INTEGRATED ONION PEST AND DISEASE MANAGEMENT

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1015428
• Multistate No.: W-3008
• Project Start Date: Apr 26, 2018
• Project End Date: Sep 30, 2022
• Program Code: [(N/A)]- (N/A)

Recipient Organization
NEW MEXICO STATE UNIVERSITY
1620 STANDLEY DR ACADEMIC RESH A RM 110
LAS CRUCES,NM 88003-1239

Performing Department
Plant and Environmental Sciences

Non Technical Summary
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.

Animal Health Component

50%

Research Effort Categories

Basic

50%

Applied

50%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1451	1081	50%
212	1451	1081	25%
211	1451	1081	25%

Knowledge Area
212 - Pathogens and Nematodes Affecting Plants; 211 - Insects, Mites, and Other Arthropods Affecting Plants; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1451 - Onion, garlic, leek, shallot;

Field Of Science
1081 - Breeding;

Keywords

onion breeding

iysv resistance

thrips resistance

genetics

Goals / Objectives
Evaluate onion germplasm for resistance to pathogens and insects.

Project Methods
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.

Progress 10/01/18 to 09/30/19

Outputs
Target Audience:The target audience for this research is the numerous individuals and companies involved in the United States and New Mexico onion industry. These interested parties include growers, shippers, handlers, brokers, dealers, and salespersons. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training of graduate and undergraduate students with regards to trait measurement, instrument use, plant pathogen maintenance, pathogen inoculation, seed cleaning, proper seed storage, statistical analysis, and data collection. How have the results been disseminated to communities of interest?A presentation was made at the 2019 annual meeting of Multistate Research Project W3008: Integrated Onion Pest and Disease Management on July 24, 2019 regarding research work on onion thrips. Three presentations were made at the 2019 International Allium Research Conference, 2019 National Allium Research Conference, and 2019 National Onion Association Annual Convention in Madison, WI on July 27, 2019 regarding research work on breeding for Fusarium basal rot resistance. What do you plan to do during the next reporting period to accomplish the goals?No changes.

Impacts
What was accomplished under these goals? Seeds of original, intermediate, and advanced Fusarium basal rot (FBR)-selected populations and one resistant and two susceptible checks were sown in fields at the Fabian Garcia Science Center (FGSC) in Oct. 2018. There were a total of 54 entries in the study that were replicated four times. In Mar. 2019, cultures of FOC isolate CSC 515 were initiated from infected, frozen wheat straw. Onion bulbs were inoculated with mycelium and spores from these cultures. The pathogen was reisolated from infected basal plate tissues of these inoculated bulbs. Small sections of infested basal plate tissue were placed on petri plates of PDA to encourage pathogen growth. After 10 days, spores were rinsed from the plates with distilled water and the resulting spore suspension was saved. These spores were mixed with cooled, autoclaved PDA media to result in a final spore concentration of 3 x 104 spores?ml-1 of PDA in the poured plates. From May to June, bulbs were harvested from the planted populations once plants had reached maturity. After harvest, the basal plate of all bulbs from the plot was cut transversely and a 1 cm diameter plug of PDA inoculum was applied to the cut surface. Bulbs were placed in plastic crates and crates were placed in black plastic bags for 1 day. After 21 days from inoculation, the basal plate of each bulb was cut again and the basal plate was rated. Bulbs, that were rated as a 9, were discarded while all other bulbs were saved to produce seed for the following year. The average disease severity was calculated from the first 20 bulbs selected arbitrarily from the plot. As in the previous year, the inoculation method was very effective at causing disease in most bulbs. This effectiveness is very important for selecting FBR resistant bulbs. The susceptible check entries exhibited a high level of disease severity while the resistant check exhibited less. Of the FBR-selected populations, recent selections of NuMex Crimson, NuMex Crispy, NuMex Sweetpak, NuMex Vado, and Serrana exhibited less disease consistently over years than previous generations and the susceptible checks. The most recent FBR-resistant selections of NuMex Camino, NuMex Chaco, and NuMex Mesa exhibited less disease than the susceptible checks. In some instances, the most recent selection exhibited less disease than the FBR-resistant check. This result indicates that breeding for FBR resistance has been successful in producing germplasm that is more resistant than currently-available short-day commercial cultivars. In Oct. of 2018, bulbs selected from the third generation lines of all seven cultivars were placed into separate locations in a field at the FGSC to produce seed of each line in the following year. In Apr. 2019, those bulbs produced seedstalks and began the flowering process. Crossing cages were constructed and placed over the flowering bulbs. In May, pollinators were introduced into the cages to pollinate flowers. These pollinators remained in the cages for 3 additional weeks until flowering had finished. In July, seed capsules were harvested and seed cleaning was initiated. Seed was produced from a total of 17 different germplasm lines associated with this project. This seed will be used for further evaluations to ascertain additional progress made for resistance to FBR. Our results from this past year confirm that the developed inoculation protocol is successful at identifying resistant bulbs. This protocol could be used by other onion breeding programs to develop FBR resistant cultivars. If the levels of FBR resistance observed this past year is consistent over years, FBR-resistant germplasm will be released to commercial breeding programs for the development of FBR-resistant cultivars. The onion industry in New Mexico and the US is valued at farm gate annually at $80-90 million and $900-1,000 million, respectively. Onion stakeholders have identified onion thrips and Iris yellow spot virus (IYSV) as the greatest pest threats to onion yield and economic sustainability. Germplasm from the NMSU onion breeding program has been identified in previous studies to possess fewer thrips per plant and less severe Iris yellow spot (IYS) disease symptoms than commercial cultivars. A study is needed to understand the mechanisms involved in these trait expressions and to conduct additional cycles of selection for thrips tolerance and reduced disease expression. The potential impacts of this study are the offsets of yield reduction caused by IYS and onion thrips and the cost of chemical control of thrips. The potential economic impacts of this research could be 10-15% of the current farm-gate value that is estimated to be lost due to injury from IYS and onion thrips. In addition, the cost of chemical control of thrips, that is estimated at $7.5-12 million, could be saved with the availability of a thrips-tolerant onion cultivar. In Oct. 2018, onion bulbs were placed on the first and last bed and at the front and back borders of an onion thrips/IYS study at the FGSC. Seed of NuMex Freedom was sown at the same time on every seventh bed to ensure that thrips are spread throughout the field. In Jan. 2019, seed of four NMSU germplasm lines and Rumba, an IYS-susceptible cultivar was sown in flats. Plants were transplanted to 3.3 m long field plots in Mar. 2019 with 2 rows of plants per plot and 7.5 cm between plants within the row. Plants were irrigated using drip irrigation tape that was placed 10 cm beneath the surface of the bed and centered on the bed. The field was arranged using a split-plot design with irrigation as whole plots and selections as subplots. Each whole plot was replicated three times and within whole plots, selections were arranged in a RCBD with four replications. On 21 Apr., irrigation treatments of well-watered (not to exceed 30% managed allowed depletion [MAD] based upon crop evapotranspiration) and water-limited conditions (50% MAD) were initiated. Ten plants were randomly-selected from each plot and identified with a plastic label. Starting on 7 May and every two weeks afterwards, plant height, leaf number, and sheath diameter were measured for each of the ten plants. Starting on 8 May and four additional times two weeks apart, the number of adult and juvenile thrips were counted from each of the ten plants from each plot. On 5 Jun., the severity of Iris yellow spot symptoms was rated for each of the ten plants on a scale of 0 to 4, where 0 = no symptoms; 1 = 1-2 small lesions per leaf; 2 = more than 2 medium-sized lesions; 3 = lesions coalescing on more than 25% of the leaf tissue; 4 = more than 50% leaf is dead. These ratings were repeated for two additional times two weeks apart. At 8 and 10 weeks after transplanting, plants of Rumba possessed more juvenile and total thrips than plants of the four NMSU germplasm lines when averaged over irrigation treatments. At 12 weeks, plants of Rumba grown under deficit irrigation had fewer juvenile and total thrips than plants grown under the well watered treatment. For both irrigation treatments, plants of Rumba exhibited more thrips than plants of the NMSU germplasm lines when thrips were counted at 12 weeks. After 12 weeks, the number of thrips per plant decreased for all entries except for NMSU 12-337. At 16 weeks, plants of NMSU 12-337 possessed more juvenile and total thrips than plants of other entries. This difference was mainly due to the maturity of plants of NMSU 12-243, 12-236, and 12-238, the poor performance of Rumba plants, and the actively growing plants of NMSU 12-337. When averaged over all entries, plants grown under the well watered treatment exhibited a greater number of leaves, plant height, and sheath diameter than plants grown under deficit irrigation from 10 to 16 weeks after transplanting. At 12, 14, and 16 weeks, plants of Rumba exhibited more severe IYS than plants of all other four entries.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Singh, N. and C.S. Cramer. 2019. Improved tolerance for onion thrips and Iris yellow spot in onion plant introductions after two selection cycles. Horticulturae 5:18. doi 10.3390/horticulturae5010018.

Progress 04/26/18 to 09/30/18

Outputs
Target Audience:The target audience for this research is the numerous individuals and companies involved in the United States and New Mexico onion industry. These interested parties include growers, shippers, handlers, brokers, dealers, and salespersons. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training of graduate and undergraduate students with regards to plant pathogen maintenance, pathogen inoculation, seed cleaning, proper seed storage, statistical analysis, and data collection. How have the results been disseminated to communities of interest?A presentation was made at the 2018 annual meeting of the American Society for Horticultural Science in Washington, DC on August 1, 2018 regarding research work on breeding for Fusarium basal rot resistance. What do you plan to do during the next reporting period to accomplish the goals?No changes.

Impacts
What was accomplished under these goals? Fusarium basal rot (FBR) is a soil-borne fungal disease that causes a disintegration of the onion bulb basal plate (compressed stem) thus killing a plant growing in the field. Once a bulb becomes infected with the fungal pathogen, the disease and the resulting decay it causes cannot be halted. Any plants exhibiting foliage symptoms consistent with the disease must be discarded, thus reducing yield. Soil fumigation, although costly, and crop rotation cycles of five years or more can reduce the frequency of the disease, but will not prevent it from occurring. FBR-resistant cultivars currently do not exist. Since onions have been grown in New Mexico for more than 100 years, many fields have had multiple onion crops in their history. In addition, as agricultural land becomes sequestered into residential development or perennial agricultural crops, such as pecan, the number of fields available for adequate rotation decreases and the rotation time between successive onion crops decreases to three years or less. The FBR pathogen also has the ability to infect other plant species and to survive on dead plant matter in the soil, thus increasing its longevity in the soil and decreasing the benefits of crop rotation. Seeds of original, intermediate, and advanced FBR-selected populations and one resistant and two susceptible checks were sown in fields at the Fabian Garcia Science Center (FGSC) in October 2017. There were a total of 55 entries in the study that were replicated four times. In March 2018, cultures of FOC isolate CSC 515 were initiated from infected, frozen wheat straw. Onion bulbs were inoculated with mycelium and spores from these cultures. The pathogen was reisolated from infected basal plate tissues of these inoculated bulbs. Infected bulbs served as an inoculum source for generating fresh inoculum and to maintain pathogen virulence. Small sections of infested basal plate tissue were placed on petri plates of PDA to encourage pathogen growth. After 10 days, spores were rinsed from the plates with distilled water and the resulting spore suspension was saved. These spores were mixed with cooled, autoclaved PDA media to result in a final spore concentration of 3 x 104 spores?ml-1 of PDA in the poured plates. From late May to late June of 2018, bulbs were harvested from the planted populations once plants had reached maturity. After harvest, the basal plate of all bulbs from the plot was cut transversely and a 1 cm diameter plug of PDA inoculum was applied to the cut surface. Bulbs were placed in black plastic crates and crates were placed in black plastic bags for 1 day to encourage mycelium growth and infection. After 21 days from inoculation, the basal plate of each bulb was cut again and the basal plate was rated. Bulbs, that were rated as a 9, were discarded while all other bulbs were saved to produce seed for the following year. The average disease severity was calculated from the first 20 bulbs selected arbitrarily from the plot. Disease incidence was calculated as the percentage of diseased bulbs. Data were statistically analyzed to determine entry means for disease severity and incidence. Single-degree-of-freedom contrasts were calculated to determine statistical differences between pairs of entry means. These analyses were conducted to determine if selection had resulted in a reduction in disease severity and incidence. The inoculation method was very effective at causing disease in most bulbs. This effectiveness is very important for selecting FBR resistant bulbs. The susceptible check entry exhibited a high level of disease severity and incidence while the resistant check exhibited less disease severity. Of the FBR-selected populations, recent selections of 'NuMex Crimson', 'NuMex Mesa', and Serrana' exhibited less disease consistently over years than previous generations. The most recent FBR-resistant selection of 'NuMex Mesa', 'NuMex Sweetpak', and 'NuMex Vado' exhibited less disease than previous generations and the susceptible checks. In some instances, the most recent selection exhibited less disease than the FBR-resistant check. This result indicates that breeding for FBR resistance has been successful in producing germplasm that is more resistant than currently-available short-day commercial cultivars. In October of 2017, bulbs selected from the second and third generation lines of all seven cultivars were placed into separate locations in a field at the FGSC to produce seed of each line in the following year. In April 2018, those bulbs produced seedstalks and began the flowering process. Crossing cages were constructed and placed over the flowering bulbs. In May 2018, pollinators (honeybees and blue bottle flies) were introduced into the cages to pollinate flowers. These pollinators remained in the cages for 2-3 additional weeks from then once flowering has finished. In July 2018, seed capsules were harvested and seed cleaning was initiated. Seed was produced from a total of 40 different germplasm lines associated with this project. This seed will be used for further evaluations to ascertain additional progress made for resistance to FBR. Our results from this past year confirm that the developed inoculation protocol is successful at identifying resistant bulbs. This protocol could be used by other onion breeding programs to develop FBR resistant cultivars. If the levels of FBR resistance observed this past year is consistent over years, FBR-resistant germplasm will be released to commercial breeding programs for the development of FBR-resistant cultivars.

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: Kamal, N. and C.S. Cramer. 2018. Selection progress for resistance to Iris yellow spot in onions. HortScience 53:1088-1094.