the well-being of the overall SC.

54 ENVIRONMENTAL SCIENCES↗

Enhancing physicochemical, bioactive, and nutritional properties of sweet potatoes: Ultrasonic contact drying with slot jet nozzles compared to hot-air drying and freeze drying

Sweet potatoes are a rich source of nutrients and bioactive compounds, but their quality can be impacted by the drying process. This study investigates the impact of slot jet reattachment (SJR) nozzle and ultrasound (US) combined drying (SJR + US) on sweet potato quality, compared to freeze-drying (FD), SJR drying, and hot air drying (HAD). SJR + US drying at 50 °C closely resembled FD in enhancing quality attributes and outperformed HAD and SJR in key areas such as rehydration, shrinkage ratios, and nutritional composition. Notably, SJR + US at 50 °C produced the highest total starch (36.84 g/100 g), total dietary fiber (8.48 g/100 g), total phenolic content (158.19 mg GAE/100 g), total flavonoid content (119.08 mg QE/g), DPPH antioxidant activity (6.44 μmol TE/g), β-carotene (31.98 mg/100 g), and vitamin C (5.27 mg/100 g). It also exhibited higher glass transition temperatures (Tg: 14.49 °C), indicating better stability at room temperature. The hardness values for SJR + US samples were similar to FD, while HAD samples had the highest hardness. SJR + US at 50 °C resulted in the lowest total color changes (ΔE), indicating minimal impact on appearance. Additionally, FTIR analysis revealed that peaks in specific spectral regions indicated superior preservation of bioactive compounds in SJR + US samples compared to other methods, which was also confirmed by principal component analysis (PCA) and heatmap visualization. Overall, these findings suggest that SJR + US is an effective alternative to conventional drying techniques, significantly improving the quality of dried sweet potatoes.

Color↗

Predictive analytics of selections of russet potatoes

We explore the application of machine learning algorithms specifically to enhance the selection process of Russet potato (Solanum tuberosum L.) clones in breeding trials by predicting their suitability for advancement. This study addresses the challenge of efficiently identifying high-yield, disease-resistant, and climate-resilient potato varieties that meet processing industry standards. Leveraging manually collected data from trials in the state of Oregon, we investigate the potential of a wide variety of state-of-the-art binary classification models. The dataset includes 1086 clones, with data on 38 attributes recorded for each clone, focusing on yield, size, appearance, and frying characteristics, with several control varieties planted consistently across four Oregon regions from 2013 to 2021. We conduct a comprehensive analysis of the dataset that includes preprocessing, feature engineering, and imputation to address missing values. We focus on several key metrics such as accuracy, F1-score, and Matthews correlation coefficient (MCC) for model evaluation. The top-performing models, namely a feedforward neural network classifier (Neural Net), a histogram-based gradient boosting classifier (HGBC), and a support vector machine classifier (SVM), demonstrate consistent and significant results. To further validate our findings, we conducted a simulation study using the aims, data-generating mechanisms, estimands, methods, and performance measures (ADEMP) framework, simulating different data-generating scenarios to assess model robustness and performance through true positive, true negative, false positive, and false negative distributions, area under the receiver operating characteristic curve (AUC-ROC) and MCC. The simulation results highlight that non-linear models like SVM and HGBC consistently show higher AUC-ROC and MCC than logistic regression, thus outperforming the traditional linear model across various distributions, and emphasizing the importance of model selection and tuning in agricultural trials. Variable selection further enhances model performance and identifies influential features in predicting trial outcomes. The findings emphasize the potential of machine learning in streamlining the selection process for potato varieties, offering benefits such as increased efficiency, substantial cost savings, and judicious resource utilization. Our study contributes insights into precision agriculture and showcases the relevance of advanced technologies for informed decision-making in breeding programs.

60 APPLIED LIFE SCIENCES↗

Development of POTATO for 2S Module Grading for the CMS Phase-2 Outer Tracker Upgrade

Due to the High Luminosity-Large Hadron Collider (HL-LHC) upgrade, several detectors of the Compact Muon Solenoid (CMS) will need to be replaced, specifically the new Outer Tracker (OT) that will be assembled with 13,200 silicon modules. The OT is composed of two types of modules; the PS (pixel-strip) and the 2S (strip-strip) modules. With a large influx of production of modules, extensive testing is required to ensure quality of the modules. This research introduces POTATO (Phase-II Outer Tracker Analyzer of Test Outputs), a specialized software developed in C++ to analyze, grade, and store results in a centralized database. Module data will be collected from various international production facilities. The implementation of POTATO will facilitate with selecting the best performing modules for the Outer Tracker upgrade. This research is focused on the implementation of the analysis of 2S Module results within POTATO.

Klupshas, Anna↗

Development of POTATO for 2S Module Grading for the CMS Phase-2 Outer Tracker Upgrade

Due to the High Luminosity-Large Hadron Collider (HL-LHC) upgrade, several detectors of the Compact Muon Solenoid (CMS) will need to be upgraded, specifically the new Outer Tracker detector that will be composed of 13,200 silicon modules. The Outer Tracker features two types of modules; the PS (pixel-strip) and the 2S (strip-strip) modules. With a large influx of production of modules, extensive testing is required to ensure they fulfill the performance requirements. This research introduces POTATO (Phase-II Outer Tracker Analyzer of Test Outputs), a specialized software developed in C++ to analyze, grade, and store results in a centralized database since module data will be collected from various international production facilities. The implementation of POTATO will facilitate the selection of the best performing modules for the Outer Tracker upgrade. This paper is focused on the implementation of the analysis of 2S Module results within POTATO.

43 PARTICLE ACCELERATORS↗

Elucidating the modes of incorporation of the ferulic acid amides feruloyltyramine and feruloyloctopamine into the lignin-suberin fraction of potato periderms

Ferulic acid amides are naturally present in the cell walls of potato (Solanum tuberosum) periderms. In this study, we investigated their modes of incorporation into the periderm cell wall polymers. A lignin/suberin-enriched fraction was isolated and analyzed by GPC, DFRC, and 2D-NMR. The analyses revealed that the lignin domain of this fraction was predominantly composed of G-lignin units, with an H:G:S ratio of 2:70:28 (S/G ratio of 0.40). More importantly, the data also indicated the presence of two ferulic acid amides, feruloyltyramine and feruloyloctopamine, that are incorporated into the lignin/suberin structure of potato periderms through a variety of linkages, including 8-O-4' and 4-O-beta' ether linkages, as well as 8-5' linkages forming a phenylcoumaran structure involving the ferulate moiety. Although the phenolic groups of the tyramine and octopamine moieties could theoretically undergo oxidation, potentially creating additional sites for radical coupling, our research indicates that these groups remain predominantly as free phenolic entities that do not participate in radical coupling. On the other hand, all the phenolic groups of the ferulate moieties are bound through ether linkages reinforcing the conclusion that the feruloyltyramine and feruloyloctopamine moieties are linked to lignin/suberin within the cell wall via radical coupling reactions.

59 BASIC BIOLOGICAL SCIENCES↗

Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

Background: Potato is the third most consumed crop in the world. Breeding for traits such as yield, product quality and pathogen resistance are main priorities. Identifying molecular signatures of these and other important traits is important in future breeding efforts. In this study, a progeny population from a cross between a breeding line, SW93–1015, and a cultivar, Désirée, was studied by trait analysis and RNA-seq in order to develop understanding of segregating traits at the molecular level and identify transcripts with expressional correlation to these traits. Transcript markers with predictive value for field performance applicable under controlled environments would be of great value for plant breeding.Results: A total of 34 progeny lines from SW93–1015 and Désirée were phenotyped for 17 different traits in a field in Nordic climate conditions and controlled climate settings. A master transcriptome was constructed with all 34 progeny lines and the parents through a de novo assembly of RNA-seq reads. Gene expression data obtained in a controlled environment from the 34 lines was correlated to traits by different similarity indices, including Pearson and Spearman, as well as DUO, which calculates the co-occurrence between high and low values for gene expression and trait. Our study linked transcripts to traits such as yield, growth rate, high laying tubers, late and tuber blight, tuber greening and early flowering. We found several transcripts associated to late blight resistance and transcripts encoding receptors were associated to Dickeya solani susceptibility. Transcript levels of a UBX-domain protein was negatively associated to yield and a GLABRA2 expression modulator was negatively associated to growth rate.Conclusion: In our study, we identify 100’s of transcripts, putatively linked based on expression with 17 traits of potato, representing both well-known and novel associations. This approach can be used to link the transcriptome to traits. We explore the possibility of associating the level of transcript expression from controlled, optimal environments to traits in a progeny population with different methods introducing the application of DUO for the first time on transcriptome data. We verify the expression pattern for five of the putative transcript markers in another progeny population.

59 BASIC BIOLOGICAL SCIENCES↗

The CMS Phase 2 Outer Tracker Analyzer of Test Outputs - POTATO!

The Phase-2 upgrade of the Large Hadron Collider (LHC), also known as the High-Luminosity LHC (HL-LHC) is designed to achieve peak instantaneous luminosities which is about an order of magnitude higher than the nominal design value of $10^{34}~cm^{-2}s^{-1}$ delivering a total of atleast $3000 fb^{-1}$ data over 10 years of operation at $\sqrt{s}~=~14~TeV$. One crucial aspect of the CMS Phase-2 detector upgrade is the replacement of the existing tracking detector in order to deal with the extreme HL-LHC conditions, retaining and further expanding the physics performances achieved in the previous years. The outer part of the upgraded tracker (OT), will be equipped with over 13,000 macro Pixel-Strip (PS) and Strip-Strip (2S) modules! Module production is distributed across centers worldwide and necessitates coordinated efforts and standardized procedures. Along with production and assembly of the modules, Fermilab OT group is also working on a tool, Phase 2 Outer Tracker Analyzer of Test Outputs (POTATO) that will analyze, grade, upload and manage the large quantity of files to be stored in the centralized Database (DB). In this contribution a brief overview of the module testing and the power and dire need of POTATO to handle this large number of test outputs will be presented.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The CMS Phase 2 Outer Tracker Analyzer of Test Outputs - POTATO!

The Phase-2 upgrade of the Large Hadron Collider (LHC), also known as the High-Luminosity LHC (HL-LHC) is designed to achieve peak instantaneous luminosities which is about an order of magnitude higher than the nominal design value of $10^{34}~cm^{-2}s^{-1}$ delivering a total of atleast $3000 fb^{-1}$ data over 10 years of operation at $\sqrt{s}~=~14~TeV$. One crucial aspect of the CMS Phase-2 detector upgrade is the replacement of the existing tracking detector in order to deal with the extreme HL-LHC conditions, retaining and further expanding the physics performances achieved in the previous years. The outer part of the upgraded tracker (OT), will be equipped with over 13,000 macro Pixel-Strip (PS) and Strip-Strip (2S) modules! Module production is distributed across centers worldwide and necessitates coordinated efforts and standardized procedures. Along with production and assembly of the modules, Fermilab OT group is also working on a tool, Phase 2 Outer Tracker Analyzer of Test Outputs (POTATO) that will analyze, grade, upload and manage the large quantity of files to be stored in the centralized Database (DB). In this contribution a brief overview of the module testing and the power and dire need of POTATO to handle this large number of test outputs will be presented.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Generation, analysis, and transformation of macro-chloroplast Potato (Solanum tuberosum) lines for chloroplast biotechnology

Abstract Chloroplast biotechnology is a route for novel crop metabolic engineering. The potential bio-confinement of transgenes, the high protein expression and the possibility to organize genes into operons represent considerable advantages that make chloroplasts valuable targets in agricultural biotechnology. In the last 3 decades, chloroplast genomes from a few economically important crops have been successfully transformed. The main bottlenecks that prevent efficient transformation in a greater number of crops include the dearth of proven selectable marker gene-selection combinations and tissue culture methods for efficient regeneration of transplastomic plants. The prospects of increasing organelle size are attractive from several perspectives, including an increase in the surface area of potential targets. As a proof-of-concept, we generated Solanum tuberosum (potato) macro-chloroplast lines overexpressing the tubulin-like GTPase protein gene FtsZ1 from Arabidopsis thaliana . Macro-chloroplast lines exhibited delayed growth at anthesis; however, at the time of harvest there was no significant difference in height between macro-chloroplast and wild-type lines. Macro-chloroplasts were successfully transformed by biolistic DNA-delivery and efficiently regenerated into homoplasmic transplastomic lines. We also demonstrated that macro-chloroplasts accumulate the same amount of heterologous protein than wild-type organelles, confirming efficient usage in plastid engineering. Advantages and limitations of using enlarge compartments in chloroplast biotechnology are discussed.

Occhialini, Alessandro (ORCID:000000021162798X)↗