Enhanced pan-genomic resources at the maize genetics and genomics database.

Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genomes within a clade, are more useful than single reference genomes for studying species diversity. This is especially true for a species like Zea mays, which has a particularly diverse and complex genome. Presenting pan-genome data, analyses, and visualization is challenging, especially for a diverse species, but more so when pan-genomic data is linked to extensive gene model and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures as is the case at MaizeGDB. Here, we describe MaizeGDB's expansion to include the genic subset of the Zea pan-genome in a pan-gene data center featuring the maize genomes hosted at MaizeGDB, and the outgroup teosinte Zea genomes from the Pan-Andropoganeae project. The new data center offers a variety of browsing and visualization tools, including sequence alignment visualization, gene trees and other tools, to explore pan-genes in Zea that were calculated by the pipeline Pandagma. Combined, these data will help maize researchers study the complexity and diversity of Zea, and to use the comparative functions to validate pan-gene relationships for a selected gene model.

PanEffect: a pan-genome visualization tool for variant effects in maize.

SUMMARY: Understanding the effects of genetic variants is crucial for accurately predicting traits and functional outcomes. Recent approaches have utilized artificial intelligence and protein language models to score all possible missense variant effects at the proteome level for a single genome, but a reliable tool is needed to explore these effects at the pan-genome level. To address this gap, we introduce a new tool called PanEffect. We implemented PanEffect at MaizeGDB to enable a comprehensive examination of the potential effects of coding variants across 50 maize genomes. The tool allows users to visualize over 550 million possible amino acid substitutions in the B73 maize reference genome and to observe the effects of the 2.3 million natural variations in the maize pan-genome. Each variant effect score, calculated from the Evolutionary Scale Modeling (ESM) protein language model, shows the log-likelihood ratio difference between B73 and all variants in the pan-genome. These scores are shown using heatmaps spanning benign outcomes to potential functional consequences. In addition, PanEffect displays secondary structures and functional domains along with the variant effects, offering additional functional and structural context. Using PanEffect, researchers now have a platform to explore protein variants and identify genetic targets for crop enhancement. AVAILABILITY AND IMPLEMENTATION: The PanEffect code is freely available on GitHub (https://github.com/Maize-Genetics-and-Genomics-Database/PanEffect). A maize implementation of PanEffect and underlying datasets are available at MaizeGDB (https://www.maizegdb.org/effect/maize/).

Developing a Decision-making Tool for Agricultural Surface Water Decontamination Using Ultraviolet-C Light.

Ultraviolet-C (UV-C) light-assisted water treatment systems are an increasingly investigated alternative to chemical sanitizers for agricultural surface water decontamination. However, the relatively high concentration of particulate matter in surface water is a major challenge to expanding its application in the production of fresh produce. The objective of this project was to test the efficacy of two commercial UV-C devices to reduce the microbial risk of agricultural water in order to develop a web application to assist growers in decision-making related to the on-farm implementation of UV-C technologies for agricultural water treatment. An on-farm study using three agricultural water sources was performed to determine the microbial reduction efficacy of a low power, low flow (LP/LF; 1-9 gallons per minute (GPM), 1.34-gallon capacity) and a high powered, high flow (HP/HF; 1-110 GPM, 4.75-gallon capacity) device at flow rates of 6, 7, and 9 GPM. A threshold of 30% UVT for the HP/HF device was observed, wherein lower water transmissibility significantly impacted microbial inactivation. Although less effective at lower %UVT, the LP/LF device costs less to install, maintain, and operate. The observations were used to design an online tool for growers to calculate the predicted reduction of generic Escherichia coli using either device based on the %UVT of their water source. However, because this study utilized an exploratory and proof-of-concept approach, the experimental flow rates were limited to reflect the capacities of the smaller unit (9 GPM) for direct comparison to the larger unit. Thus, the preliminary model and tool are largely limited to the experimental conditions. Yet, these results of this study demonstrate the utility of UV-C light in reducing the microbial risk of agricultural water, and future studies using different UV-C devices and higher flow rates will expand the use of the decision-making tool.

The Potential for Cover Crops to Reduce the Load of Escherichia coli in Contaminated Agricultural Soil.

Cover crops are plants seeded before or after cash crops to improve soil health, reduce weed pressure, and prevent erosion. Cover crops also produce various antimicrobial secondary metabolites (i.e., glucosinolates, quercetin), yet the role of cover crops in moderating the population of human pathogens in the soil has rarely been investigated. This study aims to determine the antimicrobial capacity of three cover crop species to reduce the population of generic Escherichia coli (E. coli) in contaminated agricultural soil. Four-week-old mustard greens (Brassicajuncea), sunn hemp (Crotalaria juncea), and buckwheat (Fagopyrum esculentum) were mixed into autoclaved soil and inoculated with rifampicin-resistant generic E. coli to achieve a starting concentration of 5 log CFU/g. The surviving microbial populations on days 0, 4, 10, 15, 20, 30, and 40 were enumerated. All three cover crops significantly reduced the population of generic E. coli compared to the control (p < 0.0001), particularly between days 10 and to 30. Buckwheat resulted in the highest reduction (3.92 log CFU/g). An inhibitory effect (p < 0.0001) on microbial growth was also observed in soils containing mustard greens and sunn hemp. This study provides evidence for the bacteriostatic and bactericidal effect of particular cover crops. More research regarding the secondary metabolites produced by certain cover crops and their potential as a bio mitigation strategy to improve on-farm produce safety is warranted.

The Attenuation of Microbial Reduction in Blueberry Fruit Following UV-LED Treatment.

Ultraviolet-C (UV-C) irradiation is a well-recognized technology for improving blueberry postharvest quality, and previous literature indicates that it has the potential for dual-use as an antimicrobial intervention for this industry. However, the practicality and feasibility of deploying this technology in fresh blueberry fruit are significantly hindered by the shadowing effect occurring at the blossom-end scar of the fruit. The purpose of this study was to determine if treating the blueberry fruit within a chamber fitted with UV-Light Emitting Diodes (LEDs) emitting a peak UV-C at 275 nm could minimize this shadowing and result in improved treatment efficacy. Ten blueberry fruits were dip-inoculated with E. coli at a concentration of 105 CFU/mL and irradiated within the system at doses of 0, 1.617, 3.234, 9.702, and 16.17 mJ/cm2 (0, 30, 60, 180, and 300 s). Statistical analysis was performed to characterize the extent of microbial survival as well as the UV-C inactivation kinetics. A maximum of 0.91-0.95 log reduction was observed, which attenuated after 60 s of treatment. The microbial inactivation and survival were thus modeled using the Geeraerd-tail model in Microsoft Excel with the GInaFIt add-in (RMSE = 0.2862). Temperatures fluctuated between 23 ± 0.5°C and 39.5°C ± 0.5°C during treatment but did not statistically impact the treatment efficacy (P = 0.0823). The data indicate that the design of a UV-LED system may improve the antimicrobial efficacy of UV-C technology for the surface decontamination of irregularly shaped fruits, and that further optimization could facilitate its use in the industry.

Protocol for Evaluating the Microbial Inactivation of Commercial UV Devices on Plastic Surfaces.

With the plethora of commercially available UV-C devices exhibiting different intensity and lifespans, it is critical to consumer safety that companies verify and clearly communicate the efficacy of their devices as per the intended use. The purpose of this study was to define a low-cost protocol for investigating the antimicrobial efficacy of commercial UV devices for industry use. The tested devices included: a wall-mounted unit (Device A), a troffer unit (Device B), and an induction lamp unit (Device C). The devices were installed within an enclosed tower to prevent the transmission of UV-C radiation outside of the testing area. The procedure details determining the devices' antimicrobial efficacy using plastic coupons inoculated with Escherichia coli or Staphylococcus aureus. The protocol includes suggested time-distance treatments according to the potential application of each device type and reports the results as log CFU/mL reduction or percent reduction.