W4008: Integrated Onion Pest, Disease and Weed Management

(Multistate Research Project)

Status: Active

W4008: Integrated Onion Pest, Disease and Weed Management

Duration: 10/01/2022 to 09/30/2027

Administrative Advisor(s):

NIFA Reps:

Non-Technical Summary

Statement of Issues and Justification

Onion, Allium cepa, is the third most consumed vegetable in the U.S., behind tomato and potato. The per capita consumption of onion in the U.S. is over 20 pounds per year, which has increased 70% over the past 20 years (https://www.onions-usa.org/all-about-onions/consumption). Onion also is one of the most economically important specialty crops with a farm-gate value averaging nearly $1 billion per year over the past 5 years (USDA NASS 2021) and over $70 million in added value after processing. In addition, over 20% of the world’s onion seed is produced in the U.S. and is valued at over $100 million per year. More than 138,000 acres of onions have been harvested annually over the past 5 years and the crop is grown in over 20 states with a majority produced in California, Idaho-Eastern Oregon and Washington in the west, Texas and New Mexico in the south, and Georgia and New York in the east (USDA NASS 2021).

The need as indicated by stakeholders. Onion crops are damaged by a spectrum of pests and pathogens throughout the U.S. For example, infestations of fly maggots (Delia spp.) can reduce plant stands by over 50% if not controlled (Nault et al. 2006), while a new invasive fly pest (Phytomyza gymnostoma) is raising concern (Barringer et al. 2018). Onion thrips (Thrips tabaci) feeding damage can reduce bulb yield by up to 30 to 50% (Fournier et al. 1995; Leach et al. 2020b) and it also spreads pathogens that cause devastating diseases like Iris yellow spot (IYS, caused by Iris yellow spot virus) (Gent et al. 2004, 2006; Bag et al. 2014), Stemphylium leaf blight (SLB, caused by Stemphylium vesicarium) (Leach et al. 2020a) and bacterial bulb rots (Grode et al. 2017, 2019). Multiple fungal and bacterial pathogens can cause onion yield losses in the field and in storage facilities throughout the U.S. (Schwartz and Mohan 2008). Each disease can cause up to 25 to 100% crop loss. The most important fungal diseases include SLB, purple blotch (Alternaria porri), downy mildew (Peronospora destructor), black mold (Aspergillis niger), Botrytis leaf blight (Botrytis squamosa) and neck rot (Botrytis species), Fusarium basal rot (FBR) (Fusarium oxysporum f. sp. cepae), white rot (Sclerotium cepivorum), pink root (Pyrenochaeta terrestris) and powdery mildew (Leveillula taurica). The most important bacterial diseases include sour skin (Burkholderia cepacia), slippery skin (Burkholderia gladioli pv. Alliicola), center rot (Pantoea ananatis and P. agglomerans), leaf streak (Pseudomonas viridiflava), soft rot (Pectobacterium carotovorum and Dickeya spp.), and Enterobacter bulb decay (Enterobacter cloacae). Serious weeds include yellow nutsedge (Cyperus esculentus), ragweeds (Ambrosia spp.), pigweeds (Amaranthus spp.), lamsquarters (Chenopodium album), perennial sowthistle (Sonchus arvensis) and others. Growers continue to abandon onion production in some regions because one or more of these organisms have caused catastrophic losses. Consequently, we propose to address managing the most serious pests, diseases and weeds of onion through the following objectives: 

  • Evaluate onion germplasm for resistance to pathogens and insects.

  • Investigate the biology, ecology and management of onion insect pests.

  • Investigate the biology, epidemiology and management of onion plant pathogens.

  • Investigate the biology, epidemiology and management of weedy plant species that impact onion production. 

Importance of the work, and consequences if it is not done. The work proposed is critical for solving the most important pest, disease and weed problems facing the U.S. onion industry. We are not aware of other public or private entities that will be as organized across state borders to solve these problems as the W4008 group, particularly given the successful foundation set by the preceding multistate onion projects (W1008: Biology and Management of Iris yellow spot virus (IYSV) and Thrips in Onions, from 2005-2010; W2008: Biology and Management of Iris yellow spot virus (IYSV), Other Diseases and Thrips in Onions, from 2011-2016; and W3008: Integrated Onion Pest and Disease Management, from 2017 to 2022). The most significant change to our proposed multistate project is that we will include a weed biology and management objective. Similar networking successes are anticipated for weed scientists working in onion cropping systems across the country, just as they have occurred with entomologists and plant pathologists during our previous multistate projects. 

We expect that results from our research and extension activities will continue to contribute significantly to science and agriculture as we communicate new knowledge about the biology, ecology and management of these pests, pathogens and weeds through peer-reviewed publications, presentations at professional meetings, field days, and web-based resources for stakeholders. Consequences of not addressing these significant issues include further reductions in U.S. onion acreage due to limited ability to manage the pests, diseases, and weeds mentioned above, reduced profits as a result of decreased bulb yields, reduced quantities and/or qualities of onion seed produced, greater competition from other regions of onion bulb and seed production in the world, and greater pesticide and fertilizer inputs, as well as potential environmental and human health concerns associated with greater fertilizer and pesticide use. 

Technical feasibility of the research. Participants of our proposed project will include researchers at institutions that have the resources, laboratories, land for research and personnel required to conduct the studies described herein. Project objectives are designed to include short-term, medium-term, and longer-term research studies that should reasonably be completed within the 5-year duration of this project. A majority of the members of this project have a proven track record of effective, collaborative onion research and extension programs, including involvement in the W1008, W2008, and W3008 multistate projects that laid the foundation for the next iteration, the W4008. 

Advantages for doing the work as a multistate effort. The principal advantage of doing this work as a multistate effort is that this proposal builds on three previous, highly successful multistate projects that were described above. Indeed, the W3008 project team was awarded the 2018 Excellence in Multistate Research Award given by the Western Association of Agricultural Experiment Station Directors. We anticipate that participants of our proposed project will continue to include most of those who are leaders in their respective areas of onion breeding, horticulture, entomology, plant pathology, virology, microbiology, and weed science. Past participants have included public and private researchers, extension professionals, onion growers and seed industry personnel throughout the U.S. who have formed productive collaborations. Many of the problems affecting onion production occur in most regions in the U.S., so our project brings together those with similar interests in solving the issues. The proposed research is synergized by interactions this group has developed over the past 17 years, which we anticipate will continue. The research and extension contributions from members in all major regions of onion production in the U.S. adds efficiency, pooled expertise, and synergies that are greater than the sum of each individual research and extension program. At least three multi-state, multi-disciplinary, 4-year proposals funded by the USDA NIFA Specialty Crops Research Initiative were developed as a result of collaborations in the W1008, W2008, and W3008 multistate projects, and we anticipate continued success of this group at garnering such resources to address the pests, diseases, and weed issues of concern to onion stakeholders across the country. 

Likely impacts from successfully completing the work. This project is expected to have positive impacts on the economy, environment and society. The cost of onion production should be reduced through implementation of new management tactics that utilize new onion cultivars with greater resistance to thrips, IYSV and FBR, and reduced inputs such as pesticides and fertilizers. More judicious use of insecticides, fungicides, bactericides, herbicides, action threshold-based pesticide application programs, and optimal pesticide application techniques and strategies that mitigate insecticide, fungicide, and herbicide resistance risks will contribute directly to improved environmental stewardship and sustainability. This project is expected to enhance our understanding of how cultural practices can be optimized to mitigate the risks of these pests, diseases, and weeds, further contributing to reduced expenses and enhanced environmental stewardship. Society will benefit from the training of graduate and undergraduate students as well as post-doctoral associates working with faculty on this project, preparing the next generation of researchers, extension specialists and agricultural professionals in public roles and private industries who will shape the future of production agriculture.

Related, Current and Previous Work

We seek to continue the success of previous multistate projects (W1008, W2008, and W3008) by broadening the scope of this project to include new studies for solving the U.S. onion industry’s most important problems. Below are notable accomplishments over the past five years. 

Breeding for disease and insect resistance. The most promising and sustainable means for long-term onion thrips and IYSV management is deploying cultivars with resistance or tolerance to both. In New Mexico, several second-generation breeding line selections (NMSU 12-279, 12-255, 12-258, 12-289, and 12-298) derived from plant introduction accessions exhibited fewer thrips per plant than their first-generation breeding lines and a thrips-attractive cultivar, Rumba (Singh and Cramer 2019). In more locally adapted germplasm, breeding lines NMSU 12-236, 12-239, 12-243, 12-335, 12-337, and 12-796 that were selected twice for reduced IYS expression exhibited less severe disease and fewer thrips than their unselected populations and ‘Rumba’ (Kamal et al. 2021). Using standard commercial practices for thrips management in Oregon, three advanced lines (NMSU 14-81, 14-208 and 14-240) had lower thrips densities and IYS damage than several commercial cultivars (Reitz et al. 2016). Recent research in other countries have shown some resistance or tolerance to onion thrips in onions. In India, ‘NIKSP-86’, ‘T-821’, and ‘Ceylon’ were characterized as resistant to thrips (Raut et al. 2020). Cultivars Vale Ouro IPA 11, BRS Alfa São Francisco, Franciscana IPA 10, and Sirius F1 produced large average bulb yields while under thrips pressure when grown in semi-arid regions of Brazil (de Oliveira et al. 2017). In Tanzania, breeding lines VI038512 and AVON 1067 were characterized as resistant, while VI038552 was characterized as highly resistant (Njau et al. 2017). In Texas, short-day sweet onion germplasm TAM Experimental (Expt) #31034 (2 thrips per plant) showed tolerance to thrips compared with TAM Expt #50153 (17 thrips per plant) at Uvalde, TX whereas TAM Expt #50014 and TAM Expt #50084 (2 thrips per plant) were tolerant to thrips as compared to TAM Expt #40051 (45 thrips per plant) at Weslaco, TX. More research is needed to elucidate these results. 

With regards to breeding for reduced IYS disease symptoms, breeding lines NMSU 10-575-1, 10-577-1, and 10-582-1 selected from PI accessions exhibited less severe IYS symptoms than those accessions when all were grown using conditions conducive for disease development (Singh and Cramer 2019). Gains for reduced IYS symptoms have also been observed after one or two cycles of selection within onion germplasm adapted to growing in New Mexico (Kamal and Cramer 2018; Kamal et al. 2021). Onion breeding efforts in the US must develop cultivars that are highly resistant to IYSV and thrips. Until such cultivars become available commercially, more effort is needed to evaluate existing cultivars for thrips and IYSV resistance. 

Fusarium basal rot (FBR) is a devastating soilborne disease of onion in which complete resistance is limited in all onion germplasm pools. Research efforts have focused on developing FBR-resistant onion germplasm. In New Mexico, a new technique was developed for advancing resistance development efforts (Mandal and Cramer 2020) that was an improvement over currently used screening methods (Mandal et al. 2020). Through multiple cycles of phenotypic recurrent selection using artificial inoculation of fungal conidia, FBR severity and incidence were reduced in several NMSU cultivar populations (Mandal and Cramer 2021b). Additional sources of potential resistance to FBR were identified in several PI accessions using mature bulb and seedling screening methods (Mandal and Cramer, 2021c). The use of digital image analysis for FBR disease scoring has been shown to be as accurate as visual scoring and may offer additional benefits in developing FBR cultivars (Mandal and Cramer 2021a). An evaluation and selection of onion germplasm for FBR resistance utilizing a seedling screening resulted in the identification of quantitative trait loci on chromosomes 2 and 4 associated with resistance (Straley et al. 2021). These studies should help in the development of onion germplasm that is resistant to FBR. 

Pink root continues to be a major soilborne disease in onion. In Texas, a preliminary study was designed to evaluate 23 TAM elite germplasm lines for pink root resistance. Yellow H6 had the least pink root severity (10%) followed by TAM Expt #31034 (18%). TAM Expt #34036 had the highest disease severity of 85%. An additional 220 TAM preliminary lines also were evaluated for pink root resistance. Ten germplasm lines (TAM Expt #: 33015, 40026, 40027, 40060, 40061, 40066, 40067, 90519, 92007 and 92021) had pink root severity ratings of only 5%, indicating that these lines have resistance against the disease. 

Onion thrips ecology and management. Advancements were made in understanding interactions between onion thrips and major pathogens of onion that cause IYS, SLB and bacterial bulb rot. In a controlled experiment study, onion thrips adults infected with IYSV lived 1.1 to 6.2 days longer (average of 3.6 days) than non-viruliferous adults, which lived for 16.6 ± 0.9 days (Leach et al. 2019a). Fecundity of viruliferous and non-viruliferous onion thrips was similar with 2.0 ± 0.1 and 2.3 ± 0.3 larvae per female per day, respectively. Consequently, the longer lifespan of viruliferous onion thrips adults may allow them to infect more plants, thereby exacerbating IYSV epidemics (Leach et al. 2019a). Because IYSV epidemics continue to be common in some production regions, the role of various habitats contributing to viruliferous onion thrips populations and IYSV epidemics were explored in New York onion fields. The abundance of dispersing onion thrips adults, including those that were viruliferous, was recorded from habitats known to harbor both IYSV and its vector. While viruliferous thrips were encountered in all habitats, transplanted onion fields accounted for 50% of the total estimated numbers of viruliferous thrips in the cropping system (Leach et al. 2018). During early to mid-season, transplanted onion sites had 9 to 11 times more viruliferous thrips than the other habitats (Leach et al. 2018). Results indicated that transplanted onion fields were the most important habitats for generating IYSV epidemics, suggesting that growers should control thrips in transplanted fields early in the season to minimize risk of IYSV epidemics later in the season. Research is needed to evaluate the impact that early-season thrips control in transplanted onion fields has on the incidence of IYSV later in the season. 

In a controlled environment study, onion thrips transferred S. vesicarium conidia to onion plants resulting in 2 to 14% of plants becoming infected (Leach et al. 2020a). Additionally, a reduction in onion thrips feeding decreased S. vesicarium colonization of onion leaves by 2.3 to 2.9 times, resulting in a 40–50% reduction in leaf dieback. In field trials in New York, the use of insecticides to control thrips reduced symptoms and colonization of SLB by 27 and 17%, respectively (Leach et al. 2020a). 

Onion plants inoculated with the bacterial pathogen, P. ananatis, and then infested with varying densities of onion thrips in a controlled environment showed more symptoms of bacterial disease as thrips density increased (Grode et al. 2017). Similarly, onion thrips densities were positively correlated with increasing incidence of bacterial disease caused by the pathogen P. agglomerans in Michigan onion fields (Grode et al. 2019). While insecticide use to reduce onion thrips infestations was suggested as an approach to mitigate bacterial disease (Grode et al. 2019), the incidence of bacterial bulb rot in commercial onion fields in New York was reduced in only one of four trials when insecticides were used to reduce onion thrips infestations. More research is needed to elucidate the role that thrips management may have in reducing bacterial bulb rot incidence (Leach et al. 2020b). 

Onion thrips and bacterial bulb rot are primary constraints to onion production, and choice of onion cultivar, fertility regime and insecticide use may be important tactics for managing both. In New York onion fields containing muck soils that are high in organic matter, experiments were conducted to evaluate the impact of a moderately thrips-resistant onion (cv. Avalon), multiple nitrogen and phosphorous fertilization regimes, and a season-long, action threshold-based insecticide program on thrips abundance and bacterial rot incidence (Leach et al. 2020b). Results indicated that Avalon experienced lower thrips densities, but suffered 58% more bacterial rot, which reduced onion yields overall by 9%. Nitrogen and phosphorus fertilizer had limited impact on onion thrips abundance, incidence of bacterial bulb rot, and onion yield. For example, thrips abundance was not impacted by the amount of fertilizer applied. Nitrogen fertilizer additions increased bacterial bulb rot in one of two years. In both years, low rates of fertilizer (67 kg/ha N or 56 kg/ha P) produced statistically similar yields to plants supplemented with highest rates of fertilizer. Insecticide use reduced thrips densities and increased bulb yield in both years, but did not consistently reduce bacterial bulb rot. Results indicated that IPM programs should be evaluated to consider multiple biotic constraints simultaneously within the onion production system as IPM tactics can be counterproductive. Additional research is needed to identify new management tactics for onion thrips that do not exacerbate damage by other pests and diseases in the crop. 

Among the various IPM tactics evaluated for onion thrips control in conventional and organic onion production systems, insecticides continue to be the most effective and reliable tool (Leach et al. 2017, 2020b; Iglesias et al. 2021b). In most conventional onion fields, abamectin, cyantraniliprole, spinetoram, spirotetramat and co-applications of methomyl and lambda-cyhalothrin continue to work reasonably well (Harding and Nault 2021, Moretti and Nault 2019, Waters and Darner 2017). For onion thrips management in organic onion fields, spinosad is the most effective, especially when co-applied with neem oil (Iglesias et al. 2021a). No new, highly effective insecticide active ingredients were registered on onion for onion thrips control over the past five years. However, isocycloseram (PLINAZOLIN® technology) has been highly effective in research trials and should be commercially available for thrips control in onion in the near future. 

The possibility of resistance to insecticides used for onion thrips control continues to be a concern for growers. Adesanya et al. (2020) reported onion thrips resistance to methomyl and abamectin in the western US. In New York, there was concern that onion thrips populations were developing resistance to spinetoram, but results showed that populations were susceptible when evaluated in laboratory bioassays (Moretti et al. 2019, Yannuzzi et al. 2021). 

Onion thrips management has been improved by developing a program based on two insecticide resistance management (IRM) principles: rotating classes of insecticides during the growing season and applying insecticides following an action threshold (Leach et al. 2019b). In New York, onion growers (n=17) increased their adoption of insecticide class rotation from 76% to 100% and use of the action threshold for determining whether to apply insecticides from 57% to 82%. Growers who always used action thresholds successfully controlled onion thrips infestations, applied significantly fewer insecticide applications (1-4 fewer applications) and spent $148/hectare less on insecticides compared with growers who rarely used the action threshold. Growers who regularly used action thresholds and rotated insecticide classes did so because they were primarily concerned about insecticide resistance development in thrips populations. Similar success has occurred in eastern Oregon where this IRM-based thrips management strategy has resulted in fewer insecticide applications and similar yields compared with a calendar-based application strategy. More effort is needed to develop extension-based programs that involve regular and interactive meetings with growers in other production regions to increase their adoption of IRM and related integrated pest management tactics. 

Fungal pathogens and management. Stemphylium leaf blight (SLB). SLB is capable of causing severe defoliation to onion crops in disease-conducive years. SLB occurs annually throughout New York (Hay et al., 2019, 2021) and is an emerging threat to onion production regions in Michigan, Georgia and the Treasure Valley of eastern Oregon and southwestern Idaho. Control of SLB using fungicides can result in a 33-40% increase in bulb weights and a 29% increase in the number of jumbo grade (>7.6 cm diam.) bulbs (Hoepting 2018a, 2018b). Growers earn a premium for larger bulbs and this has been particularly important in PA where either a 40 lb-box or 4 lb bag of jumbo-sized and colossal-sized bulbs are worth ≥ $1/lb more than standard-size bulbs. Management of SLB has become challenging in New York because populations of S. vesicarium have rapidly developed resistance to several fungicides with different modes of action including the FRAC 2, 7, 9 and 11 groups (Hay et al., 2019, 2021). Some fungicides, such as the FRAC 7 boscalid (Endura) and fluxapyroxad (in Merivon) and FRAC 11 azoxystrobin (Quadris) have been rendered almost completely ineffective, and can no longer be used alone for SLB control. Other fungicides, such as the FRAC 7, fluopyram (in Luna Tranquility), FRAC 2 (iprodione in Rovral) and FRAC 9 (pyrimethanil in Scala) have shown a substantial reduction in field efficacy over the years, but still provide some level of control. Similarly, fungicide resistance to the major fungicides used to control SLB has been observed in the Treasure Valley (OR/ID). Currently in New York, the FRAC 3 fungicide active ingredients tebuconazole (a component of Viathon and Luna Experience), propiconazole (the active ingredient of Tilt) and difenoconazole (a component of Quadris Top and Inspire Super) are the most effective fungicides against SLB. However, it appears that the FRAC 3 group is also under threat as disease control only can be achieved using high rates of combinations of FRAC 3 products (e.g. Viathon + Tilt). The development of widespread fungicide resistance to SLB in New York has occurred despite considerable adoption of fungicide resistance management strategies. The severity of SLB can be exacerbated by other abiotic (e.g. herbicide burn) or biotic (diseases and pests) stresses on onion. For example, onion hrips damage also has been shown to increase the severity of SLB (Leach et al., 2020a). 

Botrytis leaf blight (BLB). BLB is another common and often severe leaf disease of onion in many U.S. production areas. Recently in Georgia, B. squamosa was the principal contributor to an estimated 2.5% reduction in onion crop value amounting to $2.4 million dollars. BLB is primarily managed using fungicides. Historically, this has been through the use of the protectant chlorothalonil (Bravo), which has multi-site modes of action, and low risk for fungicide resistance. However, co-applications of chlorothalonil with insecticides reduces the efficacy of the insecticides (Nault et al. 2013). Growers are now utilizing other fungicides in FRAC groups 2, 3, 7 and 9, with single-site modes of action for control of BLB, which increases the risk for resistance development. For example in New York,  recent on-farm trials evaluating Rovral (FRAC 2) and Scala (FRAC 9) resulted in poor or no control of BLB in Oswego Co., (2018, 2020), Elba (2019) and Wayne Co., (2019) (Hoepting, pers. comm.). Resistance of BLB to Rovral (FRAC 2) has also been reported in Quebec and in Ontario, Canada (Hervé van der Heyden). In Georgia, there are reports of reduced efficacy of Rovral (FRAC 2), Scala (FRAC 9) and Quadris Top (FRAC 3 against SLB, but resistance has not been confirmed. There is an urgent need to determine the status of fungicide resistance to BLB, and to develop strategies to manage it. 

There is a need to identify fungicides that are effective against BLB, especially when co-applied with insecticides without compromising insecticide efficacy, and that belong to different FRAC groups. Recent on-farm trials in New York have indicated that the multi-site protectant Mancozeb (FRAC M3) is effective when used at a low rate (1 lb/A) when BLB is first detected, rather than using the common industry standard at higher rates (up to 3 lb/A) and an action threshold of 1 BLB spot/leaf (Hoepting, pers. comm.). Similarly, Lifegard (FRAC P06), Oso (FRAC 19) and Howler (FRAC PM02) have shown some efficacy against BLB in New York field trials (Hoepting pers. comm.). Other products (e.g., fenpicoxamid) also need to be evaluated. 

To improve management of BLB, the symptomatology of the disease needs to be better understood. When BLB first occurs in June and early July, lesions appear as tiny yellow necrotic spots surrounded by a silvery halo (= BLB halo). Often, the necrotic spot in the center of the lesion is absent, leaving just the silvery halo. During the second half of July, BLB lesions often do not have the silvery halo. Instead, they have yellow spots, sometimes yellowish-white spots as they get larger, with a round defined border, that are pin-prick to 1 mm or slightly larger in size (= BLB necrotic spots). By August, BLB necrotic spots are dominant, while BLB halos are difficult to find, especially in western New York. BLB halos tend to linger for the duration of the season in central New York (Hoepting pers. comm.). BLB necrotic spots become severe in appearance during August, but the effect on yield is unclear. The relationship between BLB halo spots and BLB necrotic spots is also unknown. Recently, differences in efficacy among fungicides were observed for control of BLB halo and BLB necrotic spots. Inspire Super had the most striking results where it failed to control BLB halos, but was the best fungicide in the trial for control of BLB necrotic spots (Hoepting pers. comm.). Evaluation of fungicides against both BLB halo and necrotic spots, including optimizing fungicide timing, is necessary to identify proper fungicide placement in programs for effective season-long BLB control. 

BLB halos and necrotic spots likely exacerbate the incidence and severity of SLB. Attempts to ascertain this relationship have yielded mixed results in New York. In 2019, there were moderate positive correlations between final SLB severity ratings and BLB halo lesion abundance on 3-5 July and total BLB halo + necrotic lesions on 7-9 August, which indicated that BLB may predispose onion plants to increased infection by SLB. There is a need to determine the effect of BLB severity mid-season on SLB severity later. The extent of this relationship will dictate the importance of BLB control and consequent fungicide recommendations. 

Fusarium bulb rot. In 2021, several growers in Utah lost 20-30% of their onions after harvest from Fusarium bulb rot caused by Fusarium proliferatum. This disease does not occur very often and therefore little is known. The affected growers need recommendations on how to prevent and manage this disease. A survey of growers will be undertaken to better understand the prevalence of Fusarium bulb rot, and the relationship between grower practices and weather on disease severity. In addition, field trials will be undertaken to evaluate fungicides and examine topping procedures as a means of providing management options. 

Pink root. Pink root is caused by a soil-borne fungus that infects onion roots, causing a pink to purple discoloration. Roots are killed leading to poor uptake of water and nutrients and small bulbs and low yields. Pinkroot is managed through expensive fumigation in the Treasure Valley. There is a need to develop and integrate methods of soil testing for pink root to improve its management. 

White rot. White rot is a devastating fungal disease spread by small sclerotia produced on decayed bulbs and roots. As few as one sclerotium per liter of soil can result in significant crop losses. Control of white rot is difficult because sclerotia survive in fields for 30 years or more, remaining dormant in the absence of Allium hosts and germinating only in response to compounds released from Allium roots. Sclerotia reductions of up to 90% have been observed when certain sulfur-containing compounds (specifically diallyl-disulfide, or DADS) or products containing DADS (e.g. garlic oil) are applied to fields in the absence of an Allium host, which results in sclerotia germination and death. A previous study was conducted to encapsulate diallyl disulfide and garlic oil with β-cyclodextrin to protect oil volatiles against oxidation, heat, and light degradation and evaporation, and inclusion complexes between DADS or garlic oil and β-cyclodextrin were prepared by the co-precipitation method. A laboratory trial was conducted to evaluate encapsulated garlic oil and DADS. Both the dry and wet formulations of encapsulated garlic oil and DADS reduced sclerotia counts by approximately 75%, similar to the standard DADS-treated control under laboratory conditions. More research is needed before commercialization of this material. 

Bacterial bulb rots (multiple pathogens). The American Phytopathological Society lists >10 bacterial diseases of onion caused by >16 bacterial genera and species (Schwartz and Mohan 2008). These pathogens cause diverse foliar diseases and bulb rots that cause losses in all U.S. onion production regions because highly effective management strategies are not available (Schwartz and Mohan 2008; Schwartz et al. 2012). These pathogens are estimated to cause >$60 million/year in losses to the U.S. onion industry. The ability to manage bacterial diseases is limited compared to many fungal diseases because of unique epidemiological and management aspects of bacteria. Losses can be particularly severe for stored onions as bacterial bulb rots primarily develop after bulbs are harvested and placed in storage, i.e., all production costs have been incurred, with losses ranging from 5 to 100% for individual fields. Onion grower and packer losses from bacterial rots, and research and extension efforts to address these losses, have been a primary feature in the last 5-10 years at meetings of the National Onion Association (NOA) and National Allium Research Conference (NARC). Several W3008 members developed a USDA NIFA Specialty Crops Research proposal to garner resources for comprehensive research and extension to mitigate losses to bacterial diseases of onion. The proposal was funded in 2019 and has fostered very productive collaborations across the U.S. 

The spectrum of bacteria that cause losses in onion differs among regions of onion production in the U.S. (Schwartz and Mohan 2008). Burkholderia cepacia, which causes sour skin, is prevalent in the Midwest, northeast, and southeast but is uncommon in the inland Pacific Northwest. Burkholderia gladioli pv. alliicola causes slippery skin and is very prevalent in western states. Onion growers in many areas battle Enterobacter cloacae and related species that cause Enterobacter bulb decay, but these pathogens are less virulent than Burkholderia spp. and Pantoea spp. (Schroeder et al. 2010). Xanthomonas axonopodis pv. allii occurs primarily in the Rocky Mountains and southeast, causing a leaf blight but not a bulb rot. Pantoea ananatis causes center rot and is prevalent in the northeast, southeast, Midwest, and Rocky Mountain states, but not in the Pacific Northwest. P. agglomerans causes bacterial stalk and leaf necrosis and bulb rots in all onion production regions of the U.S. Furthermore, onions often are colonized by a complex of bacteria, including non-pathogenic bacteria, which can confound the ability to determine accurately which bacterium (bacteria) initiated development of the disease. This is particularly true given the lack of robust DNA-based detection methods for a majority of bacterial pathogens of onion, particularly for species that have both pathogenic and non-pathogenic strains, such as P. agglomerans. 

Bacterial bulb rots are difficult to manage when weather conditions favor bacterial pathogens because of the lack of highly effective, systemic bactericides. Coppers (e.g., copper hydroxide) are the most effective bactericides available to onion growers, but they have limited efficacy at best (Schwartz and Mohan 2008). These bactericides are purely protectant, i.e., they cannot cure existing infections, are not absorbed into plant tissues, and must be applied prior to colonization of plants by bacteria to prevent disease outbreaks. In multiple years of field trials in various states, applications of copper hydroxide and other bactericides, biocontrol products, and disinfectants either did not control bacterial bulb rots, even when applied weekly, or were inconsistent among seasons in their level of efficacy (e.g., Dutta and Foster 2021; Dutta et al. 2020; du Toit et al. 2021c; Hoepting et al. 2021). Additional management strategies are being evaluated to reduce losses from bacterial bulb rots, with a focus on late-season cultural practices such as the timing of topping, undercutting, and rolling of tops (du Toit et al. 2021b); careful irrigation frequency and quantity as well as nitrogen application quantity and timing during the second half of the season (Belo et al. 2021; Pfeufer 2014); selection of irrigation methods (da Silva et al. 2021); selection of bulb harvest equipment and methods (Dutta and Tyson 2021a, 2021b); effective control of thrips as mentioned above (Dutta et al. 2014; Stumpf et al. 2021.); and postharvest applications of disinfectants to onion bulbs (du Toit et al. 2021a). In plasticulture systems, reflective or silver-on-black plastic mulches reduce soil temperature, which reduces bacterial disease incidence at harvest (Pfeufer 2014). The relationship between in-season foliar nitrogen tissue levels and loss at harvest and post-harvest is being examined so that growers can make harvest timing and marketing decisions (Mazzone 2017). Similarly, if foliage is infected with bacteria late in the growing season, there is a possibility of preventing bulb infection by harvesting early; however, this often means sacrificing bulb size for marketability. In Pennsylvania, a visual bacterial disease severity rating scale on foliage effectively predicted disease incidence at harvest. This tool was validated on commercial farms and will help growers determine when to harvest to minimize rot. 

The severity of bacterial bulb rots caused by E. cloacae, B. gladioli pv. alliicola, and B. cepacia during postharvest curing were exacerbated by high temperature and duration of curing (Schroeder and du Toit 2010, Schroeder et al. 2012). Bulb rot was most severe at high temperatures (35-40°C vs. 25-30°C) and when cured for 14 versus 2 days prior to cold storage. Severity of bulb rot was greater with a longer duration of storage after curing, and the effects were greater for cv. Vaquero than Redwing. Therefore, postharvest curing at <35°C for a limited duration should reduce severity of these bacterial rots in storage. When storage cultivars were evaluated in Washington for resistance to Enterobacter bulb decay, cvs. Redwing, Red Bull, T-433, Centerstone, and Salsa had low bulb rot severity ratings, whereas cvs. Montero, OLYS05N5, Caveat, and Granero had severe bulb rot ratings (Schroeder et al. 2010, Wohleb et al. 2012). Field trials in Washington in 2020 and 2021 were designed to evaluate a method of screening onion cultivars for relative susceptibility to bacterial pathogens when grown with overhead irrigation that does not confound maturity of the cultivar with the timing of inoculation and susceptibility to bacterial pathogens (du Toit et al., unpublished data). In Georgia, a collection of >600 Allium accessions is being screened for resistance to P. ananatis to try and identify germplasm with resistance that can be utilized in onion breeding programs (Dutta et al., unpublished data). 

Ecology and management of weedy plant species that impact onion production. Onion is a very poor competitor with weeds as onion accumulates biomass at a much slower rate than weed species. Research has demonstrated that a few weeds in an onion field, especially during the first few weeks of onion growth, may reduce stands and bulb yields. Losses from uncontrolled weeds in onions can be severe with some control failures resulting in total crop loss or crop abandonment. Nationwide, there are over 56 weed species that interfere with onion production (Nissen and Waters 2013). Among them, yellow nutsedge (YNS), Cyperus esculentus, is the most common and difficult to control (Hoffmann et al. 1996; Nissen and Waters 2013). YNS is an aggressive perennial weed that belongs to the sedge family and has an extensive underground system of specialized roots and tubers that gives it extraordinary survival and reproductive capacity. One plant can produce several hundred to several thousands of tubers during a single growing season, and each tuber can produce two or three more plants. More research is needed to manage this weed. 

Use of herbicides is the first line of defense for managing weeds in conventional onion production with pre-emergent herbicides pendimethalin (WSSA group 3) and metalochlor/dimethenamide (WSSA group 15) and post-emergent herbicides oxyfluorfen (WSSA group 14), flumioxazin (14) and bromoxynil (WSSA group 6) being the most commonly used nationwide. Herbicide programs for onions can vary widely among different production systems (summer, overwinter, direct seeded, transplanted), soil types (sandy, loam, muck, etc.) and climatic conditions. Optimal weed control in onions includes striking the perfect balance between effective weed control and minimal crop injury. There has been a paucity of new herbicide modes of action. Consequently, identifying solutions to current weed control issues has involved developing programs that include tank mixes, improved timing, new formulations and strategies using existing herbicides. Also, various active ingredients that were initially dismissed for onion production such as bicyclopyrone (WSSA group 27), pyroxasulfone (WSSA group 15) and linuron (WSSA group 7) are now being revisited and reformulated for improved crop safety. 

The economic stimulus to the herbicide industry caused by the evolution of herbicide-resistant weeds, especially glyphosate-resistant weeds and modern methods of target site discovery are beginning to yield new herbicide modes of action that will need to be evaluated for their suitability in onion. For example, in New Mexico, 11 herbicide programs that included registered and potential new herbicides were evaluated to find cost-effective weed control programs (Schutte et al. 2022). Bensulide and DCPA applied at seeding followed by bromoxynil at the 2-leaf stage provided the best weed control program with least need for hand weeding. However, this weed control program was the most expensive. A delayed pre-emergence application of pendimethalin after onion seeding showed promise as a cost-effective weed control program in New Mexico. 

Occasionally, a plant species emerges as a new weedy species in onion production for which there is little information on its control. Seaside petunia (Calibrachoa parvifolia) is a low growing, mat forming species that has recently started to impact onion production in the southwestern United States. Based upon the results of a plant control study using various herbicides, oxyfluorfen and flumioxazin showed promise for preemergence control of seaside petunia while bromoxynil showed promise of postemergence control (Schutte et al. 2021). 

Because the same herbicides with limited WSSA group diversity have been used for weed control in onion for decades, it is important to monitor weeds in onion production for herbicides resistance, especially in muck-onion producing regions where crop rotation is less prevalent. In New York, common ragweed (Ambrosia artemisiifolia) and perennial sowthistle (Sonchus arvensis), and Powell pigweed (Amaranthus powellii) are being monitored for herbicide resistance to clopyralid (WSSA group 4) and WSSA group 14 herbicides, respectively.  

In almost all cases, hand weeding is still required in onion production, despite judicious herbicide use, which can cost $100 to $500 per acre depending on the severity of weed escapes. Unfortunately, weeding can be disruptive by displacing onions and reducing yields. With labor issues on the rise including availability of workers, increased minimum wage and a maximum 60-hr, work-week, reducing the need to hand weed onion is highly desirable. Alternatives to herbicides and hand labor include mechanical cultivation, robotic weeding and electricity. Such approaches will be challenging to adopt in onion production because onions are planted in high densities and weed complexes and soil types can be highly variable. Recently, Nexus Robotics developed a new prototype “La Chevre” that is able to navigate and remove weeds in muck-grown onions autonomously.


  1. Evaluate onion germplasm for resistance to pathogens and insects
  2. Investigate the biology, ecology and management of onion insect pests
  3. Investigate the biology, epidemiology and management of onion plant pathogens
  4. Investigate the biology, epidemiology and management of weedy plant species that impact onion production


The proposed studies will be conducted in fields, greenhouses and laboratories to improve our understanding about the biology, ecology, epidemiology and management of the major pests, diseases and weeds impacting onion production and quality. Research will be collaborative, conducted by project participants, and coordinated annually by the leadership of this Project. 

Objective 1. Evaluate onion germplasm for resistance to pathogens and insects. Onion breeding evaluation research will be conducted during all 5 years of this project in the Pacific Northwest, Southeast and Southwest. In the Southwest, responses of advanced breeding lines, cultivars and germplasm accessions will be evaluated for their responses to IYS and onion thrips under field conditions that support short-day and/or intermediate-day onion types. Additional screening and identification of promising materials will continue to be promoted for use in onion cultivar improvement efforts by public and private onion breeders. Trials will be conducted following methodology known to generate high IYSV and onion thrips pressure. Trials will be randomized with a minimum of 3 replicates per entry. Assessments will be made by visually recording the number of thrips per plant from 10 randomly-selected plants per entry per replicate 4 weeks pre-bulbing, 2 weeks pre-bulbing, bulbing, 2 weeks post-bulbing and 4 weeks post-bulbing. IYS severity will be rated on 10 randomly selected plants per entry per replicate at bulbing, 2 weeks post-bulbing, and 4 weeks post-bulbing using the following scale: 0 = no symptoms, 1 = 1-2 small lesions, 2 = 3-10 medium lesions, 3 = 11-25 medium to large lesions, and 4 = more than 25 medium to large lesions per infected leaf. 

Onion germplasm will be evaluated for resistance to FBR using a mature bulb artificial inoculation method. Transversely-cut surfaces of stem basal plates from mature bulbs will be inoculated with 3 x 104 spores ml-1 of a virulent F. oxysporum f. sp. cepae (FOC) isolate. After 21 days of incubation, basal plates of inoculated bulbs will be recut and tissue rated on a scale of 1-9, where 1 represents no diseased tissue and 9 represents 70% or more of symptomatic tissue. Surviving bulbs that exhibit no disease will be selected, planted, and seed produced. The subsequent generations will be evaluated in a similar fashion for FBR resistance. 

Also in the Southwest, onion germplasm will be evaluated for resistance to pink root in a field known to have high pressure. The severity of the disease will be rated from 10 randomly selected plants in each plot. The rating will be based on percentage of root damaged (0 to 100%). Foliar dieback also will be recorded on a scale of 0-9, where 0 = immune and 9 = >90% or more necrotic/chlorotic. 

Onion germplasm also will be evaluated for resistance to bacterial pathogens prevalent in different regions of production. For example, P. ananatis will be evaluated in the southeast winter production region, while B. gladioli and P. agglomerans will be evaluated in Pacific Northwest. Diverse germplasm from culture collections and public and private onion breeders will be screened in these locations using standardized methods of inoculation in replicated, randomized plots, under conditions that favor development of the pathogens (e.g., overhead irrigation). In the Pacific Northwest, onion cultivars will be blocked based on maturity groups for inoculation with bacterial suspensions at the same relative stage of growth to avoid confounding daylength sensitivity with susceptibility to these bacterial pathogens. Consistency in response will be evaluated over multiple years in each location. Results will be compared to develop more effective screening methods that can then be used by all onion breeders. 

Objective 2. Investigate the biology, ecology and management of onion thrips and other pests. Onion insect research is planned for all 5 years of this project throughout the Great Lakes and Pacific Northwest. Research efforts will focus primarily on improving knowledge about the biology, ecology and management of onion thrips and maggots (onion and seedcorn) across all regions. However, the biology and management of other pests like the allium leafminer (specific to the northeastern US) will be addressed in New York. 

Management of onion thrips will be evaluated using new insecticides and use patterns. For example, efficacy of new insecticides like isocycloseram (PLINAZOLIN® technology) will be evaluated in small-plot field trials. This product may become commercially available as soon as 2023, so we must know how best to use it beforehand to inform growers. Insertion of isocycloseram into a season-long insecticide program must be evaluated in both production regions. In the Pacific Northwest, onions are irrigated primarily via center pivot or drip irrigation, and insecticides are typically applied either as foliar sprays or via chemigation. Management of thrips using insecticides applied by sprinkler and drip chemigation will be compared with standard foliar applications. Understanding the most effective application methods for specific insecticides will help growers customize and optimize insecticide programs on their farms. 

Onion thrips are generally controlled following a season-long sequence of insecticides that are applied based on action thresholds, but outbreaks continue to occur and IYS disease epidemics are getting worse in some areas. Adult thrips infected with IYSV are likely overwintering within and adjacent to onion fields. In the spring, adults emerge and are likely colonizing and spreading IYSV during the first half of the season. Movento and Senstar (spirotetramat) are systemic and highly effective against onion thrips larvae, but much less effective against adults. In the Great Lakes, Movento and Senstar are usually the first insecticides applied during the season to manage thrips infestations and their use occurs no earlier than mid- to late June. Typically, after two applications of Movento or Senstar (late June through mid-July), a different insecticide is used that likely has better control of adults. The consequence of this thrips management strategy is that the onion crop may be vulnerable to attack by adults infected with IYSV from mid-June through mid-July. Therefore, insecticides that are highly effective against adults must be identified and used early in the season to determine if this will reduce levels of IYS later in the season. Small-plot studies will be conducted initially to identify the most effective adulticide and then field-level experiments will be conducted using that adulticide early in the season in production regions where IYS is common. IYS levels in fields where adulticides are used early will be compared with those where they are not. 

Research also is needed to evaluate commercially available onion cultivars that may be less vulnerable to thrips and IYS. Preliminary results in a 2021 study in New York indicated that thrips feeding damage generally increased as days to maturity of the cultivars decreased. However, there was a cultivar in each maturity class that had more thrips feeding damage than the others. For example, cvs. Trailblazer, Braddock and Redwing had more thrips damage in the early, main and late maturity classes, respectively, than the other entrees. The cv. Crockett (118 days) had the least thrips feeding damage in the trial. There is a need to repeat this research and identify cultivars that may be less vulnerable to thrips and IYS damage. 

Chlorpyrifos is no longer an option for maggot control in the U.S. Additionally, there likely will be a short-term loss of Regard SC seed treatment (spinosad) until formulation issues are resolved with the new registrant (Corteva). Therefore, novel active ingredients for maggot control are needed more than ever. Small-plot field experiments will be conducted to evaluate the novel chemistry, isocyclorseram (PLINAZOLIN® technology), as a seed treatment. Positive controls will be included such as cyromazine (Trigard OMC) and spinosad (Regard SC) either alone or in combination with thiamethoxam (Cruiser 5FS). Multiple rates of isocycloseram seed treatments will be examined to determine the lowest rate that provides the highest level of maggot control. Additionally, laboratory bioassays will be conducted to determine the sensitivity of maggots from populations in CA, OR, WA, WI and NY to each active ingredient. This information will be helpful to assess areas where insecticide resistance in maggot populations may be developing. 

Objective 3. Investigate the biology, epidemiology and management of onion plant pathogens. Onion disease research is planned for the duration of the 5-year project in production regions throughout the Great Lakes, Pacific Northwest and Southeast. 

Iris yellow spot virus. Interactions between IYSV and onion at the transcriptome level will be studied using next generation sequencing. Using the complete IYSV genomic sequence as a reference, virus-specific small RNA profiles will be determined from cultivars susceptible and those with tolerance to IYSV. Profiles will help identify regulatory pathways potentially affected by IYSV infection, and could lead to development of molecular markers associated with virus resistance/tolerance. 

Fungal pathogens. Stemphylium leaf blight. Field trials in NY with methods similar to (Hoepting 2018a, 2018b) will be conducted annually to evaluate new fungicides and rates in different FRAC groups and examine different use patterns. Information generated will optimize placement of fungicides in season-long programs needed to maintain control of SLB while minimizing the development of fungicide resistance. The accuracy of environmental forecasting models such as BSPcast (Montesinos et al. 1995) also will be assessed in a field trial to determine their utility for scheduling fungicide sprays at strategic times. If a high level of prediction can be achieved in experimental trials, the model will be evaluated in commercial fields. 

Epidemiological studies of SLB will be conducted (NY, OR) to determine the timing of spore release over the season, to underpin decisions as to when the fungicide program for SLB should be initiated. The relationship between thrips damage and SLB severity also will be studied in field trials (OR) to determine if improved thrips management can reduce SLB. 

Botrytis Leaf Blight. Field trials in NY will identify fungicides effective against BLB following similar procedures as Hoepting (2018a, 2018b). Products will include Mancozeb (FRAC M3) at 1 lb/A, at first detection of BLB, in comparison to the industry threshold of higher rates (3 lb/A) applied later, i.e. 1 BLB spot/leaf. Trials will also evaluate Lifegard (FRAC P06), Oso (FRAC 19), Howler (FRAC PM02) and fenpicoxamid. Efficacy will be based on different symptom types of BLB (halo and necrotic spots). Field trials in NY also will examine the relationship between BLB severity early to mid-season and the severity of SLB mid-late season. SLB often invades necrotic tissue of onion, and previous trials in NY have shown some association between the severity of BLB earlier in the season, and SLB later. The extent of this relationship will dictate the importance of BLB control and consequent fungicide recommendations. 

Field trials in GA will evaluate fungicide efficacy against BLB in Vidalia onions. Treatments will include FRAC group fungicides 1, 3, 7, 9 and 11 and a combination of these groups. Disease severity will be assessed at a weekly interval starting with first appearance of BLB symptoms as percent leaf area with symptoms per plot. Also in GA, fungicide resistance to BLB will be assessed from Vidalia onion fields. Botrytis spp. isolates will be collected and laboratory assays conducted to determine sensitivity of these isolates against a panel of commonly used fungicides. Sensitivity of isolates to difenoconazole, (FRAC 3), pyrimethanil (FRAC 9), fluazinam (FRAC 29), and iprodione (FRAC 2) will be determined. Insensitive isolates will be subjected to molecular screening for the detection of gene-specific mutations such as fungicide target site genes (CYP51 gene for DMIs and SDH gene subunits for SDHIs). Sequences of BcOS1 genes will be identified for iprodione, sequenced and then compared to determine if any target site mutations are present that could confer fungicide resistance. Similar studies will be undertaken in NY. 

Fusarium bulb rot. Growers in UT recently lost 20-30% of their onions after harvest to Fusarium bulb rot caused by Fusarium proliferatum. A survey of growers will be undertaken to better understand the prevalence of Fusarium bulb rot, and the relationship between grower practices and weather on disease severity. Field trials aslo will be conducted to identify fungicides and topping procedures that may be effective management options. 

Pink root. The soil-borne disease pink root is managed through expensive fumigation in the Treasure Valley (ID/OR). A real-time PCR assay will be developed to detect and quantify Pyrenochaeta terrestris in soil, and trials will be undertaken to integrate the assay with alternative means of managing the pathogen. 

White rot. Research efforts in OR in 2022 will focus on evaluating encapsulated DADS and garlic oil inclusion complexes applied to infested microplots for their efficacy at reducing white rot sclerotia under field conditions. 

Bacterial bulb rot pathogens. Surveys to determine the diversity of pathogenic and non-pathogenic bacterial pathogens prevalent in multiple major onion production areas over multiple seasons will be conducted. Additionally, isolates for whole genome sequencing will be used to identify regions of the genome associated with pathogenicity, following the work of Agarwal et al. (2021) and Stice et al. (2021). Regions of genomes of pathogenic strains will be used to design DNA detection tools that will facilitate more rapid detection and diagnosis of the causal agents of onion bacterial rots. 

Field trials in GA, PA, and WA will be conducted to determine the impact of nitrogen applications on bulb rot incidence (primarily by P. ananatis and P. agglomerans) at harvest and after a duration in storage. In PA, harvest timing recommendations will be fine-tuned based on visual symptom thresholds that growers can use as a guideline to help minimize bacterial movement from the leaves into the bulb. Similarly, field trials to evaluate the amount and timing of irrigation, particularly when to taper and cease overhead irrigation, will be evaluated in field trials in multiple states (CA, CO, GA, OR, and WA) under different irrigation systems (drip and overhead irrigation), along with comparisons of the impacts of drip vs. overhead irrigation on the risk of onion bacterial diseases. 

Field trials evaluating applications of diverse copper products, resistance inducing products, biocontrol products (e.g., Lifegard), disinfectants (e.g., Oxidate), etc. will be evaluated in CA, CO, GA, NY, OR, UT, and WA. Combinations of treatments with greater or more consistent efficacy, including the timing of applications and rate(s) of application will be evaluated for developing more comprehensive and effective bactericide programs. Potential interactions of bactericides with insecticides and herbicides on control of bacterial diseases will be assessed to ensure that products are compatible (i.e., no phytotoxicity). Field research on optimizing late-season cultural practices and postharvest treatments of onion bulbs (e.g., disinfectant applications, postharvest heated/forced air curing vs. in-field curing) for reducing the risk of bacterial bulb rots will continue in GA, CO, NY, and WA. 

Onion growers and private industry stakeholders will be consulted regularly during these trials to ensure the trials are designed with realistic understanding of what growers can do, and in consultation with economist Greg Colson at the Univ. of Georgia to assess the economic feasibility of the practices evaluated for controlling onion bacterial diseases. 

Objective 4. Investigate the biology, epidemiology and management of weedy plant species that impact onion production. Herbicide efficacy trials will be conducted in the Great Lakes and Pacific Northwest. Treatments will include novel herbicides, application timings, and tank mixes to control the most important weeds relevant to each region. For pre-emergent treatments, weed control and visual crop injury will be evaluated at the 1-2, 2-3, 4-5 leaf stages and again 10 weeks after planting. For post-emergent treatments, weed control and visual crop injury will be evaluated 7, 14, 21 and 28 days after treatment. Overall weed control and crop injury will be visually estimated on a 100% scale where 0% = no weed control/no crop injury and 100% = perfect weed control/onions completely dead. Depending on the weed species and herbicide(s) being evaluated, some weed control assessments may include an herbicide injury rating per weed size, fresh biomass or % ground coverage. Stand will be quantified at the 2-leaf stage, and % stunting will be visually estimated, or onion plants measured at 2-3, 4-5 and 6-7 leaf stages. Onions will be harvested, size-graded and bulb size distribution by weight determined.  

In NY, the efficacy of clopyralid (Stinger) for controlling perennial sowthistle (PST) and ragweed (RW) will be assessed. Healthy PST rhizomes will be collected from five conventional fields prior to any herbicide applications to prevent injury that could impact the vigor of the rhizomes. In large bins in the greenhouse, we will let the rhizomes grow into mother plants for 6 months, then fragment them and then let the daughter plants grow out for three additional months (to achieve sufficient above- and below-ground biomass), and then treat with clopyralid. This will ensure that all of the daughter plants involved in the formal screening process were derived from parents grown under identical environmental conditions. A suitable range of 8-10 rates of clopyralid will be applied when the daughter plants are at the mid-rosette stage. Two weeks after treatment, both the above-ground leaves and below-ground rhizomes will be harvested and fresh biomass for each determined. This bioassay will be replicated 4 times for each PST population collected from an onion field, as well as a nearby nontreated population. 

Also in NY, clopyralid will be evaluated for RW control. Two weeks after clopyralid is applied, ~25 surviving RW plants will be potted and grown to seed in the greenhouse. Seed will be harvested from these plants and used to screen 8-10 rates of clopyralid, which will be applied when RW is 1-2 inch in size. RW mortality will be assessed 7, 14 and 28 days after treatment. 

Pendimethalin has been utilized for post planting, postemergence weed control in onions after seedlings have developed two true leaves. In some onion production regions, a special local needs registration has been obtained in order to apply pendimethalin at a time when onion seedlings have one true leaf or prior to onion seedling emergence. The currently registered herbicides for application at seeding in NM are expensive and potentially hazardous to the environment. A project will be initiated to evaluate the weed control effectiveness and onion injury when pendimethalin is applied after onion seeding, but prior to seedling emergence. Information gathered from this study will be used to seek a special local needs registration in NM for pendimethalin applied in the stated manner. 

In all regions, weed control using non-chemical tactics will be examined. Tactics may include robotic mechanisms as well as electricity.

Measurement of Progress and Results


  • Improved onion breeding lines and cultivars will possess increased levels of resistance to IYSV, thrips and/or FBR. New resistant cultivars will become available to onion growers in all growing regions in the US.
  • Insecticide programs will be refined and then integrated into production systems to manage season-long infestations of onion thrips and will ensure compatibility with management of pathogens and weeds
  • New approaches for thrips management to mitigate IYSV outbreaks will be explored
  • The resistance of onion cultivars to thrips and IYSV will be evaluated
  • New insecticide seed treatments will be developed for maggot management in onion
  • Resistance of SLB and BLB to fungicides will be determined
  • Relationship between plant stress (e.g. thrips and BLB) and SLB will be quantified, and means of alleviating plant stress to minimize the impacts of this disease will be identified
  • The utility of forecasting models as a means of scheduling fungicides for control of SLB will be determined
  • Onion cultivars tolerant to the onion foliar disease complex will be identified
  • Effective fungicide programs will be identified to manage SLB and BLB while reducing selection pressure for fungicide resistance
  • Practices to reduce the severity of Fusarium basal rot will be determined
  • A molecular assay to quantify the Pink root pathogen in soil will be developed and tested for use as part of an integrated management strategy
  • Encapsulated DADS and garlic oil inclusion complexes will be assessed for their efficacy at reducing white rot sclerotia under field conditions
  • Cultural, chemical, and postharvest management practices will be optimized for management of bacterial bulb rots
  • Better understanding of the diversity in onion bacterial pathogens across the U.S. and interactions among the complexes (microbiomes) of bacteria associated with onion plants and bulbs (pathogenic and non-pathogenic)
  • Greater ability to detect and diagnose the diseases rapidly and robustly as a result of developing molecular diagnostic tools based on virulence factors identified in the genomes of bacteria surveyed across the U.S.
  • Efficacy and crop tolerance data will be generated for several herbicide products and programs for the major weed species of concern in onion production
  • Presence and degree of herbicide resistance, if any, will be quantified for perennial sowthistle and common ragweed in New York. It is likely that through the duration of this project that herbicide resistance will be monitored in other species and in other production regions as well
  • Onion growers will see autonomous hand weeders in action in their growing region suited to their scale of production
  • Growers will have new herbicide recommendations and resources available

Outcomes or Projected Impacts

  • Improved, high yielding onion cultivars with increased resistance to IYS and/or thrips may dominate regional and national production. Areas planted to these new cultivars may increase by more than 10%, leading to substantial yield increases in the participating states. The commercial value of new cultivars is expected to exceed $100 million annually.
  • Adoption of multiple-pest resistant cultivars may reduce pesticide use by 20% or more, resulting in savings to producers and positive impacts on the environment.
  • Adoption of season-long, insecticide programs to manage thrips and IYSV will increase profitability by at least 10%. These programs will reduce damage and pesticide inputs that will increase marketable yield and quality. Environmental quality is expected to improve as a result of using 20-50% fewer pesticide applications as well as replacing broad-spectrum pesticides with reduced-risk products.
  • Adoption of commercially available cultivars that suffer less damage by thrips and IYS symptoms will increase profitability by at least 10%. These cultivars will help the onion industry continue to be competitive and profitable.
  • Registration and adoption of a new insecticide seed treatments for maggot control will increase profitability by at least 5%. Moreover, this novel seed treatment belongs to a new class of chemistry can be used in a resistance management program to mitigate resistance development.
  • Development and adoption of a fungicide program that is cost-effective for controlling Stemphylium leaf blight, and Botrytis leaf blight while minimizing fungicide resistance. Estimations of reducing leaf dieback caused by Stemphylium leaf blight by 20% may increase yield by 10 to 15%, or an estimated $520 to $780 per acre. Bulb quality will be improved by reducing bacterial bulb decay associated with plants dying from excessive leaf dieback.
  • Development of an assay to quantify pink rot in soil will reduce production costs and provide improved environmental outcomes for the onion industry by reducing unnecessary prophylactic applications of costly soil fumigants.
  • Successful development of germination stimulants for white rot control would allow growers to produce a profitable onion crop on land that was previously infested with white rot, negating the need for lengthy rotations to crops other than onion for 10-20 years, and reduce the potential for further spread of this disease to new production areas.
  • Improved understanding and management of Fusarium basal rot will mitigate losses to individual growers of over 20-30% in storage.
  • Adoption of optimized cultural, chemical, and postharvest management practices will reduce losses to onion bacterial diseases by at least 25% and will help keep the US onion industry profitable and sustained.
  • Phenotypic methods of screening for relative resistance of onion germplasm will be developed and adopted or adapted by onion breeding programs to increase the efficiency of developing cultivars with greater resistance to onion bacterial pathogens.
  • New herbicide products, timings, tank mixes and strategies will be dentified to improve weed control in onion. Grower adoption of such recommendations will improve overall weed control in onion, thus, improve yield by 10-30%, and bulb quality, while reducing need to hand weed by $50-$200 per acre.
  • Labels of current herbicides will be expanded to include new timings, tank mix partners, weed species and states where they were not previously labeled.
  • At least one herbicide with novel mode of action will be identified that has potential to be used in onion production.
  • Robotic autonomous weeders will be adopted on 2-5 onion farms.


(2023):• New breeding lines will be evaluated for resistance to thrips, IYSV, FBR, pink root and bacterial bulb rots in field trials • New insecticides will be evaluated for maggot, thrips and IYSV control in field trials • Cultivars that produce high yields under high thrips and IYSV pressure will be evaluated in field trials • New fungicides will be evaluated for SLB, BLB and FBR control in field trials • SLB and BLB resistance to fungicides will be evaluated • SLB risk will be determined by comparing several forecasting models • Molecular assays will be developed to quantify PR • DADS and garlic oil will be assessed for white rot control in field trials • Bacterial rot species will be identified in all regions • New bactericides will be evaluated for bulb rot control in field trials • Cultural and postharvest practices will be evaluated for bulb rot control • New herbicides will be evaluated for weed control in field trials • PST and RW will be evaluated for resistance to herbicides • Non-chemical weed control tactics will be tested in field trials

(2024):• The best breeding lines from 2023 will be evaluated for resistance to thrips, IYSV, FBR, pink root and bacterial bulb rots in field trials • New insecticides will be evaluated for maggot, thrips and IYSV control in field trials • Cultivars that produce high yields under high thrips and IYSV pressure will be evaluated in field trials • New fungicides will be evaluated for SLB, BLB and FBR control in field trials • SLB and BLB resistance to fungicides will be evaluated • SLB risk will be determined by comparing several forecasting models • Molecular assays will be developed to quantify PR • DADS and garlic oil will be assessed for white rot control in field trials • Bacterial rot species will be identified in all regions • New bactericides will be evaluated for bulb rot control in field trials • Cultural and postharvest practices will be evaluated for bulb rot control • New herbicides will be evaluated for weed control in field trials • PST and RW will be evaluated for resistance to herbicides • Non-chemical weed control tactics will be tested in field trials

(2025):• The best breeding lines from 2024 resistant to thrips, IYSV, FBR, pink root and bacterial bulb rots will be tested in field trials • New season-long insecticide programs will be evaluated for thrips and IYSV control in commercial fields • New insecticide seed treatments will be tested in commercial fields • Cultivars that produce high yields under high thrips and IYSV pressure will be evaluated in commercial fields • New forecasting models and season-long fungicide programs will be evaluated for SLB and BLB control in commercial fields • A new molecular assay will be used to quantify Pink root pathogens in commercial fields • DADS and garlic oil will be assessed for white rot control in commercial fields • New bactericide programs, cultural and postharvest practices will be evaluated in commercial fields and storage facilities • New herbicide programs and non-chemical strategies will be evaluated for weed control in commercial fields

(2026):• The best breeding lines from 2025 resistant to thrips, IYSV, FBR, pink root and bacterial bulb rots will be tested in field trials • New season-long insecticide programs will be evaluated for thrips and IYSV control in commercial fields • New insecticide seed treatments will be tested in commercial fields • Cultivars that produce high yields under high thrips and IYSV pressure will be evaluated in commercial fields • New forecasting models and season-long fungicide programs will be evaluated for SLB and BLB control in commercial fields • A new molecular assay will be used to quantify Pink root pathogens in commercial fields • DADS and garlic oil will be assessed for white rot control in commercial fields • New bactericide programs, cultural and postharvest practices will be evaluated in commercial fields and storage facilities • New herbicide programs and non-chemical strategies will be evaluated for weed control in commercial fields

(2027):• The best breeding lines from 2026 resistant to thrips, IYSV, FBR, pink root and bacterial bulb rots will be tested in field trials • Season-long insecticide programs for thrips and IYSV control will be implemented in commercial fields • New insecticide seed treatments will be implemented in commercial fields • Cultivars that produce high yields under high thrips and IYSV pressure will be implemented in commercial fields • A new forecasting model and season-long fungicide program will be implemented for SLB and BLB control in commercial fields • A new molecular assay will be used to quantify Pink root pathogens in commercial fields • DADS and garlic oil will be implemented for white rot control in commercial fields • New bactericide programs, cultural and postharvest practices will be implemented in commercial fields and storage facilities • New herbicide programs and non-chemical strategies will be implemented for weed control in commercial fields

Projected Participation

View Appendix E: Participation

Outreach Plan

The outreach plan will include disseminating information to stakeholders in the onion industry at local, regional and national meetings as well as in newsletters, extension articles, eXtension, peer-reviewed publications and resources located on the internet like https://alliumnet.com/. Annual meetings for W4008 will be held to share information, update participants on current research and extension efforts, identify potential sources of support for research and extension needs, and establish cooperative approaches to research and extension projects. When possible, our committee will schedule the annual W4008 meeting in conjunction with NARC and NOA. Formal and informal participation at these meetings will be encouraged from all participants from all organizations, regions and countries. Participants may include scientists and extension professionals and those from the onion industries in California, Colorado, Georgia, Idaho, Michigan, New Mexico, New York, Oregon, Pennsylvania, Texas, Utah, Washington, Wisconsin and USDA-ARS. Additionally, prior to each annual meeting, an individual or smaller groups of participants will engage stakeholders about current research and extension results at local and regional meetings, including field days and twilight meetings. Research results from each sub-project will be published in refereed and non-refereed journals, extension bulletins, the trade magazine Onion World, and posted on the web sites of individual programs or institutions or other media outlets. 

An annual report, including summaries and impact statements from each participant will be generated along with the minutes of the annual meeting, sent to committee members, archived on the NIMSS web site, and posted on Alliumnet. The annual report will also be sent to appropriate university Deans and Agricultural Experiment Station Directors, key legislators, and other stakeholders. 

All major onion grower associations, seed companies and chemical companies will continue to be engaged by members of the W4008 and invited to provide feedback on projects and results of this team.


Directors of Agricultural Experiment Stations receive requests from researchers to join Multi-State Projects, like our proposed W4008. Future members of W4008 will elect officers of the Executive Committee. The project is considered a Western Regional Research Project, but has substantial participation by those in other onion producing regions across the US as well as those with the USDA-ARS. The Executive Committee officers include a Chair, Vice-Chair, and Secretary. The Vice-Chair will succeed the Chair and the Secretary will succeed the Vice-Chair. A new Secretary will be elected by the end of each annual meeting. If a person declines to serve a subsequent office (e.g., the Secretary does not want to serve as Vice-Chair), an election will be held to refill that position by the end of the annual meeting. The Western Association of Agricultural Experiment Station Directors selects the Administrative Advisor for W4008. This person will not have voting rights. Tracy Dougher is currently the Administrative Advisor for the W3008 project and will likely to serve for the W4008 project. 

The responsibility of the Chair is to organize and moderate the annual meeting. Organizing the meeting includes making local arrangements, which may be in conjunction with NOA and/or NARC planning committees; preparing the annual meeting program agenda; and inviting the Executive Committee and other participants to attend the meeting, and advertising the annual meeting to the onion industry. The Chair should maintain the most updated W4008 participant contact information list. 

Responsibilities of the Vice-Chair include coordinating the writing of the annual report and sending it to the Administrative Advisor for submission onto the NIMSS website. The Vice-Chair should also distribute the annual report to the Executive Committee, other participants, and other stakeholders. The annual report may be further summarized for inclusion in Onion World

Responsibilities of the Secretary are to record the minutes from the annual meeting and submit them to the Administrative Advisor for submission onto the NIMSS website. 

The Executive Committee will meet annually, unless otherwise planned, at a place, and on a date designated by a majority vote of the committee. Minutes will be recorded and an annual progress report will be prepared by the Executive Committee, and both submitted through relevant channels. At the annual meetings, participants are updated about current research and extension results on the major pest and diseases of onion as described in the Outreach Plan. New and upcoming publications and other educational and outreach resources will be discussed, as well as collaborations with other relevant projects related to onions. Formal and informal participation is encouraged from participants of all organizations from all regions and countries. The committee will help facilitate development of teams with relevant expertise for preparing regional and federal grant proposals to enhance onion production in the US. 

Current Executive Committee Members of the W3008 Regional Project (2021-2022): 

Chair: Peter Rogers, Sr. Scientist Phytopathology, BASF, Brooks, OR 

Vice-Chair: David Burrell, National Onion Labs Inc., Collins, GA 

Secretary: Frank Hay, Sr. Extension Associate, Plant Pathology and Plant Microbe Biology Section, Cornell University, Geneva, NY 

Past Chair: Bhabesh Dutta, Associate Professor & Extension Vegetable Disease Specialist, Dept. of Plant Pathology, University of Georgia, Tifton, GA 

W4008 proposal rewrite coordinator: Brian Nault, Professor & Program Leader, Department of Entomology, Cornell University, Geneva, NY

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