2023 NARC/NOA meeting

Current Status of Stemphylium Leaf Blight in the Treasure Valley

James Woodhall (jwoodhall@uidaho.edu), Madeline Kinnear, Ben Wood, Joshua Rosnow, Mack Murdock, Silas Shumate, Hayden Woods, Chris Ballou and Christian Cumagun

University of Idaho, Parma Research and Extension Center

Stemphylium leaf blight (SLB) is an important disease of onions, infection results in small, tan to brown lesions on the leaves and/or a necrotic dieback of the leaf tips. These lesions and dieback can progress leading to defoliation and yield loss. In the Treasure Valley, the impact of the disease is variable. In 2019, onset of the disease appeared to be late and only lesions were present. However, in 2020, leaf tip damage was observed as early as June. Limited SLB was observed in 2021 and 2022 but in 2023 lesions and leaf tip dieback were observed from August onwards. To understand the population dynamics of Stemphylium vesicarium, spore trapping was conducted using a Burkard Multi-vial cyclone trap and a species-specific real-time PCR was used to quantify S. vesicarium DNA. Abundance of spores was related to the weather conditions each year and the severity of disease.

Airborne Stemphylium Vesicarium Spore Concentrations and
Disease Development in Commercial Michigan Onion Fields

Abdelrazek S. Abdelrhim^1,3, Douglas S. Higgins^2,3, Mary K. Hausbec (hausbec1@msu.edu)³

¹Minia University, Egypt, ²Virginia Tech Eastern Shore AREC, Painter VA and ³Michigan State University, East Lansing MI, USA

Leaf blight caused by Stemphylium vesicarium is a serious foliar disease of onion in Michigan. We monitored airborne concentrations of ascospores and conidia, environmental conditions, and disease development in commercial Michigan onion fields located in Hamilton (20 April to 23 August [2021]; 5 May to 2 September [2022]) and Grant (10 May to 8 September [2022]). Burkard volumetric traps recorded peak concentrations of airborne ascospores (19 [Hamilton 2021]; 5 [Hamilton 2022]; 18 [Grant 2022] ascospores m³/air) in May; ascospore numbers at all sites declined in June. The first onions with lesions containing S. vesicarium conidia were observed on 24 June (Hamilton 2021) and 28 June (Hamilton and Grant 2022). In the 10 days prior to the observation of disease, there were a total of 162 (Hamilton 2021), 35 (Hamilton 2022), and 26 (Grant 2022) conidia and 1 (Hamilton 2021), 6 (Hamilton 2022), and 8 (Grant 2022) total ascospores recorded. In the same period, 9.7 cm (Hamilton 2021), 3.4 cm (Hamilton 2022), and 2.7 cm (Grant 2022) of rain was recorded. The presence of S. vesicarium spores and disease conducive conditions at early growth stages could have important implementations for disease management strategies.

The Challenges of Managing Stemphylium Leaf Blight of Onion

Emily McFaul¹, Julia Scicluna¹, Michael Kooy, Kevin Vander Kooi¹, Geoff Farintosh, Bruce Gossen²,and Mary Ruth McDonald (mrmcdona@uoguelph.ca)¹

¹University of Guelph, Guelph, ON, Canada and ²Agriculture and Agri-Food Canada, Saskatoon, SK, Canada

Stemphylium leaf blight of onion (SLB), caused by the fungus Stemphylium vesicarium, is an important disease of onion many parts of the world. The disease kills leaves and can reduce yield.  Managing SLB is challenging.  Field trials were conducted in the Holland Marsh, Ontario in 2022 and 2023 to evaluate fungicides and disease forecasting programs. Biocontrols T-77 (Trichoderma aroviride) and Serifel (Bacillus  amyloliquifaciens) were evaluated and fungicides  Merivon (pyraclostorbin and fluxapyroxad), Miravis Duo (pydiflumetofen and difenoconazole), Revysol (mefentrifluconazole), Sercadis (fluxapyroxad) and Dithane (mancozeb). Disease severity was low in 2022 and moderate in 2023 and there were no differences in disease severity or yield.  Disease forecasting based on temperature and leaf wetness showed no differences in disease severity in 2022 and small differences in 2023. Spray timing based on regular intervals had lower cumulative disease severity than the nontreated control, but was not different from fungicides applied based on forecasting programs.  Isolates of the fungus from the region are known to have high resistance to azoxysrobin and fluopyram.  Recent assessments found resistance to penflufen and fluxapyroxad.  Effective management of Stemphylium leaf blight requires effective fungicides and disease forecasting programs that indicate when there is low risk of disease development.

Managing Stemphylium Leaf Blight of Onion in the Face of Severe Fungicide Resistance in New York

Christy Hoepting (cah59@cornell.edu)¹, Daniel Heck² and Frank Hay²

¹Cornell Cooperative Extension Vegetable Program, Albion, NY USA and ²Dept. of Plant Pathology and Plant Microbe Biology, Geneva, NY USA

In New York, onions are predominantly grown in pockets of muck soil where production is unique and intensive. Stemphylium leaf blight (SLB) is a polycyclic foliar disease of onion that causes target spots and leaf dieback, and when it is severe, reduced yield and bulb quality is common. Since its resurgence in 2013, SLB has developed resistance to five fungicide resistance groups including FRAC (Fungicide Resistance Action Committee) groups 2, 3, 7, 9 and 11 despite judicious use of fungicides. Annual on-farm fungicide trials have vigorously tested dozens of active ingredients and tank mixes, from which spray programs were designed that used products belonging to multiple FRAC groups in rotation to effectively control SLB while halting further development of fungicide resistance.  Fungicide sensitivity testing of SLB isolates collected from commercial onion fields was used to track the development of fungicide resistance, which was related to fungicide use. In 2022, use of no more than two double FRAC 3-product treatments per season appeared to halt further development of fungicide resistance to FRAC 3. This treatment was often used in rotation with a FRAC 7 premix product in combination with a FRAC 2, M5 and/or FRAC P07 product for effective SLB control.

The Potential of On-Site Testing for Onion Pathogens Using Isothermal Methods

James Woodhall (jwoodhall@uidaho.edu), Ben Wood, Madeline Kinnear and Christian Cumagun

University of Idaho, Parma Research and Extension Center

On site testing can offer several advantages such as preventing the movement of infected material, engagement with the grower and a rapid turnaround of results. Advances in molecular testing technology and the availability of robust reagents have made on-site testing a possibility in recent years. One method suitable for on-site testing is Loop-mediated isothermal AMPlification (LAMP). Due to its isothermal nature, sensitivity and tolerance from inhibitors, LAMP tests can be performed in a simple and rapid manner in a laboratory-free environment when combined with simple and effective nucleic acid extraction techniques. Here we will discuss the development and validation of LAMP assays for three onion pathogens: Stromatinia cepivora, Pantoea agglomerans and Stemphyllium vesicarium, and their use in diagnosis.

Survey of Genetic Diversity, Mycotoxin Production Capability, and Potential Fungicide Resistance of Aspergillus Niger in Vidalia Onions

Jake C. Fountain¹ (jfount1@uga.edu), S.E.A. Joson¹, Alison K. Adams¹, Christopher T. Tyson², Angelos Deltsedis³, and Bhabesh Dutta³

¹University of Georgia, Griffin, ²University of Georgia, Lyons, and ³University of Georgia, Tifton

Black mold (Aspergillus niger) is a common postharvest disease issue encountered by Vidalia onion producers. Black mold is typically introduced in the field following excessive rainfall near harvest and can propagate in storage if onions are not dried in a timely fashion. Here, a survey was conducted to isolate black mold from production environments for characterization of pathogen genetic diversity along with potential mycotoxin production and fungicide resistance in the pathogen population. Fifty-five isolates were obtained from culled onions from two commercial packing houses, and from research plots at the UGA Vidalia Onion and Vegetable Research Center by single spore isolation on PDA amended with chloramphenicol. PCR-based characterization of these isolates is underway to confirm their species identification using a Multi-Locus Sequence Typing (MLST) approach with three genes: ITS1/4, BenA, and CaM. Additionally, PCR-based detection of mycotoxin production genes, specifically ota1, ota2, ota3, and ota5 for ochratoxin A, and fum10 for fumonisin B2 is also being performed along with screening for mutations in the cytochrome B (CYTB) gene associated with azoxystrobin resistance. These results will shed light on the genetic diversity of this pathogen and will inform further experiments on optimizing storage conditions and practices to mitigate black mold issues.

Fusarium Basal Rot Diversity and Ecology in California Allium Crops, from Seed to Storage

Cassandra Swett (clswett@ucdavis.edu), Thomas Turini, Robert Wilson, Megan Gastelum, Brian Caine, Rachel Hallmark and Claire Theberge

University of California

Fusarium-driven bulb rots are becoming increasingly problematic in California garlic and onion production. Disease ecology and epidemiology are poorly understood, making it challenging to develop management methods. Studies focused on fresh market garlic indicate that pathogen infection initiates very early in the season, with at least 10% of infections deriving from seed and up to 100% of plants infected within four months of planting. Fungicides applied at planting and mid-season resulted in up to a 75% and 33% reduction in pathogen infection incidence within three months of application, respectively, indicating potential for early season fungicide-based management. Studies of garlic seed production indicate that across fields, ~30% of seed bulbs have basal rot at harvest, and following storage, this increases to ~55% of bulbs indicating opportunity for seed infection management both in-season and during storage. In studies of nitrogen-mediated effects, application of 150 lbs N resulted in a 2.25-fold increase in Fusarium proliferatum colonization vs. 39 lbs N, and increased F. oxysporum colonization from zero to 75% of bulbs mid-season, indicating that high N levels used in this industry may play a role in enhancing infection. Downstream, further study is needed to refine in-season management in both seed and fresh market garlic production, and to better understand whether this disease may have similar early season infection activity (and thus management opportunity) in onion.

Limiting Fusarium Basal Rot Losses in Allium Crops: AN SCRI Planning Grant to Establish National Needs and Priorities for Improving Management

Cassandra Swett (clswett@ucdavis.edu), Brenna Aegerter, Mary Campbell, Chris Cramer, Lindsey du Toit, Jeremiah Dung, Frank Hay, Christy Hoepting, Alicyn Smart, Crystal Stewart, Robert Wilson, Tom Turini, Michael Havey, Anne van Diepeningen, John Clarkson, Claudia Nischwitz, Amanda Hodson, Olena Sambucci, Mary Ruth McDonald, Pierre Merel, and Justine Beaulieu

Onions and garlic are a dietary staple for most U.S. households. Fusarium basal rot (FBR) is a widespread disease driving up to 40% loss in onion and garlic across the U.S., representing up to a $10m loss for affected producers, with downstream impacts on increased costs to consumers. Impacts are pervasive across seed, fresh market, and processing production systems. In clonally produced garlic seed, cryptic infections often go undetected, enabling widespread pathogen expansion. Existing decision support and management resources are inadequate at mitigating losses effectively. Lack of accurate diagnostic tools for FBR results in rampant misdiagnoses and subsequent use of inappropriate management tools can lead to costly losses. We have brought together a diverse suite of 21 researchers and extension professionals from the public and private sector, representing major impacted states including California, Oregon, Washington, Utah, New Mexico, Wisconsin, New York, Maine and Georgia. The goals of this one-year SCRI planning grant are to: (1) identify needs of stakeholders via listening sessions; (2) bring together researchers, breeders and extension personnel actively working on FBR, to provide a platform for information exchange around this issues; (3) leverage efforts to develop a review article on Fusarium basal rot of onion and garlic; (4) collate information generated from these joint efforts to develop a cohesive set of research and extension goals that will be addressed with a full SCRI-SREP proposal.

A Micro- and Macro-Perspective of Bacterial Pathogens Affecting Onion in Georgia, USA

Bhabesh Dutta¹ (bhabesh@uga.edu), M. Zhao¹, G, Shin², and B. Kvitko²

¹Department of Plant Pathology, University of Georgia, Tifton, GA and ²Department of Plant Pathology, University of Georgia, Athens, GA

Onion bacterial diseases are caused by diverse bacterial pathogens. Interestingly, virulence factors employed by these bacteria to infect onion are diverse. For example, Pantoea ananatis and some onion-adapted strains of P. stewartii subsp. indologenes utilize distinct phosphonate biosynthetic gene clusters, “HiVir” and “Halophos”, respectively, to infect onion. The thiosulfinate tolerance cluster “alt” in Pantoea spp. aids in colonization of the thiosulfinate-rich environment in onion bulbs. Two closely related Pseudomonas species, P. viridiflava and P. alliivorans are also associated with onion. While an “alt” gene cluster is present in both, alt makes greater contributions to symptom development in P. viridiflava than in P. alliivorans. Onion pathogenic strains of Rouxiella badensis utilize a lipopeptide gene cluster, the “rot” cluster, to infect onion. Management of these bacterial pathogens is based primarily on applications of copper-based bactericides at susceptible crop growth stages. Cultural practices, e.g., use of a chain digger for mechanical harvest, also reduced internal bacterial bulb rot in field trials. Clipping onion necks at least 5 cm above the bulb reduced bacterial rot in storage compared to shorter necks. Together, advances in onion-pathogen interactions and applied aspects of onion production will aid in sustainable reduction of losses to bacterial rots.

Exporting Intuition: Harnessing the Power of Natural Language
Processing for Determining Thiosulfinate Tolerance-Like Gene Clusters Across a Spectrum of Bacterial Species

Brendon K. Myers¹, Brian H. Kvitko², Bhabesh Dutta (bhabesh@uga.edu)¹

¹University of Georgia, Tifton GA and ²University of Georgia, Athens GA.

Colonization of onion bulbs is challenging for necrotrophic bacteria due to the hosts’ phytoanticipins and phytoalexins. In response, some bulb-colonizing bacteria possess a thiosulfinate tolerance gene cluster (allicin tolerance ‘alt’ in Pantoea ananatis) that aids their survival in thiosulfinate-rich environments, such as the onion bulb.  Understanding the range and diversity of ‘alt’ gene clusters may aid in predicting bulb colonizing ability of invading bacteria. Here, we utilized natural language processing techniques to train an artificial neural network to identify alt-like genes within more than 200,000 bacterial genomes from the NCBI RefSeq database. Post-processing sequence redundancy filtering resulted in a final collection of 47 representative alt-like gene clusters. Guilt-by-association of gene neighbors is only one piece of evidence for gene cluster function, and so we further predicted protein function with multi-sequence alignment, 3D protein superimposition, and small-molecule-binding prediction. Multiple sequence alignment shows that several of these proteins have little sequence similarity, but high predicted 3D structural similarity with validated alt-like proteins. These results indicate that alt-like gene clusters are not unique to onion bulb colonizing bacteria but are present in a wide range of bacteria from diverse ecological niches.

Evaluation of Systematic Spray Programs to Reduce Onion Center Rot

Savannah Tanner, Chris Tyson (tysonc@uga.edu), Ross Greene, Aubrey Shirley, Derrick Bowen, Steven Powell, Jason Edenfield, Lauren Stanley, and Bhabesh Dutta

University of Georgia Extension

The bacterial disease, Center Rot (Pantoea spp.) is the leading cause of loss in Vidalia Onions each year. For the past three years, local agricultural agents have evaluated four systematic approaches to center rot incidence in Vidalia Onions including a Low Input, Growers Standard, High Input, and Organic approach.  Agents planted Vidalia Onion Varieties ‘Pirate’ or ‘Century’ in 20-ft plots consisting of 4 replications of each treatment with a 3-ft bare-ground buffer between each plot. All applications were made based on the input levels during the growing season. Treatments were applied with a backpack sprayer calibrated to deliver 33 gal/A at 40 psi through TX-18 hollow cone nozzles. Natural infection was relied upon for center rot contamination. Center rot bulb symptoms were assessed 14 days after harvest following incubation at 28℃ and 50% RH. Marketable yield, input costs, and total revenue were calculated for each treatment. The study showed that despite an increase in input cost the high input approach had not only a higher yield but also a higher total revenue.

Rolling Onions that are “Dying Standing Up” to Stop the Rot

Christy Hoepting (cah59@cornell.edu)

Cornell Cooperative Extension Vegetable Program, Albion, NY US

Bacterial bulb rot is one of the most economically important diseases of onion nationally with New York being no exception. Normally, as onion plants mature the neck tissue softens, which allows the foliage to fall over. This is called lodging. When onion foliage is ravaged by disease or insect feeding, it often does not have enough weight to lodge and the plants “die standing up”. Previous studies have shown that onions that die standing up are more likely to rot, presumably because bacterial pathogens living in the soil are introduced by splashing rain into the exposed neck area allowing for bacterial infection to take place. Three on-farm small-plot research trials were conducted to investigate whether the pre-harvest practice of gently rolling onions that are dying standing up could reduce bacterial bulb rot. Rolling onions that were dying standing up reduced bacterial bulb rot by 35-57% compared to those that were left standing in 2 of the 3 trials. In these studies, the onion plants were rolled when they had 30-50% leaf dieback, which was 13 and 24 days before the onions were pulled out of the ground and windrowed. Finally, a cheap, easy and effective tactic to Stop the Rot!

Maggot Mayhem: How to Protect Onions from Maggots in an Era Without Lorsban?

Brian A. Nault¹ (ban6@cornell.edu), Leonardo D. Salgado¹, Alan G. Taylor¹, Mary Ruth McDonald², Rob G. Wilson³, and Timothy D. Waters⁴

¹Cornell University, Geneva, NY USA, ²University of Guelph, Guelph, ON, Canada, ³University of California, Tulelake, CA USA, ⁴Washington State University, Pasco, WA USA

Maggots (Delia antiqua and Delia platura) attack onions across North America and can cause significant plant stand reduction and bulb damage if not controlled. Management of maggots has relied on insecticides applied either at planting as a soil treatment or as a seed treatment, and sometimes both. Chlorpyrifos (e.g., Lorsban) applied in-furrow at planting was a popular choice for maggot control, but its recent banning and paucity of reliable at-plant alternatives leaves insecticide seed treatments as the only option. Research from coast to coast has focused on identifying highly effective insecticide seed treatments for protecting onions from maggots. Our results have identified options that are effective, but not all options are effective across production regions. Guidelines for maggot management in onion for each region as well as strategies for their deployment that should mitigate insecticide resistance development will be discussed.

Efficacy of Chemical and Biological Nematicides for the Management of Stem and Bulb Nematode, Ditylenchus dipsaci, in Garlic

Kevin Vander Kooi (kvander@uoguelph.ca), Tyler Blauel and Mary Ruth McDonald

University of Guelph, Ontario Crops Research Centre – Bradford, King ON L7B 0E9, ON Canada

Stem and bulb nematode (Ditylenchus dipsaci) is one of the most destructive pests of garlic in Ontario, Canada. Conventional nematicides were evaluated and compared to an organic product, Promax (thyme oil). The trials were conducted over three garlic growing seasons (October – July) between 2020 and 2023. All products were applied as a seed clove soak prior to planting. Velum Prime (fluopyram) treatments were applied either as a seed clove soak for two or four hours prior to planting, or an over the row drench at two rates at planting. Efficacy was assessed as emergence, survival, height, symptoms of nematode damage and yield. Incidence and severity of symptoms, and populations of the nematode in cloves and soil, were assessed at harvest. Velum Prime applied as a drench or a seed soak significantly reduced damage and resulted in higher marketable yields. The 2-hour soak with Velum Prime was as effective as the 4-hour soak for disease severity and marketable yield. The organic product did not provide effective control of the nematodes compared to the nematicides. This research has assisted in the recent registration of the drench application of fluopyram for use on garlic in Canada.

Improving Irrigation and Nitrogen Management Practices in California Desert Onions

Jairo Diaz¹ (jdiazr@ucanr.edu), Roberto Soto², and Daniel Geisseler³

¹University of California, Desert Research and Extension Center, ²Universidad Autónoma de Baja California, Instituto de Ciencias Agrícolas, ³University of California – Davis, Department of Land, Air and Water Resources

California is the largest onion producer in the nation. Imperial County onion production is about 13,000 acres. Adoption of improved irrigation and nutrient management practices by growers is needed in order to reduce water usage and water pollution from excess nutrients in California’s low desert region. The main goal of this project was to evaluate the effects of irrigation management and nitrogen fertilization rates on yield and quality of fresh onion bulb production in arid regions. Field assessments were performed during three growing seasons at the University of CA Desert Research and Extension Center – UCDREC, Holtville, CA. Four irrigation levels were established: 40, 70, 100, and 130% of crop evapotranspiration (ETc). Four in-season nitrogen treatments were assessed: 0, 75, 150, and 225 lbs N per acre. Onion size, yields, and total soluble solids (brix) were influenced by irrigation rates. Onion size distribution and total yield did not respond to nitrogen rates when pre-plant ammonium and nitrate (PPAN) in the top foot of the profile ranged from 104 to 353 lb/ac. However, onion size distribution and total yield responded to nitrogen rates in a field with only 54 lb/ac of PPAN in the top foot.

Influencing Soil Temperature to Maximize Onion Yield and Quality

Kyler Beck¹, Mike Thornton² (miket@uidaho.edu), Ransey Portenier², and Oksana Morgan²

McCain Foods¹, Fruitland, ID and ²University of Idaho, Parma, ID

High temperatures during late June of the 2021 growing season were blamed for generally lower onion yield and bulb size across the Treasure Valley region of ID and OR. To explore the relationship between soil temperature and onion crop productivity an experiment was carried out during 2022 and 2023 that sought to modify soil temperatures by addition of materials that reflect (straw mulch, kaolinite clay) or adsorb (charcoal powder, pelleted biochar) sunlight.  The treatments were applied in mid-June and soil temperatures at the 2-inch depth were monitored by Vegetronix sensors placed in the onion row.  Soil temperature in the straw and clay treatments was up to 7^oF cooler than the non-treated check, while the charcoal and biochar treatments increased soil temperature by up to 3^oF. Despite relatively small soil temperature differences among treatments, the charcoal and biochar treatments resulted in significantly lower yields and smaller bulb size compared to the check, while the straw and clay treatments tended to have the highest yields and largest bulb size.  Additional studies are needed to further define the optimum soil temperature for onion growth and the best timing and placement of sunlight reflecting treatments to mitigate the effects of high temperatures.

Adaptation of Agrobotics for Onion Production in High Organic Soils

Geoff Farintosh (jfarinto@uoguelph.ca), Kevin Vander Kooi, and Mary Ruth McDonald

University of Guelph, ON, Canada

The Holland Marsh is home to some of the most intensive agriculture in Canada. While the high organic matter soil is ideal for growing onions, weeds also thrive. The lack of registered herbicides and increasing herbicide resistance necessitates hand-weeding, but with labor shortages and increased costs, growers are looking to alternative methods. Robots such as the FarmDroid FD20 and Naio Orio could provide the solution if they can be adapted to work in onion production. Trials conducted at the Ontario Crops Research Centre – Bradford and in surrounding grower fields evaluated these two robots for growing onions, carrots and beets on a commercial scale. In the first year of the project, the FarmDroid FD20 was used to seed and weed onions on a commercial farm with weed control issues. The Naio Orio was supplemented with a camera-guided hitch attached to a cultivator and a custom twin-boom band sprayer. Data on speed, costs, resources, uptime, crop emergence, weeding efficiency and yield were collected and compared to controls grown using conventional techniques and equipment. Early results show potential for robots to cut down labour costs and increase weeding efficacy, but more data is needed to validate the long-term benefits and true costs.

Spatial Variability of Soil Characteristics are Associated with Vidalia Onion Pungency and Yield

Daniel Jackson¹ (djackso@uga.edu), Jay Lessl¹, and Matt Levi²

¹UGA Agricultural & Environmental Services Labs and ²UGA Crop & Soil Sciences Department

Vidalia onions are short-day, Granex type, sweet yellow onions (Allium cepa (L.) only grown in portions of 20 counties in Georgia, USA and represent an annual farm gate value of $150 million. Previous research has shown that variability in soil properties (e.g. soil type, texture, and A horizon thickness, sulfur concentration) can affect both nutrient availability and onion pungency. This study characterized the spatial variability in soil properties within four onion fields in the region to explore relationships with onion yield and flavor profiles during the 2020 and 2021 growing seasons). Each 25- acre field was sampled on 0.5-acre grids (1-acre grids at the reference Evans County field) to collect matching soil and onion samples. Analyses included soil physical and chemical characteristics, plant nutrient status, onion yield, bulb storability, and the concentrations of flavor-associated compounds within onion bulbs. Results indicated a considerable degree of variability within individual fields for many of the properties analyzed. For example, within the Emanuel County field, the soil A horizon thickness ranged from 15-94 cm, onion dry weights ranged from 37-209 g bulb^-1, and pyruvic acid in the onion bulb ranged from 0.78-6.38 µmole ml^-1. The soil A horizon thickness was identified as major factor in nutrient availability and onion yield and quality, with the depth to the Bt horizon having a significant negative relationship to the concentrations of onion pungency compounds, S content in the soil A horizon, and total plant weight. These results indicate that the physical and chemical differences among soils collected within 25-acre areas of onions fields in GA, is sufficient to affect nutrient availability and alter onion yield and quality at the field scale. This suggests that site-specific fertilizer recommendations and management plans may be needed in the Vidalia region to ensure consistency of onion quality and yield.

Digital Imaging of Onion Bulbs for Selection and Market Class Assignment

Madeline Oravec and Irwin Goldman (ilgoldma@wisc.edu)

Department of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, WI

A digital imaging system developed for the analysis of carrot and beet roots was modified for onion bulb shapes, and fourteen distinct types of onions, based on shape, were quantified in this system. Images include a QR matrix barcode that contains identifying information for the sample as well as a scale for converting pixel measurements to physical distances. Images were acquired with a digital camera, and processed using a set of custom Python scripts which convert RGB images to grayscale. Images were smoothed and used to generate binary masks. Bulb size was measured as the total area of the binary mask. Contour of the lower portion of the bulb was measured as the interior angle formed by the line segments connecting the tip of the bulb to contour points located 10% up the length toward its top, while shoulder area was considered the area encompassed by background pixels in the rectangular region bounding the top 10% of the bulb.  Principal component analysis of the root profile can be utilized to provide measures of variability in shape and size. This phenotyping pipeline allows for for precise characterization of root shape, calculation of various shape parameters, and accurate assignments to market class.

Toward Transgene-Free Gene Editing in Onion

Cameron De La Mora¹, Michael Havey¹, Stephen Jackson², and Patrick Krysan (pjkrysan@wisc.edu)¹

¹Department of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, WI and ²School of Life Sciences, Warwick University, Coventry, UK

Gene editing technology has the potential to allow scientists to develop improved crop varieties.  This technology has been deployed in a wide range of crop species, but there have been few reports of gene editing in onion.  Our research group has been focused on developing protocols that will allow for the production of transgene-free, gene edited onion plants.  The approach that we are taking involves using biolistic transformation to introduce either plasmid DNA constructs that expresses gene editing machinery or Cas9/sgRNA ribonucleoprotein complexes into immature embryo explants from onion.  We have established tissue culture conditions that allow for the efficient regeneration of onion plants from immature embryo explants, and we have also optimized a biolistic transformation protocol for these explants.  Transformation efficiency is monitored using fluorescent protein reporter constructs. Using these protocols, we have demonstrated efficient transient gene editing in onion immature embryos using a cytosine base editor construct targeting the onion centromeric histone 3 (CENH3) gene.  Our interest in targeting the onion CENH3 gene involves the potential for the resulting mutant lines to serve as haploid inducers that may be useful for developing doubled-haploid lines. We are currently working on screening regenerated plants to determine if gene edited plants can be recovered using this approach and will provide an update on our progress towards this goal.

Extraction and Identification of Antifungal Steroidal Saponins to Combat Fusarium Basal Rot in Short-Day Onion Cultivars

Suman Sharma¹, Maha Abutokaikah², F Omar Holguin¹, and Christopher S Cramer (cscramer@nmsu.edu)¹

¹Department of Plant and Environmental Sciences and ²Chemical Analysis & Instrumentation Laboratory, New Mexico State University, Las Cruces, NM, USA

Fusarium basal rot (FBR), one of the most destructive diseases of onion, is caused by the soil-borne fungus Fusarium oxysporum f. sp. cepae (FOC). FBR-resistant cultivars are yet to be developed for short-day onions. An effective biochemical screening may speed up the process for selecting FBR-resistant onions. Steroidal saponins are a group of secondary metabolites in Alliums possessing antifungal activity. The study aimed to identify saponins involved in FBR resistance. In this experiment, selected populations of three New Mexican short-day onion cultivars along with two checks, ‘NuMex Crimson’ (FBR-susceptible) and ‘Serrana’ (partially FBR-resistant), were planted in a randomized complete block design with four replications. Artificial inoculation was performed on mature bulbs via a conidial inoculation by applying the virulent FOC isolate and were rated for FBR severity on 21^st day after inoculation. Saponins were extracted by collecting tissue samples at 0, 5, 10, and 15 days after inoculation from FOC-inoculated and uninoculated basal plates which were analyzed using ultra high-performance liquid chromatography coupled with high-resolution mass spectrometry. Twenty-six out of 42 previously identified saponins were differentially expressed among populations. Two potential saponins were identified based on their negative correlation with FBR severity which might be responsible for imparting FBR resistance.

High-Throughput Phenotyping for Estimating Thrips Damage and Iris Yellow Spot Severity on Onion Foliage

William Peebles (wpeebles@nmsu.edu) and Christopher S. Cramer

¹Dept. of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM

High-throughput phenotyping methods using aerial imagery to estimate disease severity in other crop species have successfully replaced visual scoring methods due to increased measurement precision and accuracy. Because onion foliage is vertically oriented and thrips damage and Iris yellow spot (IYS) require high image resolutions to identify lesions, existing high-throughput workflows using orthomosaic image analysis are poorly suited for estimating thrips damage and IYS in onion. To address these challenges, we developed a phenotyping method using high-resolution RGB imagery collected at multiple angles near the plants, processed into 3D leaf models where leaf area was classified as healthy, unhealthy, thrips damage, or IYS using colorimetric and texture-based image analysis approaches. Severity of thrips damage and IYS was determined as the percentage of total leaf area classified as thrips damage or IYS. This method produced comparable results to visual disease scoring as well as image-based disease scoring using the same image analysis approach on destructively harvested leaf samples. Because this method is highly accurate and non-destructive, plant breeders and trial evaluators can make finer selections for thrips and IYS-resistant breeding lines and may also be able to estimate disease severity of other foliar diseases of onion.

Genetic Analyses of Day-Length Effects on Bulbing Of Onion

Michael J. Havey (mjhavey@wisc.edu)

Department of Plant and Agroecosystem Sciences, University of Wisconsin, Madison WI

The formation of onion bulbs is affected by day length and onion germplasm is commonly classified as short- (SD), intermediate, or long-day (LD) types.  In this study, a segregating family from the cross of doubled haploids (DH) of LD and SD onions was used for genetic analyses of day length effects on bulbing.  Segregating progenies and DH parents were grown in a greenhouse under lengthening days and the diameters of the neck constriction and pseudostems were measured weekly, and a bulbing index was calculated.  Single nucleotide polymorphisms (SNPs) were genotyped and a genetic map of 112 SNPs was constructed.  Genetic analysis revealed two highly significant quantitative trait loci (QTL) affected bulbing under increasing day lengths; both QTL showed significant additive effects with no dominance.  The potential relationship will be discussed between these QTL and the FT homologs known to affect bulbing under different day lengths.