W3008: Integrated Onion Pest and Disease Management

(Multistate Research Project)

Status: Active

W3008: Integrated Onion Pest and Disease Management

Duration: 10/01/2017 to 09/30/2022

Administrative Advisor(s):

NIFA Reps:

Statement of Issues and Justification

Onion, Allium cepa L., is the third most consumed vegetable in the U.S., behind tomato and potato. The per capita consumption of onions in the U.S. is about 20 pounds per year, which has increased 70% over the past 20 years (https://www.onions-usa.org/all-about-onions/consumption). Onion is also one of the most economically important specialty crops with a farm-gate value of nearly $1 billion USD/year (https://www.nass.usda.gov/Publications/Ag_Statistics/2015/Chapter04.pdf) 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 over $100 million/year. Onion is grown on 125,000 acres across at least 20 states with a majority produced in California, Colorado, Georgia, New Mexico, New York, Oregon, Texas and Washington.

The need as indicated by stakeholders. Onion crops are damaged by a similar spectrum of pests and pathogens throughout the U.S. For example, onion thrips, Thrips tabaci Lindeman, damages onion by feeding on leaves that significantly reduces onion bulb yield and quality (30 to 50%) (Fournier et al. 1995). Onion thrips also is notorious for developing resistance to insecticides (Shelton et al. 2003, 2006; Allen et al. 2005) and spreading plant pathogens like Iris yellow spot virus (IYSV), which also reduces bulb yield and quality as well as seed production (Gent et al. 2004 & 2006, du Toit and Pelter 2005). There are multiple fungal and bacterial pathogens that can cause onion yield losses in the field and in storage facilities throughout the U.S. (Schwartz and Mohan 2005). Each disease can cause up to 25 to 100% crop loss. The most important fungal diseases include Stemphylium leaf blight (SLB), Stemphylium vesicarium, purple blotch (PB), Alternaria porri, downy mildew (DM), Peronospora destructor, black mold, Aspergillis niger, Botrytis leaf blight (BLB)/ blast and neck rot, Botrytis species, powdery mildew, Leveillula taurica, and white rot, Sclerotium cepivorum. 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 sp., and Enterobacter bulb decay, Enterobacter cloacae. Over the past several years, growers in some regions have abandoned onion production because of losses due to problems caused by one or more of these organisms. Consequently, stakeholders have identified onion thrips, IYSV and these fungal and bacterial pathogens as significant threats to sustainability of the U.S. onion industry http://www.ipmcenters.org/pmsp/pdf/USonionPMSP.pdf).

The importance of the work, and what the consequences are if it is not done. The work proposed is critical for solving the most important pest and disease problems facing the US 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 W3008 group, particularly given the successful foundation set by the preceding multistate projects (W1008: Biology and Management of Iris yellow spot virus (IYSV) and Thrips in Onions from 2005-2010, and W2008: Biology and Management of Iris yellow spot virus (IYSV), Other Diseases and Thrips in Onions from 2011-2016). We anticipate that results from this research and extension effort will continue to contribute significantly to science and agriculture as we communicate new knowledge about the biology, ecology and management of these pests and pathogens 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 US onion acreage due to limited ability to manage the pest and diseases mentioned above, reduced profits as a result of decreased bulb yields, reduced quantities and/or qualities of onion seed produced, and greater pesticide and fertilizer inputs, as well as potential environmental and human health concerns associated with greater fertilizer and pesticide use.

The technical feasibility of the research. Participants of this 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 proposed project.

The 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 two previous, highly successful multistate projects (W1008 from 2005 to 2010, and W2008 from 2011 to 2016). 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 and microbiology. Past participants have included public and private researchers, extension professionals, onion growers and seed industry personnel throughout the US who have formed productive collaborations. Many of the problems affecting onion production occur in most regions in the US, 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 11 years, which we anticipate will continue.

What the likely impacts will be 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 other pests and diseases, and reduced inputs such as pesticides and fertilizers. More judicious use of reduced-risk insecticides and fungicides, action threshold-based pesticide application programs, and optimal pesticide and fertilizer application techniques and strategies that mitigate insecticide and fungicide resistance risks will contribute directly to improved environmental stewardship and sustainability. Reduced fertilizer use should reduce watershed pollution caused by nutrient runoff or leaching, and will reduce production costs. Society will benefit from the training of graduate and undergraduate students working with faculty on this project, preparing the next generation of researchers, extension specialists and agricultural professionals who will shape the future of production agriculture.

Related, Current and Previous Work

We seek to continue the success of previous multi-state projects (W1008 and W2008) by broadening the scope of this project to include new studies for solving the US onion industry’s most important problems. Below are some of our accomplishments.

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 to both. Entries have been evaluated in germplasm nurseries from 2012 to 2015 in Colorado, New Mexico, Oregon, and New York. In New York, Diaz-Montano et al. (2012) observed cultivars Tioga, Vaquero, Cometa, NMSU 03-52-1, Colorado #6, Mesquite and Granero to be partially thrips resistant. In New Mexico, Cramer et al. (2012) reported that plants of Cometa and NMSU 05-35-1 were more tolerant to IYS and also had lower levels of IYS than other entries. Singh (2013) reported that NMSU 10-575-1, 10-577-1 and 10-582-1 exhibited less severe IYS than their original populations. In Colorado, accessions 258956, 264320, 546140 and 546188 had fewer symptoms than other accessions (Boateng et al. 2014). In New Mexico, Cramer et al. (2014) reported that PIs 239633 and 546192 exhibited fewer IYS symptoms, while PI 289689 had fewer thrips per plant. Kamal (2016) reported that breeding lines selected for reduced IYS symptom expression (NMSU 10-776, 10-782, 10-785, 10-807 and 10-813) had lower thrips densities, disease severity and incidence than unselected breeding lines. Kamal (2016) also reported plants from breeding lines NMSU 12-239 and 12-243 that were selected twice for reduced IYS expression had less severe disease and fewer thrips than an unselected population NMSU 07-53-1 and a susceptible cultivar Rumba. 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). 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 in conjunction with other management tactics.

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 2016c) and several selected breeding lines exhibited less disease (Mandal and Cramer 2016a). Improvements have been made to the inoculation procedure with regards to host and inoculum preparation, inoculum concentration, and incubation period that have resulted in greater disease expression and disease response (Mandal and Cramer 2016a, 2016b). In Wisconsin, disease evaluations entail a seedling screen (Marzu 2015), with survivors retained for seed production. Past studies have shown significant correlations between seedling evaluation and field resistance to FBR (Retig et al. 1970).

Onion thrips ecology and management. Advancements were made in understanding how abiotic factors influence onion thrips dispersal in onion fields. Adult dispersal was monitored passively in the air using both clear sticky cards and trap-equipped unmanned aerial vehicles in onion fields, with on-site weather conditions recorded. Sub-samples of thrips captured by these traps were tested for IYSV using RT-PCR assays. Results indicated that time of day, temperature and wind speed were important factors influencing thrips flight. Adults dispersed almost exclusively during the day with peak dispersal around one hour before sunset. Thrips dispersed most often when temperatures were between 21 and 28°C and when wind speeds were low, <0.6 m/s (Smith et al. 2016a). Thrips were more likely to disperse later in the season (August) than earlier in the season (June). Regardless of season, most thrips dispersed short distances, but a small percentage dispersed long distances. IYSV was detected in dispersing thrips during the entire season, but most tested positive in August (54%) than earlier in the season (2 to 22%). Approximately 15 to 20% of long-distance dispersing thrips tested positive for IYSV (Smith et al. 2015). Results indicated that onion thrips, including those likely to vector IYSV, engage in short-distance and long-distance dispersal late in the season and may contribute to the spread of IYSV both locally and regionally in New York. While this research was done in the eastern US, more research is needed in the western US to improve our understanding of thrips dispersal and movement of IYSV, particularly between onion bulb and seed production fields, as onion seed production is concentrated in the western US.

Over the past five years, severe losses in onion bulb yield attributed to thrips damage have become less common because new insecticides such as abamectin, cyantraniliprole, spinetoram and spirotetramat have become registered for use on onions and used by growers (Groves et al. 2013, Nault et al. 2014, Waters and Skoczylas 2015a, 2015b, 2015c). Additionally, thrips management has been improved by making insecticide applications based on action thresholds (Nault and Shelton 2010, Nault and Huseth 2016), following specific sequences of insecticide products applied during the season (Nault and Shelton 2012, Byrne and Szendrei 2013, Reitz 2014), and using surfactants co-applied with insecticides (Nault et al. 2013). Despite these advancements, thrips control using insecticides has been inconsistent in many regions of the US. Control failures can be attributed to ineffective insecticide delivery approaches, poor timing of insecticide applications, greater thrips pressure, insecticide resistance developing in thrips populations, or combinations of these factors. Research is needed to identify regions where thrips resistance is developing to insecticides, determine if there are better approaches than aerial application or chemigation to deliver insecticides, and help growers adopt relevant onion thrips management programs for their farms.

Measures have been established to mitigate resistance to newly registered insecticides for thrips management in onion bulb and seed crops. For most new products, only two consecutive applications one week apart should be made to minimize the number of thrips generations exposed to the insecticide (e.g., one generation), thereby reducing selection pressure and mitigating resistance development. However, multiple generations of thrips are likely exposed to the same insecticide on some farms where multiple onion cultivars varying in maturity are grown in proximity. In New York, Smith et al. (2016b) documented thrips adults dispersing from mature onion fields that had been treated previously with insecticides into adjacent immature onion fields where additional insecticides were applied. Because virtually all onion fields are sprayed with spinetoram, the same thrips population will be exposed to spinetoram at least twice in each of several fields. Research is needed to determine if resistance has developed in thrips populations to spinetoram, and develop additional recommendations to mitigate development of resistance in the future.

Management tactics need to be integrated to improve thrips control in onion bulb and seed crops. Selecting cultivars with thrips resistance, reducing the rate of nitrogen applied at planting, and judicious use of reduced-risk insecticides are promising tactics (Buckland et al. 2013, Cramer et al. 2014, Nault and Huseth 2016). In New York, combinations of varying levels of nitrogen and insecticide use were evaluated for thrips control in onion cultivars that ranged from moderate to high thrips susceptibility, cv. Avalon, Delgado and Bradley. Within each cultivar, combinations of nitrogen applied at planting (e.g., 60, 90, and 125 lbs per acre) and insecticide regimes (e.g., a standard weekly spray program or an action threshold-based program) were evaluated for thrips management and impacts on yield. Results indicated that, regardless of cultivar, nitrogen fertilizer rates applied at planting had no effect on either thrips densities or bulb yields. Across cultivars, the standard and action threshold-based programs provided excellent control, but 33 to 50% fewer applications were made following the action-threshold program than the standard program. Insecticide programs reduced thrips densities by 60 and 81% compared with densities in untreated plots. Onion yields in standard and action threshold insecticide programs also were statistically similar and averaged 10 to 54% greater yields in comparison with untreated controls. The frequency of insecticide applications and quantity of nitrogen at planting both could be reduced without compromising bulb yield or thrips control. However, more research is needed to determine whether timing of nitrogen applications (split applications) may impact thrips population levels and bulb yield, and the impact of total available soil N (residual N from the previous year’s cropping rotations plus N fertilizers applied in-season).

Iris yellow spot virus population genetics and detection. A global analysis of IYSV nucleocapsid gene (N gene) sequences was conducted to compare genetic population structure, and spatial and temporal dynamics of genetic diversity and evolution (Iftikhar et al. 2014). A total of 98 N gene sequences from 23 countries were characterized by in-silico RFLP analysis, with 94% of the isolates grouped into either the IYSV Netherlands genotype (NL) or the Brazilian genotype (BR). The proportion of NL and BR types was 46 and 48%, respectively. A temporal shift toward BR types over NL types occurred only before 2005. Inherent differentiation and infrequent gene flow between BR and NL types was detected, corroborating the geographical confinement of the genotypes. Overall, results suggested that diversity in IYSV populations and a temporal shift in BR genotype are attributable to genetic recombination, purifying selection, insignificant positive selection and population expansion. Restricted gene flow between the two IYSV genotypes emphasizes the role of genetic drift in modeling population architecture and evolutionary lineage. This information improves our understanding of IYSV epidemiology that may be important in management programs.

An ELISA-based assay was developed for detecting IYSV in individual thrips and groups of adult thrips (Bag et al. 2014), using polyclonal antiserum produced against the nonstructural protein (NSs) coded by the small (S) RNA of IYSV. The assay enabled estimating the proportion of potential thrips transmitters in a large number of thrips collected from plants. This practical and inexpensive test to identify viruliferous thrips will be useful in epidemiological studies of IYSV outbreaks.

IYSV was detected in bunching onion, Allium fistulosum, for the first time in the US (Tabassum et al. 2016). Plants had symptoms of IYS, and the virus was confirmed using a RT-PCR assay with primers specific to the S RNA. IYSV infection of A. fistulosum is a concern because this species is grown in the western US and may serve as a major source for IYSV in onion bulb production.

Fungal pathogens and management. Botrytis leaf blight (BLB), Stemphylium leaf blight (SLB), downy mildew (DM) and purple blotch (PB) are the main foliar diseases of onion in North America. These diseases can cause excessive leaf dieback, pre-mature plant mortality, and reduced bulb quality, yield and storability. In New York, SLB occurred in 100% of 22 conventionally grown fields and 10 “low input” fields. On-farm trials showed that fungicides belonging to Fungicide Resistance Action Committee (FRAC) Groups 3 and 7 provided the best control of SLB with Luna Tranquility, Merivon, Inspire Super and Quadris Top being the most efficacious. FRAC Group 11 fungicides Quadris and Cabrio failed to control SLB in field trials (Hoepting 2016a). Further investigation using fungicide sensitivity bioassays and genetic testing (G143A mutation on cytochrome b region) revealed that some SLB fungal isolates have developed resistance to azoxystrobin (Quadris) in New York. Since the SLB fungus readily infects plants that are infected with DM, effective DM control is critical for effective SLB control. Fungicide trials indicated that DM was best controlled with Orondis (FRAC Group US15), Ridomil Gold Bravo (Groups 4 and M5), Reason (Group 11), Quadris Top (Groups 3 and 11) and mancozeb (Group M3) (Hoepting 2016b). However, fungicides that are most effective for control of SLB and DM do not provide effective control of BLB. A season-long sequence of fungicides that effectively controls all three diseases while mitigating the potential for fungicide resistance development should be identified.

Onion stunting caused by Rhizoctonia spp. is an important soilborne disease on sandy soils where cereal winter cover crops are planted the previous fall to prevent wind erosion of soil. The cover crop is killed with an herbicide shortly before or after onion seeding. The dead cereal plants provide a physical barrier to protect onion seedlings against sand-blasting. The cover crop serves as a green bridge for Rhizoctonia spp. on cereal roots to colonize onion roots, causing onion stunting. To determine the effect of a glyphosate application to reduce this green bridge, three application timing intervals preceding onion planting were evaluated in Washington (Sharma-Poudyal et al. 2016). As the interval between herbicide application and onion planting increased from 3 to 27 days, the number of patches of stunted onion plants decreased by ≥55%, total area of stunted patches decreased by 54 to 63%, and patch severity decreased by 59 to 65%. Increasing the interval between herbicide application to the cover crop and onion planting provides a practical strategy to avoid onion crop stunting. Additionally, multiple field trials showed that a pre-plant, banded, incorporated application of Quadris reduced the number of stunted patches by 24 to 57%, the area of stunted patches by 33 to 68%, and severity of stunting by 44 to 81% (Sharma-Poudyal et al. 2013).

From 2010 to 2013, 251 isolates of Rhizoctonia or Rhizoctonia-like spp. obtained from soil and onion plant samples inside and outside patches of stunted plants in 29 onion fields in Washington were identified to 13 anastomosis groups (AGs) or subspecies by DNA sequencing (Sharma-Poudyal et al. 2015b). The frequency of isolation and DNA concentration of R. solani AG 8 in soil were greater inside patches of stunted onion plants than from adjacent healthy areas. For six cultivars in seven growers’ fields, onion stunting reduced average marketable bulb yield by 25 to 60% within stunted patches. Yield reduction increased with increasing disease severity. In addition, 35 onion genotypes were evaluated for resistance to stunting caused by R. solani AG 8 (Sharma-Poudyal et al. 2015a). Of the 35 genotypes, 3, 16, and 3 demonstrated partial resistance to R. solani AG 8 for plant height, root length, and total biomass, respectively. Four genotypes displayed partial resistance for at least two of the three growth parameters: PX07713218, R14885, R14888, and SN307. These could be used in onion breeding programs to develop cultivars partially resistant to stunting caused by R. solani AG 8.

Bacterial rot and management. Center rot caused by Pantoea ananatis and P. agglomerans, as well as other bacterial diseases, have the potential to cause 100% yield loss. Center rot is particularly devastating because discolored interior scales are difficult to detect at harvest. Management options include preventative copper sprays tank mixed with mancozeb, harvesting at optimum maturity and effective control of thrips, which can transmit bacteria to onions (Dutta et al. 2014). In plasticulture systems, reflective or silver-on-black plastic mulches reduce soil temperature, which reduces bacterial disease incidence at harvest (Pfeufer 2014). The nutritional status of the host can also influence the spread and multiplication of bacterial pathogens. Leaf tissue nitrogen was positively correlated with center rot incidence in a two-year field study (Pfeufer 2014). The relationship between in-season foliar nitrogen tissue levels and loss at harvest and post-harvest should be determined so that growers can make harvest timing and marketing decisions (Mazzone 2017). Similarly, if foliage is infected with bacteria late in growing season, there is a possibility to prevent 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.

Another bacterial pathogen, B. cepacia, has been difficult to manage in Georgia and New York. Crop rotation is an effective cultural strategy to manage this disease, but it has failed on some occasions. There is a possibility that bacteria may be reintroduced into fields as rhizosphere inhabitants on the roots of onion transplants. In addition, inoculum may be increasing on roots of weed hosts if weeds are not managed effectively between onion crops.

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). For all three pathogens, bulb rot was more severe at high temperatures (40 or 35°C vs. 30 or 25°C) and when cured for 14 versus 2 days prior to cold storage. Severity of bulb rot also was greater with a longer duration of storage after curing. 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. If greater temperatures are used to dry onion necks to reduce the risk of neck rot (Botrytis spp.), a shorter curing duration may be necessary to minimize bacterial bulb rots. When 69 storage cultivars were evaluated in Washington for resistance to Enterobacter bulb decay, Redwing, Red Bull, T-433, Centerstone, and Salsa had low bulb rot severity ratings, whereas Montero, OLYS05N5, Caveat, and Granero had severe bulb rot ratings (Schroeder et al. 2010, Wohleb et al. 2012). Therefore, partial resistance to Enterobacter bulb decay in onion cultivars should be selected.

Interactions among W2008 members. To facilitate more interactions between W2008 participants and the onion industry, two W2008 annual meetings have been held in conjunction with joint National Allium Research Conference (NARC) and National Onion Association (NOA) meetings (2014 and 2016). Onion growers, allied representatives from the seed and pesticide industries, and researchers and extension educators from university and government agencies attended joint sessions and events throughout both conventions. The conventions were highly successful and all three groups have decided to meet again in the future (see Milestones).

Participation in W2008 annual meetings increased by 25% compared with participation in W1008 meetings (171 vs. 137 participants). Moreover, 26% more growers and 91% more industry representatives attended W2008 meetings compared with W1008 meetings. Presentations by W2008 members increased 260% compared with those given by W1008; 83 total by W1008 (~ 21 per year); 215 total by W2008 (~ 54 per year). We intend to increase W3008 membership by expanding our objectives.


  1. Evaluate onion germplasm for resistance to pathogens and insects.
  2. Investigate the biology, ecology and management of onion thrips and other pests.
  3. Investigate the biology, epidemiology and management of onion plant pathogens.
  4. Facilitate discussions between W3008 participants and onion industry stakeholders that will advance onion pest and disease management.


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 and diseases impacting onion production and quality. Research projects will be conducted by project participants and coordinated annually by the leadership of this Project (Chair, Vice Chair, and Secretary).

Objective 1: Evaluate onion germplasm for resistance to pathogens and insects. Onion breeding research will be conducted and/or evaluated during all 5 years of this project in New Mexico, New York, Oregon, Washington and Wisconsin. We will continue to evaluate responses of onion entries (advanced breeding lines, cultivars, germplasm accessions) to IYSV and onion thrips populations under field and controlled conditions at cooperating sites with different environmental conditions that support short-day, intermediate-day, and/or long-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 at cooperating sites throughout the US. Trials will be randomized with a minimum of 3 replicates per entry. Periodically throughout the field, a row will be planted with an IYSV/thrips susceptible cultivar that is not treated with any insecticides to provide uniform pest and virus pressure to adjacent plots in the trials where the evaluated entries are located. The nurseries should be surrounded with a 3 m-wide planting of a local onion variety that receives all agronomic inputs, except insecticide treatments. Cooperators are encouraged to plant in areas with a history of IYSV and moderate to severe thrips pressure. IYSV pressure may be increased by promoting development of IYSV-infected volunteer onion plants and/ or transplanting infected plants into and around the nursery. To evaluate onion thrips without destructive sampling of plants, the number of adult and larval thrips per plant on 10 randomly selected plants per entry per replicate should be counted 4 weeks pre-bulbing, 2 weeks pre-bulbing, bulbing, 2 weeks post-bulbing and 4 weeks post-bulbing. IYSV severity should be rated on 10 randomly selected plants per entry per replicate at bulbing, 3 weeks post-bulbing, and 6 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. It is important that cultivars selected for resistance to IYSV and/or onion thrips are not especially susceptible to other diseases, which could limit their usefulness commercially.

Onion germplasm will be evaluated for resistance to Fusarium basal rot (FBR) using two approaches. Transversely-cut surfaces of stem basal plates from mature bulbs will be inoculated with 3 x 105 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 the tissue rated on a scale of 1-9, where 1 represents no diseased tissue and 9 represents 70% or more of the symptomatic tissue. For the second approach, seed is sown in a sand medium infested with FOC and maintained at 19°C until seedlings have emerged. The temperature is then increased to 28°C, at which FOC readily infects and kills susceptible seedlings. Surviving seedlings or 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.

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 in New York, Oregon, Pennsylvania, Washington and Wisconsin by participating members from those states. Research efforts will focus primarily on improving our knowledge about onion thrips biology, ecology and management. However, the biology and management of other pests like the Allium leafminer (a new invasive pest restricted to the northeastern US), onion maggot, seedcorn maggot, etc. will be addressed based on regional growers’ priorities.

Research is needed to determine if onion thrips populations have developed resistance to commonly used insecticides like spinetoram (Radiant SC). Using a laboratory bioassay, thrips populations will be examined for resistance to spinetoram and possibly other insecticides. Populations identified as resistant to spinetoram will be examined to determine the mechanism and genes that confer resistance. For example, traditional piperonyl butoxide (PBO)-based assays that determine P450-mediated metabolism will be conducted. If PBO assays indicate that P450 monooxygenases are the cause of resistance, we will sequence and compare the transcriptomes of susceptible and resistant populations in order to find the P450s that are overexpressed. If the bioassays with PBO indicate that P450-mediated metabolism is not the mechanism of resistance, we will sequence the alpha6nAChR cDNA from the most susceptible and resistant populations that are collected, following the methods from Hou et al. (2014). Based on results from these insecticide resistance studies, complementary research will address the development of insecticide resistance management programs to prolong the longevity of efficacy of insecticides like spinetoram. Such strategies may restrict the use of some products in geographic regions where resistance has developed or is developing.

Another project will concentrate on understanding dispersal of viruliferous onion thrips among onion bulb and seed crops. In some regions of the western US, onion bulb and seed crops are grown in close proximity, creating a perennial host for both thrips and IYSV. The dispersal of thrips in time and space as well as the epidemiology of IYSV where bulb and seed plantings co-occur is not well known. Likewise, the role of other “green bridge” hosts in thrips population dynamics and IYSV epidemiology is poorly understood. Densities of thrips will be monitored during the year using sticky cards and visual counts of thrips on plants, while IYSV in onions will be ascertained using DAS-ELISA and/or PCR assays. Subsamples of thrips also will be tested for IYSV using PCR assays to help identify dispersal patterns.

Management of onion thrips will continue to be evaluated using new insecticides, insecticide use patterns and alternative delivery systems. For example, efficacy of new insecticides like Minecto Pro (abamectin + cyantraniliprole) will be evaluated in small-plot field trials in the eastern and western US. Insertion of Minecto Pro and other new products into season-long insecticide programs also will be evaluated in both regions. Moreover, these season-long insecticide sequence programs will be evaluated using action thresholds on onion cultivars that are moderately resistant to thrips and grown following a fertility program that reduces onion thrips populations. These studies may be conducted in small-scale field plot trials and in commercial-scale field experiments. Compatibility of optimal, season-long insecticide sequence programs with other pesticides, especially fungicides, also will be evaluated in small-scale and commercial-scale field experiments.

In the western US, 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 producers customize and optimize insecticide programs on their farms.

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 California, Georgia, Michigan, New York, Oregon, Pennsylvania and Washington by participating members from those states.

Iris yellow spot virus. IYSV continues to be a major pathogen of importance in onion production regions in the western and northeastern US. Efforts will continue to focus on understanding the molecular epidemiology and evolution of IYSV. Using a whole genome sequencing approach, molecular characterization and genetic diversity studies of IYSV populations from the Pacific Northwest will be conducted, led by Pappu’s group, and comparative analyses carried out globally to better understand factors that might contribute to the diversity and evolution of IYSV. Interactions between IYSV and onion at the transcriptome level will be carried out 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. The 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. The biology and management of Stemphylium leaf blight (SLB), a disease that has increased in prevalence and impact in the past 5 years, will be examined primarily in the Great Lakes region. Effective management strategies involving fungicide and cultural practices will be investigated. In addition, research efforts will include downy mildew (DM) and Botrytis leaf blight (BLB) management as part of the onion foliar disease complex that commonly occurs with SLB. To confirm species identity of SLB, DNA will be extracted from 50 isolates of SLB obtained from onion fields across New York and gene sequences (Inderbitzin et al. 2009) compared with published sequences of known species. To assess potential fungicide insensitivity of the isolates, representative isolates of the SLB fungus will be tested in the laboratory with the active ingredients of fungicides commonly used in onion production, including: Scala (pyrimethanil), Rovral (iprodione), Pristine (boscalid + pyracolostrobin), Quadris (azoxystrobin), Inspire Super (cyprodinil + difenoconazole) and Merivon (fluxapyroxad + pyraclostrobin). Any insensitivity to strobilurin fungicides (e.g., azoxystrobin or pyracolostrobin) will be confirmed by DNA extraction from a subset of at least 20 isolates, and sequencing of the cytochrome b gene to identify point mutations known to be associated with fungicide resistance (Alberoni et al. 2010). Fungicide efficacy, timing and programs, and role of plant stress in SLB development will be evaluated via several on-farm, small-plot, replicated trials. Plant stress and varietal differences will be studied in greenhouse and field studies. Plant stressors will include mechanical foliage abrasion, herbicide injury and various foliar nutritional treatments to alleviate plant stress.

Another fungal pathogen, Sclerotium cepivorum, which causes white rot, is a major concern to onion growers in major onion-producing regions in the USA (e.g., California, Oregon, and the Walla Walla sweet onion production area of Washington). Since 1994, over 19,000 acres have documented white rot infestations and many fields have been abandoned from onion production, threatening the Allium industry in many areas of the western US (Nunez 2008). There is no evidence of white rot resistance in onion. Sclerotia are the resting structures of this fungus and can survive in soil for long periods, making it particularly challenging to control. White rot sclerotia germinate only in the presence of volatile sulfur compounds produced by Allium spp., an aspect of this pathogen biology that can be exploited for management of the disease. Several years of industry-funded research have shown that germination stimulants, coupled with in-furrow fungicide applications, may offer effective control of white rot (Davis et al. 2007). However, new sources of stimulants are needed. Volatile sulfur compounds in Alliums will be characterized using gas chromatography-mass spectrometry. In Oregon and California, sulfur compounds will be evaluated individually and in different combinations to identify sulfur compounds with the greatest germination stimulant activity on white rot sclerotia. Stimulants will be applied in replicated field trials, with and without fungicides, to determine the effects of potential germination stimulants and fungicides on sclerotial populations, white rot incidence and severity, and marketable yields.

In the Pacific Northwest, research will continue on the potential use of arbuscular mycorrhizal fungi inoculants in direct-seeded and transplanted onion bulb crops for enhancing onion production by increasing phosphorus use efficiency, reducing the severity of onion soilborne pathogens (particularly those causing root diseases), and promoting vigorous growth of onion plants. The impact of soil fertility levels, particularly phosphorus, on the potential benefits of mycorrhizal inoculants will be evaluated on controlled greenhouse trials and in grower-cooperator field trials under different irrigation systems to assess the importance of growers’ modifying fertilizer practices in order to benefit from using mycorrhizal inoculants. This work will be led by du Toit and Waters.

Bacterial pathogens. Management of bacterial pathogens requires an integrated approach that focuses on understanding the potential sources of bacteria (seed, transplants, soil, weeds and crop debris), their etiology and epidemiology, as well the impact of combinations of management practices to reduce losses. Efforts to reduce epiphytic bacterial populations associated with transplants through the application of pre-plant treatments will continue, as well as screening cultivars to identify reduced susceptibility.

Bacterial pathogens that cause center rot, Pantoea ananatis and P. agglomerans, are major problems in onion, especially in the eastern US. In Pennsylvania, replicated research trials will be conducted with the leadership of Gugino to evaluate the impact of timing and rate of nitrogen application on percent nitrogen in foliage and center rot incidence at harvest. 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.

In Georgia, post-harvest treatments of onion bulbs will be evaluated by Dutta and Gitaitis to reduce P. ananatis infection using novel chemistries like nanoparticles (TiO2) applied to necks, heat treatment (32°C) of bulbs, or drenching bulbs in Kocide 3000; as well as the effects of crop maturity at harvest on center rot infection, to improve management strategies against P. ananatis bulb infection. Additionally, the historic and current genetic diversity and epidemiology of P. ananatis in onion crops in Georgia will be investigated using phenotypic, physiological, and genotypic studies. This includes testing P. ananatis infection of a panel of known and unknown hosts in the Alliaceae; utilization of nutrients, growth at different temperatures and salt concentrations, and sensitivity to copper and other antibiotics; and multi-locus sequence analysis (MLSA) of P. ananatis strains using conserved housekeeping genes. Also, the effectiveness of novel control measures such as nanoparticle TiO2/Zn, Kocide 3000, and Pseudomonas fluorescens A503 will be evaluated for managing center rot.

Another bacterial pathogen, Burkholderia cepacia, which causes sour skin, is a major problem in onion production areas, especially in the southeastern US. The impact of transplanting vs. direct-seeding and weed management between cropping periods will be examined for sour skin control, led by Dutta and Gitaitis. A 4-year field trial will be established in Georgia using transplanting or direct-seeding in weedy plots vs. plots maintained weed-free, and using double-cropping of onion vs. rotation with crops that do not support the sour skin pathogen (e.g., pearl millet or carrot) vs. rotation with crops that support the bacterium (e.g., corn). A second project will examine if cross-talk occurs between mineral homeostasis and systemic acquired resistance in onion to various pathogens/pests. Onion bulbs with high vs. low levels of sour skin, and from plots treated with acibenzolar-S-methyl (Actigard) or not will be analyzed for mineral content and subjected to qPCR of extracted RNA to assess activities of PR1 (plant defense gene) activity, and Cu/Zn and Mn superoxide dismutase genes indicative of oxidative and heavy metal stress. Onions will be grown to produced bulbs high vs. low in Cu:Fe, and treated with Actigard or not treated, and subjected to the same mineral and qPCR analyses (3-year project).

Research will be continued in the semi-arid Pacific Northwest on understanding the cause(s) and management of internal dry scale and associated fungal and bacterial bulb rots that have been particularly prevalent and severe in years with periods of extreme heat stress mid-summer. The extent of internal dry scale in very warm growing seasons (e.g., 2013 to 2015 in the Columbia Basin of Oregon and Washington, and the Treasure Valley of eastern Oregon and southwestern Idaho), has resulted in 100% crop loss in some fields. Field trials on irrigation management will be carried out to assess potential alleviation of this physiological disorder using this cultural practice, along with evaluations of the timing and rates of applications of bactericides (coppers, disinfectants) and fungicides for management fungal and bacterial bulb rots. The work will be led by Waters, du Toit, and Reitz.

Objective 4. Facilitate discussions between W3008 participants and onion industry stakeholders that will advance onion pest and disease management. Participants from all states on this project will be involved in this objective. We intend to expand membership in W3008 by broadening the scope of our objectives and connecting with more stakeholders in the national onion industry. A concerted effort will be made to inform the onion industry about upcoming W3008 annual meetings via trade magazines, email, internet promotions, and a new and improved version of the www.alliumnet.com web site. Our goal is to continue to tie together effectively our collaborative research findings and disseminate the results to stakeholders at annual meetings. We have been successful in the past in this regard and have maximized our interactions with the US onion industry by having joint meetings among W2008, NARC and NOA. More details about communicating information about this project are described in the Outreach Plan.


Measurement of Progress and Results


  • New data and knowledge about the biology of the major pest and diseases of onion will be used to advance onion pest and disease management, as well as scientific knowledge.
  • 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.
  • Optimal pesticide delivery methods and reduced-risk pesticide programs will be developed and then integrated into production systems to manage season-long infestations of onion thrips and outbreaks of plant pathogens.
  • Landscape features such as size of onion production area and surrounding habitats as well as production practices related to pesticide resistance will be identified.
  • Cultural control tactics with an emphasis on reduced fertilizer application programs will be evaluated for managing onion thrips and plant pathogens.
  • Stemphylium leaf blight pathogen resistance to fungicides will be determined.
  • Relationship between plant stress and Stemphylium leaf blight will be quantified, and means of alleviating plant stress to minimize the impacts of this disease will be identified.
  • Onion cultivars tolerant to the onion foliar disease complex will be identified.
  • Effective fungicide programs will be identified to manage Stemphylium leaf blight, downy mildew and Botrytis leaf blight.
  • Volatile sulfur compounds from Alliums will be identified and evaluated individually and in combination to determine effective dosage(s) required for sclerotia germination. Field trials will determine efficacy of germination stimulants and fungicides to reduce white rot severity and increase marketable yields.
  • Cultural, chemical, and resistance tactics will be identified to improve management of bacterial bulb rots.
  • Evaluation of mycorrhizal inoculant products in growers’ production systems will help determine if such inoculants improve onion growth, nutrient use efficiency, and disease and pest tolerance.
  • Evaluation of mycorrhizal inoculant products in growers’ production systems will help determine if such inoculants improve onion growth, nutrient use efficiency, and disease and pest tolerance.
  • Collaborations among members of W3008 will synergize research and extension efforts aimed to improve US onion production.
  • Research-based information will be delivered to stakeholders through local, regional and national meetings, proceedings articles, trade journals, eXtension, peer-reviewed publications and appropriate social media.
  • Joint meetings among W3008, NARC and NOA will be held approximately every other year.

Outcomes or Projected Impacts

  • Improved, high yielding onion cultivars with increased resistance to IYSV 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, reduced-risk pesticide programs 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% fewer pesticide applications as well as replacing broad-spectrum pesticides with reduced-risk products.
  • Pesticide resistance development will be mitigated by developing insecticide resistance management programs that will retain the limited arsenal of effective pesticide products available for use in onion by at least 5 to 10 years, thereby saving growers from having to resort to more pesticide applications to manage pesticide-resistant pests and pathogens.
  • Adoption of fertilizer programs that reduce pest and pathogen populations in onions will increase profitability by at least 5%. These programs will help the onion industry become more sustainable by reducing fertilizer inputs. Additionally, environmental quality will improve by using less fertilizer.
  • Adoption of novel practices for reducing bacterial diseases of onions will keep the US onion industry profitable and sustained.
  • Identification and adoption of a fungicide program that is cost-effective for controlling Stemphylium leaf blight, downy mildew 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.
  • Identification and evaluation of sulfur compounds that promote white rot sclerotia germination will provide the onion industry with information that can be used to identify potential sources of germination stimulants. A two-pronged approach consisting of germination stimulants and fungicides may reduce sclerotia populations in infested fields, reduce the potential for further spread of the fungus to new production areas, and allow growers to produce a profitable onion crop on land that was previously infested with white rot.
  • Identification of new and emerging pests and diseases and consequently determining best management practices for them in a timely manner will shave off years of unneccesary losses and save the US onion industry million of dollars in preventable losses.
  • Identifying mycorrhizal inoculant products, formulations, and methods of application that enhance onion growth, nutrient use efficiency, and disease and pest tolerance is expected to enable growers to reduce fertilizer application rates and, potentially, reduce the numbers of pesticide (fungicide and insecticide) applications, thereby improving the economic viability of onion production.
  • Joint W3008, NARC and NOA meetings and improved outreach techniques will result in a 25% increase in onion grower participation at the W3008 and NARC meetings, and consequently increased sharing of information and collaboration among researchers, onion growers and the allied onion industry. Priority research issues and cooperative strategies to obtain funding, conduct research and information transfer will result.


(2017):Disseminate results and impacts from the 5-year W2008 project on onion thrips, IYSV and other diseases with the onion industry and other stakeholders. This has been done previously via the trade publication Onion World. Submit a formal request to renew and broaden the multi-state project (W3008), and invite participation by all interested Agricultural Experiment Stations, USDA-ARS personnel, and onion commodity groups. Research and extension activities to address the proposed objectives will be continued or initiated. If our W3008 proposal is accepted, we will meet in Grand Rapids, MI in conjunction with the Great Lakes EXPO in early December 2017.

(2018):Research and extension activities to address the proposed objectives will be continued or initiated. Relevant findings generated during this project will be published and disseminated. The annual W3008 meeting will be held in December 2018 at a venue to be determined later.

(2019):Research and extension activities to address the proposed objectives will be continued or initiated. Relevant findings generated during this project will be published and disseminated. The annual W3008 meeting will be held in conjunction with NOA and NARC meetings in Madison, WI in July 2019.

(2020):Research and extension activities to address the proposed objectives will be continued or initiated. Relevant findings generated during this project will be published and disseminated. The annual W3008 meeting will be held in December 2020 at a venue to be determined later.

(2021):Research and extension activities to address the proposed objectives will be continued or initiated. Relevant findings generated during this Project will be published and disseminated. The annual W3008 meeting will be held in conjunction with NOA and NARC meetings in December 2021.

(2022):Comprehensive management practices for thrips and pathogens of onions will be adopted readily by producers nationwide. Results and impacts from the 5-year project (W3008) on integrating management strategies for pest and diseases will be disseminated to stakeholders. A proposal to renew or terminate the regional research committee (W3008) in 2022 will be discussed and appropriate actions taken.

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. Annual meetings for W3008 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 W3008 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, and sent to committee members and archived on the NIMSS web site. 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 the W3008 (see attachment).


Directors of Agricultural Experiment Stations receive requests from researchers to join Multi-State Projects, like our proposed W3008. Future members of W3008 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 W3008. This person will not have voting rights. Steve Loring is currently the Administrative Advisor for the W2008 project and will likely to serve for the W3008 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 W3008 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 W2008 Regional Project (2016):

Chair: Tim Waters, Associate Professor/Regional Vegetable Specialist, Washington State University - WA

Vice-Chair: Lindsey du Toit, Professor, Dept. of Plant Pathology, Washington State University – WA

Secretary: Christine Hoepting, Sr. Extension Educator, Cornell Vegetable Program, Cornell University – NY

Past Chair: Mark Uchanski, Assistant Professor, Dept. of Horticulture and Landscape Architecture, Colorado State University - CO

W3008 proposal rewrite coordinator: Brian Nault, Professor, Dept. of Entomology, Cornell University - NY.

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Sharma-Poudyal, D., Paulitz, T., Porter, L., Eggers, J., Hamm, P., and du Toit, L.J. 2013. Efficacy of fungicides to manage onion stunting caused by Rhizoctonia spp. in the Columbia Basin of Oregon and Washington, 2011-2012. Plant Dis. Manage. Rep. 7:V047.

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