Progress 09/01/23 to 08/31/24
Outputs
Target Audience:A key audience target for Objectives 1, 2, 3, and 5 are coffee growers and extension agents. Data collected under Objective 1 will benefit the coffee industry in Hawaii and Puerto Rico by identifying high-quality coffee varieties that are resistant to CLR and other diseases for long-term replanting of damaged fields. In the immediate term, recommendations generated by Objectives 2 and 3 will assist growers with agronomic field management on susceptible trees. Economic analyses under Objective 5 will inform growers about the cost effectiveness of each recommendation. Specific outreach and extension efforts are described further under the Accomplishments: Communities of Interest section. Information sharing between Hawaii and Puerto Rico scientists will benefit the national and international science community. The genomic activities under Objective 4 are targeted to researchers, plant breeders and plant pathologists. Knowledge generated under this grant strengthens the coffee industry in Historically Underserved and economically depressed areas like the mountain region of Puerto Rico and the Ka'u region of Hawaii by maintaining and creating jobs in farms and coffee processing organizations. These two regions are denoted on the Federal government's Justice40 Initiative map. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Objective 1: Propagation of CLR-Resistant Varieties Four part-time students were trained in aseptic techniques and general coffee tissue culture skills at USDA ARS Hilo. Three part-time technicians were trained for coffee somatic embryogenesis and Rita® Bioreactors and eight high school interns were trained for basic tissue culture at HARC. How have the results been disseminated to communities of interest?Regular and ongoing activities have been conducted to facilitate communication and outreach to all communities of interest. Some of these Extension-specific activities are listed under the "Other Products" Section. In part with SCRI project funding, Extension provided 21 educational opportunities to 523 coffee producers and stakeholders to learn about CLR best management practices, coffee pruning, sprayer calibration, safe pesticide and respirator use, CLR resistant varieties, coffee tissue culture, coffee root-knot nematode, and coffee propagation via workshop, webinar, and field day events. During events, we provided translators and translated materials to Spanish, Ilocano, and Tagalog. Our HawaiiCoffeeEd.com website is frequently visited by over 15,300 unique viewers. Information at this site can also be translated to dozens of languages. We hosted educational booth displays during industry events such as the Kona Coffee Cultural Festival's Ho'olaulea, Kona Coffee Farmers Association Symposium, Hawaii Coffee Association's Annual Conference, and Maui Coffee Association's Seed to Cup Festival where over 4,500 people were exposed to the information provided. Also, 22 farm doctor visits were conducted throughout the state including on Kauai and the districts of Kau, Kona, Hamakua, and Waimea on Hawaii Island. Extension shared 28 events and announcements newsletters with over 1,430 online and mailer recipients. These newsletters provide agricultural information, events, research and technologies with Hawaii, California, and Puerto Rico's producers and stakeholders from UH-CTAHR, USDA, and NGOs. Scientists presented research at the Kona Coffee Farmers Association Symposium & Annual Conference (February) and the Hawaii Coffee Association Annual Conference (July). Multiple talks and updates were presented at UH CTAHR extension CBB/CLR virtual talk story sessions and webinars, events organized by the UPR-Extension Service, a local agronomy meeting in PR, and several other local pest management and coffee grower meetings/workshops. This includes two cupping workshops with CLR-resistant varieties, given at the HCA conference with over 50 participants. This workshop highlighted coffees from the same genotypes in the IMLVT and other CLR resistant coffees imported into Hawaii. This workshop was to help alleviate concerns that new CLR resistant varieties will not meet the Hawaii Specialty Coffee standards. Information was also distributed during ongoing farm visits. Continued contact and direct communication with coffee farmers is needed to understand their point of view regarding the management of CLR, which will be useful to develop an IPM program for CLR adapted to Hawaiian coffee agroecosystems. In addition, information on the cost of controlling CLR (e.g., sprays of fungicides, pruning, etc.) is critical to understand the cost-benefit of those practices and the economic viability. Consortium Project Investigators meet quarterly at an All-Team online meeting to discuss research successes and barriers. Minutes are kept, and subsequently shared. This provides regular contact and follow up for issues between objectives and disciplines. Dr. Cheng presented the latest update of this research at the XX International Plant Protection Congress in July 2024. Dr. Keith presented a poster at Plant Health 2024 in Memphis, TN. The Project Manager attends the monthly Hawaii Coffee Association and Kona Coffee Farmers Association meetings, and briefs stakeholders on SCRI grant activities. What do you plan to do during the next reporting period to accomplish the goals?Objective 1A: Field Trials of CLR Resistant Varieties WCR IMLVT lines will continue to be grown out for testing, with additional plant material to be imported to and from Hilo and Mayagüez. Plant material from remaining differential plants from CENICAFE in Colombia will be shipped to Mayagüez. Renovation of the Kona Extension Research Station demonstration fields will be conducted in late 2024 to prepare for future coffee plantings and to expand the demonstration plot. Historically, these fields have poor drainage and rock that complicates planting arrangements and causes trees to die prematurely. Objective 1B: Propagation of CLR Resistant Varieties HARC will continue propagating Maite, Obata and Fukunaga cultivars as well as any newly identified CLR-resistant cultivars. Germinated plantlets will be rooted and transplanted in the soil for acclimatization. Isolation field plots of Obata seedlings, produced via self-pollination and confirmed via DNA typing, will be established to be able to provide seeds. Objective 1C: Root-knot Nematode Resistance Trials and Enhancement of Resistance Screening Additional nematode bioassays will be conducted as more CLR-resistant material becomes available. Nematode surveys will be conducted on coffee farms on Maui and Kauai. Objective 2: CLR Surveys and Environmental Monitoring We will conduct a third (final) year of monitoring at Ka'u and Hilo, Hawaii sites to capture differences in CLR biology, coffee plant phenology, management practices, and weather (third year of Kona data collected in 2024). We will conclude PR field data collection in March 2025; analyze and write up data. Utilizing data currently collected, the consortium will collaborate with the Phenotype Screening Corporation (PSC) to assist in evaluating and modifying the ExpeRoya Coffee Leaf Rust Predictive Software Model (ExpeRoya), developed for coffee leaf rust disease incidence prediction on coffee plantations in Central America, to conditions experienced on Hawaii Island. The current model accuracy is low, and PSC will investigate three hypotheses which may explain the discrepancy: (i.) coffee leaf rust infection in Hawaii is humidity driven rather than rainfall driven as in Central America, (ii.) fungicide use in Hawaii plantations is fundamentally different than in Central America, (iii.) pruning practices are different enough to affect model accuracy. Objective 3A: Field and Laboratory Research to Identify Effective and Safe Fungicides We plan to evaluate rotation programs with the use of preventive and systemic fungicides for the full coffee season. Fungicide efficacy test will continue for new fungicides, including additional systemic fungicides and biopesticides in lab assays, greenhouse studies and in the field. Potted coffee plants are growing in preparation for these new experiments. We will estimate cost to control CLR in a rotation program based on farm records. Objective 3B: Biological Control of CLR Further testing of these and other isolates of Simplicillium and Akanthomyces, as well as others in the Cordycipitaceae family, will be conducted in the lab and eventually in the field. We will continue testing fungal isolates from Hawaii against CLR on leaf disks as treatments for CLR pre- and post-infection. Successful isolates will be selected for testing in the field. We will also survey for endophytic fungi associated with other parts of field-grown coffee plants in Hawaii for potential CLR control agents. Work is ongoing to describe two potential new species from these efforts. We plan to submit a manuscript on field application of biocontrol fungi in Puerto Rico. Objective 3C. Optimizing Field Health for CLR Management in Non-Resistant Varietals We will continue visiting farms regularly to document all agronomic practices and CLR management and conduct comparative analyses on the differences in agronomic practices and how this affects CLR. We will write a paper to characterize coffee soil/tissue nutrient deficiencies and imbalances across the State. We plan to support coffee farmers with specific recommendations for improving coffee plant nutrition based on three rounds of soil/leaf tissue sampling, previous fertilization records, elevation, planting density, tree age, and time of year. Objective 4A: Genetics of CLR Mayaguez ARS will extract DNA of CLR isolates from Costa Rica and Colombia for population genetics, and complete and analyze microsatellite data for PR samples. The Purdue lab is collaborating with Dr. Rachel Koch at Ft. Dietrick to generate a new CLR genome adequately prepared to allow haplotype phasing resolving which sets of variants along chromosomes are inherited from each parent. We are additionally collaborating with Dr. Marco Cristancho from CENICAFE to annotate the genomes of various isolates from Portugal, Perú and Brazil, which will allow us to compare multiple CLR isolates. To corroborate results on CLR origin, the Purdue lab will 1) perform additional sampling and analysis of African spores, 2) secure additional historical specimens from other herbaria, 3) secure additional current specimens that encompass most of the 50 top world coffee producer countries, and 4) samples from Hawai'i that include all coffee producing regions/islands. The lab recently received additional spores from Hawaii for infection to start other analyses (e.g. differential experiments to find genes associated with virulence and that are specific to different races of CLR). Objective 4B: Understanding Resistance Analyze transcriptomic data to determine gene expression for resistant and non-resistant plants. Objective 5: Economics We will write a report of the grower survey results and share the report for outreach purposes. We will initiate and complete the cost-benefit analysis focused on replanting new CLR resistant varieties, and initiate research plans for a market level study to understand the industry response to new varieties being grown by growers in Hawaii.
Impacts
What was accomplished under these goals?
Objective 1A: Field Trials of CLR Resistant Varieties Coffee Leaf Rust resistant lines are being propagated in Hilo (ARS) and Kunia (HARC), Hawaii and Mayaguez (ARS), Puerto Rico. Permits from USDA APHIS as well as Hawaii and Puerto Rico Department of Agriculture have been obtained for additional material to be shipped in from World Coffee Research (WCR) in El Salvador. Plant material in these new imports include coffee accessions from the WCR International Multi-Location Variety Trials and Innovea Arabica Breeding Network. In addition, differential coffee plants for identification of CLR races are being obtained from CENICAFE and CATIE and shipped to ARS-Mayagüez. Objective 1B: Propagation of CLR Resistant Varieties Coffee cultivar 'Maite' was identified in a grower's field as a CLR-resistant genotype. The material was initiated into culture and shipped from USDA ARS Hilo to HARC in May 2024. Somatic embryos have also been initiated from CLR-resistant 'Obata' and nematode-tolerant 'Fukunaga'. The Fukunaga material will be used by farmers to grow nematode-resistant rootstock for grafting new coffee cultivars. Objective 1C: Root-knot Nematode Resistance Trials and Enhancement of Resistance Screening A survey of coffee farms on Oahu was conducted to determine the spread of Meloidogyne konaensis, Kona coffee root-knot nematode. Using morphology and PCR with species-specific primers, none of the farms surveyed had M. konaensis populations. A low population of M. incognita was found at one location and other less damaging plant-parasitic nematodes including reniform, Rotylenchulus reniformis, and spiral nematodes, Helicotylenchus spp., likely associated with the orchard groundcover, were recovered. A greenhouse bioassay is ongoing to evaluate CLR-resistant lines from UH CTAHR for resistance or tolerance to M. konaensis. A hydroponic method of rearing M. konaensis was developed to produce volumes of clean nematode inoculum for large screening trials. Objective 2: CLR Surveys and Environmental Monitoring In Hawaii, a third year of monthly CLR surveys continued. Spore sampler and fruit load data were collected from 15 farms across Kona (8), Ka'u (6) and Hilo (1). An additional 9 farms were monitored for CLR in Kona and 6 in Ka'u. Data collection was completed for CLR life stage and spore germination/viability study from a subset of farms. In Puerto Rico, field data has been collected every three weeks from fifteen sites and weather stations were installed. Data was collected on CLR incidence, weather data, management activities, spore dispersal via wind, fruit load, CLR life stage, spore germination/viability, and costs of fungicide applications. Average CLR incidence is high during the harvest and post-harvest (Aug-Feb, ~30%) and low during fruit development (Mar-Jul, 5-10%). Incidence and severity are positively correlated. No significant difference was observed in incidence at varying elevations. Incidence was lower in 2024 compared to previous years. Spore capture is positively correlated with incidence. Spore germination is highest in shade vs. sun and on low vs. mid branches. Objective 3A: Field and Laboratory Research to Identify Effective and Safe Fungicides Completed two-year field trial of registered fungicides to test efficacy and duration of protection of six fungicides, with CLR incidence and leaf retention recorded from 15 trees per block. Priaxor and Badge provided significantly longer protection and greater efficacy of CLR control compared to biological and botanical products. Biological fungicides provided protection for 4-5 weeks, while copper products protected for 5-8 weeks and Priaxor (translaminar) protected leaves for 8-12 weeks.A single Priaxor spray provided the same level of protection compared to a combination of three sprays (Priaxor / Badge / Priaxor) over the same time frame. A manuscript is being prepared for submission to Crop Protection and results have been shared in webinars. Of fungicides not-yet-registered, Year-2 field trial was completed on 3 systemic fungicides and 2 commercially available biological control products, which are Azoxystrobin, Picoxystrobin, Myclobutanil, Extract of Reynoutria sachalinensis, and Pseudomonas chlororaphis strain AFS009, plus an untreated control. Three replications of each treatment and control were included. All systemic products (Abound, Alto 100SL, Aproach Prima, Aprovia Top, Excalia, and Priaxor) had significantly lower mean area under the disease progress stairs (AUDPS, p < 0.05) compared to the non-systemic products (Cafedak in rotation with Badge SC; Badge SC, Serenade ASO, Double Nickel LC rotation; PureCrop; and the Widespread Max negative control). These data show that systemic products are valuable tools for farmers to combat CLR. The industry will seek registration of the systemic fungicides for use on coffee. Objective 3B: Biocontrol Ten isolates of fungi recovered from the island-wide survey were assessed as a preventative treatment against CLR on coffee leaf disks. The fungi were five isolates of Simplicillium species, and a single isolate each of Lecanicillium/Verticillium, Chlonostachys, Chlorocillium, Acremonium, and Akanthomyces. Several isolates show promise (sporulation ranging from 15.6% to 37.5% of leaf disks, compared to the positive control which had 81.3% of disks with sporulation). Objective 3C. Optimizing Field Health for CLR Management in Non-Resistant Varietals Evaluations of agronomic practices and management of CLR were conducted on 11 coffee farms in Kona (6) and Ka'u (5). Data were gathered for fungicide and fertilizer applications, weed control, pruning style, coffee production, and nutrient deficiencies/imbalances based on soil/leaf tissue samples. As expected, agronomic practices correlate with CLR incidence. During the second part of the season, the traditional "Kona-style" pruning (trees with different aged verticals) have shown higher CLR infection (>25%) in comparison with Beaumont-Fukunaga style (< 15%), block stumping (< 10%), and hedge/umbrella style (< 5%). During the full coffee season, coffee farms that only applied preventive fungicides had high CLR infection (5-45%) in comparison with coffee farms that used a combination of the translaminar fungicide Priaxor (1- 2 times) with preventive fungicides resulting in low CLR infection (0.5- 5%). Objective 4A: Genetics of CLR We have accomplished RNA sequencing from a CLR isolate from Hawaii and one from Panama that will be used to aid in genome annotation. We have continued the population analysis using 12 SSRs and added additional samples for better geographical representation including specimens from Kenya, Rwanda, Puerto Rico, and historical samples obtained from the USDA National Fungus Collections (BPI). A preliminary analysis that included 11 SSRs and 395 samples showed evidence of potential second introductions of CLR to Brazil and Puerto Rico; and revealed that the few representative samples we currently have from Kenya and Rwanda were unique MLGs (multi-locus genotypes) not seen in other countries. This supports our hypothesis that CLR originated in the Lake Victoria region and that if sexual recombination is occurring, and therefore a potential alternate host for this rust is present, it would be present in this region. Objective 4B: Understanding Resistance RNA from 70 samples of coffee plants susceptible vs. resistant to CLR has been extracted at UPR and TARS laboratories. Differential gene expression may indicate the mechanism for resistance. Objective 5: Economics The coffee grower survey was completed, with more than 80 responses received by the end of October 2023. We used the survey data to conduct economic analysis to better understand the costs, benefits, and tradeoffs across different control strategies from the perspective of coffee growers and the larger coffee industry.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Species diversity, host range, and biogeography of the gall midges (Cecidomyiidae: Mycodiplosis) feeding on spores of rust fungi (Basidiomycota: Pucciniales). Journal of Insect Science 24(4) 18
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Achievements and challenges in controlling coffee leaf rust (Hemileia vastatrix) in Hawaii. Agrochemicals 3
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2024
Citation:
Survey of potential fungal antagonists of Coffee Leaf Rust (Hemileia vastatrix) on Coffea arabica in Hawaii, USA. Brazilian Journal of Microbiology 55
- Type:
Other
Status:
Published
Year Published:
2024
Citation:
Meisner, a coffee rootstock selection with increased tolerance to the Kona coffee root-knot nematode. University of Hawaii Cooperative Extension Bulletin FN-67:1-6.
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Progress 09/01/22 to 08/31/23
Outputs
Target Audience:A key audience target for Objectives 1, 2, 3, and 5 are coffee growers and extension agents.Data collected under Objective 1 will benefit the coffee industry in Hawaii and Puerto Rico by identifying high-quality coffee varieties that are resistant to CLR and other diseases for long-term replanting of damaged fields.In the immediate term, recommendations generated by Objectives 2 and 3 will assist growers with agronomic field management on susceptible trees.Economic analyses under Objective 5 will inform growers about the cost effectiveness of each recommendation.Specific outreach and extension efforts are described further under the Accomplishments: Communities of Interest section. Information sharing between Hawaii and Puerto Rico scientists will benefit the national and international scientific community.The genomic activities under Objective 4 are targeted to researchers, plant breeders and plant pathologists. Knowledge generated under this grant strengthens the coffee industry in Historically Underserved and economically depressed areas like the mountain region of Puerto Rico and the Ka'u region of Hawaii by maintaining and creating jobs in farms and coffee processing organizations. These two regions are denoted on the Federal government'sJustice40 Initiative map. Changes/Problems:A significant delay has arisen due to the Hawaii Department of Agriculture's (HDOA)Plant Quarantine division. Shifting protocols and loss of staff within the Department has delayed permitting under Objective 1. Each new cultivar requires a 1 year quarantine, but new protocols for completingquarantineare currently under development by the Hawaii Department of Agriculture. At this time, APHIS requires a one year quarantine, and HDOA is requiring a separate one year period, rather than running concurrently. Introducing key varieties has taken longer than the expected 1 year quarantine period.In varieties that are through quarantine, loss of plant inventory due to tissue culture contaminationhave dramatically reduced the number of plants available for propagation and subsequent field testing. Industry stakeholders are assisting grant personell in seeking a solution to this issue. The sudden retirement of the University of Hawaii PI under Objective 1b (micropropagation) has delayed the expansion of materials. This Objective has now been transferred to the Hawaii Agriculture Research Center. In Hawai'i, testing of fungal isolates under Objective 3B is still in thein vitroandin plantastages due to the sheer number of fungal isolates to test. Purduestruggled with repeatability and maintenance of in vivo CLR infections in the greenhouse under Objective 4Bbut have recently optimized the protocol for the successful in vivo maintenance of CLR in growth chambers. This protocol is being used to 1) obtain sufficient infected tissue samples for RNA extraction for genome annotation and differential experiments to find genes associated with virulence and that are specific to different races of CLR. 2) increase and maintain different races of CLR for subsequent analyses. Finding variable markers to study CLR population genetics has been difficult in Puerto Rico. The sole coffee extension agent in the state of Hawaii is currently on extended leave, which has slowed development of materials for growers. What opportunities for training and professional development has the project provided?Objective 1:Due to the delay in hiring full time technicians for this project. Limited Appointment hirings of college students have aided in getting the objectives complete while providing these students with training for their future careers. Objective 3:Field, greenhouse and laboratory experience in general microbiology and plant pathology, agricultural data collection, molecular techniques, mobile app technology, and data analysis have been provided to full- and part-time biological technicians and students working on the project in Hawai'i. Objective 4:A new post doc, Dr. Terry Torres Cruz, began in March 2023 at Purdue University. In Puerto Rico, undergraduate and graduate students, recent graduates, and a post-bac student from Hispanic Serving Institutions have been hired and trained at USDA-ARS in Mayaguez and UPR Rio Piedras on plant pathological techniques. These activities included various methods of plant propagation, DNA extraction from CLR pustules and coffee plants, inoculations procedures of CLR on susceptible coffee varieties, and inoculation techniques on leaf disks under laboratory conditions. Objective 5: a doctoral student is receiving training in survey development and data analysis How have the results been disseminated to communities of interest?Regular and ongoing activities have been conducted to facilitate communication and outreach to all communities of interest. Some of these Extension-specificactivities are listed under the "Other Products" Section. Consortium Project Investigators meet quarterly at an All-Team online meeting to discuss research successes and barriers. Minutes are kept, and subsequently shared. This provides regular contact and followup for issues between objectives and disciplines. Through June of 2023, growers, stakeholders, scientists and state agencies met on a semi-monthlyconference call organized by the Hawaii Coffee Association. In these calls, consortium members provide updates, field questions, and receive input on progress to ensure the research is meeting stakeholder needs. These calls averaged at least 30 attendees. The Project Manager attends the monthly Hawaii Coffee Association and Kona Coffee Farmers Association meetings, and briefs stakeholders on SCRI grant activities. What do you plan to do during the next reporting period to accomplish the goals?Objective 1A: Field Trials of CLR Resistant Varieties WCR IMLVT lines will continue propagating for field trials, and a few plants from each line will be acclimated to the greenhouse to send leaves for genotyping to verify the variety. These plants will also be used to confirm CLR resistance using leaf disc assays and for nematode screening (Objective 1C).Establish agreementswith tissue culture labs in the continental U.S. to import potential new cultivars following HDOA importation requirements. Objective 1B: Propagation of CLR Resistant Varieties Due to the unexpected retirement of the PI for this sub-objective, this objective will be carried out further through the Hawaii Agriculture Research Center (HARC). Cultures that were started at UHH will be acclimatized and send out for field testing to be compared against Kona Typica plants. HARC has established cultivars of Obata into somatic embryogenesis media. We are working with breeders to get permission to propagate the IMLVT lines for the Hawaii coffee growers. We also will be looking at getting material in from commercial tissue culture laboratories in the continental U.S. to test other varieties. Objective 1C: Root-knot Nematode Resistance Trials and Enhancement of Resistance Screening Additional nematode bioassays will be conducted as more material from World Coffee Research and other sources becomes available.Nematode surveys will be conducted on coffee farms on the other Hawaiian Islands. Objective 2: Conduct third year of monitoring at all sites to capture differences in CLR biology, coffee plant phenology, management practices, and weather. Objective 3A: Field and laboratory research to identify effective and safe fungicides Conduct third year of field trials to capture variation across multiple seasons. Evaluation of rotation programs with the use of preventive and systemic fungicides for the full coffee season. Continue testing the efficacy of fungicidesin vitro,in planta, and in the field. Objective 3B: Continue testing the fungal isolates from Hawai'i for antagonistic behavior towards CLRin vitroandin planta. Begin evaluating mixes of the best biological control species/isolates from Puerto Rico against CLR. Objective 3C. Optimizing Field Health for CLR Management in Non-Resistant Varietals Continue visiting farms regularly to document all agronomic practices and CLR management.Support coffee farmers with specific recommendations for improving coffee plant nutrition based on two rounds of soil/leaf tissue sampling, previous fertilization records, elevation, planting density, tree age, and time of year. Conduct comparisons and analysis on the differences in agronomic practices and how this affects CLR. Objective 4A: We are collaborating with Dr. Rachel Koch at USDA ARS Ft. Dietrick to genotype and generate complete genomes for other races. This first comprehensive genome and additional genomes from other CLR strains using Nanopore will be analyzed for comparisons. Objective 4B: Initiate inoculations of CLR on plants to conduct gene expression studies. Objective 5:The plan is to use the survey data to conduct economic analysisto better understand the costs,benefits, and tradeoffs across different control strategies from the perspective of coffee growers and the larger coffeeindustry.
Impacts
What was accomplished under these goals?
In 2022, the first year of the grant and second full year of Coffee Leaf Rust infection, Kona coffee growers reported a 50% reduction in yields due to severe defoliation from CLR. In 2023, leaf counts and subsequent yields rebounded close to average levels, significantly improving the economic situation for growers.Researchresults and extensive tech transfer under SCRI funding led to agronomic refinements in the field which facilitated this recovery.Through proper timing and use of fungicidal sprays, infection damage was reduced and crop loss was stabilized. As we learn more about the fungus' behavior in both Hawaii and Puerto Rico, and see the economic burden of maintaining susceptible trees, growers are increasingly interested in resistant varieties. Stakeholders have taken a proactive role in this project, assisting scientists with identifying varieties currently in the field and communicating their preferences on the taste profile.One producer located three trees with apparent resistance in his field and alerted ARS.The work under this grant has broad visibility in the grower community. Objective 1A: Propagation of the World Coffee Research (WCR) International Multi-Location Variety Trial (IMLVT) coffee lines is continuing. Inventory of the lines decreased due to general plant tissue culture contamination that occurred once the plants were propagated after quarantine. Select lines from the quarantined material are being acclimated in the greenhouse and/or placed in somatic embryogenesis media. In addition, in order to supplement the cultivars that have low inventory, we have imported coffee seeds and in vitro plantlets from Costa Rica under an APHIS Controlled Import Permit. Objective 1B: A Hawaii grower identified three trees that appeared resistant to CLR in his field. Laboratory tests confirmed resistance toHemileia vastatrixrace XXIV. Genotyping of these lines was completed by Dr. Dapeng Zhang, USDA ARS Beltsville. Somatic embryogenesis derived from leaf tissue was used to establish the plants in tissue culture. Objective 1C: Species-specific primers forM. konaensiswere developed to remove the sequencing step.A sterile culture was established to enable early screening of coffee cultivars for nematode resistance in tissue culture. Objective 2: Monthly surveys were conducted in 15 Hawaii farms and 10 farms in Puerto Rico.Data included CLR incidence and severity, CLR life stage, spore germination/viability, weather data, management activities, spore dispersal via wind and leaf counts. Average CLR incidence is high during the harvest and post-harvest (Aug-Feb, ~30%) and low during fruit development (Mar-Jul, 5-10%). Incidence and severity are positively correlated. No significant difference observed in incidence at varying elevations. Severe defoliation was observed from Nov 2022 through March 2023, followed by a new leaf flush. Farms in Kona are estimated to have lost 30-75% of yields in 2022, with a 18-30% recovery estimated for 2023. Spore capture is positively correlated with incidence. Spore germination is highest in shade vs. sun and on low vs. mid branches. Objective 3A: This concluded the second year of afield trial conducted in five farms testing efficacy of seven products registered for use and commonly available to growers in Hawaii. This included copper products, biologicals, the translaminar Priaxor, and a biostimulant.In addition, aYear-2 trial consisted of 5 treatments of three unregistered systemic fungicides containing Azoxystrobin, Picoxystrobin, Myclobutanil (with subsequent crop destruction) and 2 commercially available biological control products, Extract ofReynoutriasachalinensis, andPseudomonaschlororaphisstrain AFS009, plus an untreated control. Methodology for testing compatibility of CLR-targeted fungicides and Coffee Berry Borer pest-targeted BotaniGard was developed. Fourteen products were tested, resulting in 54 different combinations of product rates. Tank mixing experiments were conducted twice per product. Results showed thatBiological products provided protection for 4-5 weeks, while Copper products protected for 5-8 weeks and Priaxor (translaminar) protected leaves for 8-10 weeks.On the single organic farm examined, the botanical-based ProBlad fungicide did not outperform the foliar biostimulant CafeDak. Priaxor sprays provided better protection when conducted 8 wks apart vs. the label recommendation of 3 wks apart.The unregistered systemic fungicides all showed excellent control for extended periods. Objective 3B: Isolations of fungi from coffee leaves infected with CLRwere purified and identified using morphology and/or PCR and sequencing.Tree age and variety was also collected as well as monthly precipitation data.In total, 203 isolates were purified and identified comprising 43 genera. The number of isolates placed into long term storage for future study was 128. The isolateClonostachysshows promise, and more work is needed to verify the activity of this and remaining isolates. In Puerto Rico an experiment was completed on the effect of the fungal hyperparasiteLecanicilliumon CLR lesions. Significant effects were found, but strain efficacy differed by site. Objective 3C: Evaluations of agronomic practices and management of CLR were conducted on 11 farms.Monthly evaluations of CLR incidence, fungicide applications, weed control, pruning style, coffee production, and soil/leaf tissue samples. Coffee farms in which agronomic practices are conducted properly have shown lower CLR incidence in comparison with poorly managed farms. Data show that pruning styles significantly impact infection rates. During the full coffee season, coffee farms that only applied preventive fungicides (5-10 times) had high CLR infection (5-45%) in comparison with coffee farms that used a combination of the translaminar fungicide Priaxor (1- 2 times) with preventive fungicides (4-6 times) resulting in low CLR infection (0.5- 5%). Objective 4A. Hemileiavastatrixspores and CLR symptomatic leaves were collected from various locations on Hawaii Island and transferred to Purdue for genetic studies. The CLR genome was sequenced using three different platform technologies to obtain a comprehensive and well assembled genome. The genome for the Panama strain was assembled using HiFi reads and completed haplotype-phasing since urediniospores are dikaryotic, with 750 Mb for one nucleus and 724 Mb for the other. RNA was collected in the field for the Panama strain to aid in genome annotation. We have 2 Nanopore runs for the HI strain for comparison and are in the process of conducting RNA-sequencing on it. Population analyses of Hawai'i isolates using 12 SSRs has continued. Sampling for this analysis is nearly complete excepting some additional samples from Puerto Rico. Key historical CLR samples have also been added to this dataset and we are genotyping 4 CLR races obtained from USDA Ft. Dietrick. In Puerto Rico, DNA has been extracted from CLR collections from several sites and cultivars and microsatellite loci amplified. New candidate microsatellite loci have been tested.The microsatellite loci have shown little variation so far, and then new microsatellites have amplified well but have not been variable. Objective 4B: Puerto Rico obtained and planted coffee seeds of susceptible ('Caturra' and 'Catuai') and resistant local varieties ('Limani' and 'Fronton"). CLR inoculation on in vivo plants is a slow process. CLR infection was obtained onC.arabicacv. Caturra under laboratory conditions. Objective 5: Economics The coffee grower survey was launched in April using the membership list of various coffee organizations active in Hawaii. Response to the survey was very low for the first 3-4 months. Efforts were intensified to reach farmers in late summer, and we have now received more than 80 responses, with a goal of 100 by November 2023.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Keith, L. M., Matsumoto, T. K., Sugiyama, L. S., Fukada, M., Nagai, C., Pereira, A. P., Silva, M. C., and V�rzea, V. 2023. First report of the physiological race XXIV of Hemileia vastatrix (coffee leaf rust) in Hawaii. Plant Dis. 107:2528. doi: 10.1094/PDIS-03-23-0460-PDN.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Urbina H & Aime MC. 2023. The first USA continental record of coffee leaf rust (Hemileia vastatrix) on coffee (Coffea arabica) in southwest Florida, USA. Plant Dis. doi: 10.1094/PDIS-09-23-1869-PDN.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Myers, R., Mello, C., Nagai, C., Sipes, B., and Matsumoto, T. 2023. Evaluation of Coffee arabica cultivars for resistance to Meloidogyne konaensis. Agriculture 13:1168. https://doi.org/10.3390/agriculture13061168
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Progress 09/01/21 to 08/31/22
Outputs
Target Audience:The primary audience target for Objectives 1, 2, 3, and 5 are coffee growers and extension agents. Specific outreach and extension efforts are described further under the Accomplishments: Communities of Interest section. Most projects are in their early stages. Data collected for Objective 1 will benefit the coffee industry in Hawaii and Puerto Rico by identifying coffee varieties resistant to CLR and other diseases. Data also will benefit coffee farmers in Hawaii because CLR race 2 (detected in Puerto Rico since 1990) is not present in Hawaii, and Puerto Rico can provide information to Hawaii about resistance and how to manage this CLR race 2 in case of this race appears in Hawaii. A stronger coffee industry impacts economically depressed areas like the mountain region of Puerto Rico and the Ka'u region of Hawaii by creating jobs in farms and coffee processing organizations. The genomic activities under Objective 4 are targeted to researchers and plant breeders. Changes/Problems:Both Hawaii and Puerto Rico have a one-year APHIS plant quarantine (PQ) process for coffee materials. Hawaii State Department of Agriculture has a secondary quarantine process once the plants have left Federal custody, which can extend the quarantine to up to two years. Delay of APHIS-PPQ permits due to administrative challenges (change in permit application processes at Beltsville) have slowed the Objective 1 segment of the project. Some plant lines have been able to clear Hawaii PQ. Once the quarantined coffee plants were allowed to be propagated, we experienced a loss of plants to contamination. This was especially problematic since 20 of the 30 ILMVT lines had only a few plants (less than 30) that were sterile at the start of the quarantine. Hurricane Fiona, which struck Puerto Rico in September 2022, heavily damaged fields and roads in the mountainous coffee region. Lack of access delayed survey and data collection through December. A portion of the harvest was lost, and trees were defoliated by high winds. Beneficially, not as many trees were lost in comparison to 2017's Hurricane Maria, and the region should recover relatively quickly. The Project Investigator, Dr. Michael Shintaku, leading Objective 1b is retiring unexpectedly. This activity revolves around tissue-culturing the new varieties. This will necessitate moving the micropropagation activities from the University of Hawaii to the Hawaii Ag Research Center, a 501(c)3 entity. The budget and work timeline will be nominally the same. What opportunities for training and professional development has the project provided?Due to the delay in hiring full time technicians for this project, Limited Appointment hirings of University of Hawaii college students for Objective 1 have aided in getting the objectives complete while providing these students with training for their future careers. Undergraduate and recent graduates from Hispanic Serving Institutions have been hired and trained at USDA-ARS in Mayaguez on plant pathological techniques. These activities included various methods of plant propagation, DNA extraction from CLR pustules, inoculations procedures of CLR on susceptible coffee varieties, inoculation techniques on leaf disks under laboratory conditions. For Objective 5, a masters student in Agricultural Economics is receiving training in survey development. How have the results been disseminated to communities of interest?On a semi-monthly basis, growers, stakeholders, scientists and state agencies meet on a conference call organized by the Hawaii Coffee Association. In these calls, consortium members provide updates, field questions, and receive input on progress to ensure the research is meeting stakeholder needs. These calls average at least 30 attendees. The Puerto Rico Agricultural Experiment Station held talks with coffee growers at two events. A poster will be presented in December 2022 at a local agronomy meeting. Two manuscripts are in preparation. Multiple talks were presented at the 2022 Annual Hawaii Coffee Association Conference, CLR virtual talk story sessions, and University of Hawaii (UH) Extension webinars. Information was also distributed through extension publications, visual aids, and during ongoing farm visits. UH Extension provided 20 educational opportunities to 711 coffee producers and stakeholders to learn about CLR best management practices, coffee pruning, sprayer calibration, safe pesticide use, and coffee propagation via workshop, webinar, and field day events. Translators were provided for events such as Worker Protection Standards, sprayer calibration, and pesticide use and publications are available in languages including Spanish, Ilocano, and Tagalog. Our HawaiiCoffeeEd.com website is frequently visited by over 12,500 unique viewers. Information at this site can also be translated to dozens of languages. We also hosted educational booth displays, presented during industry events and hosted a Virtual Invasive Pest Mini Conference with 149 attendees. "Farm doctor" visits were conducted throughout the state including on Maui, Oahu, and the districts of Kau, Kona, Hamakua, and Waimea on Hawaii Island. During the statewide Invasive Pest Mini-Conference and Kauai CBB and CLR Workshop, staff presented an updated best management practices recommendation for CLR management. The recording has also been viewed by 50 individuals. Overall feedback of this mini-conference was positive with 98% of participants reporting an increase in knowledge and understanding of the topic area and 81% intending to share learned information with at least one person. During the in-person coffee pest workshop on Kauai, a total of 17 producers participatedinthis workshop. 85% of attendees responding to a post-event survey reported a significant increase in knowledge. All learned at least one new thing, and more than 30% reported learning five new things that they would apply to their operation. What do you plan to do during the next reporting period to accomplish the goals?Objective 1A: Field Trials of CLR Resistant Varieties The World Coffee Research IMLVT lines will continue propagating for field trials in Hawaii and Puerto Rico, and a few plants from each line will be acclimated to the greenhouse to send leaves for genotyping at Beltsville to verify the variety. These plants will also be used to confirm CLR resistance using leaf disc assays and for nematode screening (Objective 1C). Puerto Rico will receive 11 coffee seed differential plants from Costa Rica (the total number of CLR differential plants is 27, Costa Rica only has 11) to obtain seedlings and to start CLR evaluations. In addition, CLR from Puerto Rico will be sent to Portugal for determination of CLR race. Seeds will be obtained from controlled pollinations of the 15 IMLVT lines to obtain "pure lines" for CLR testing. Cupping trials with Extension and coffee growers will be conducted, dependent on available supplies. Objective 1B: Propagation of CLR Resistant Varieties Due to the retirement of the PI for this sub-objective, this objective will be carried out further through the Hawaii Agriculture Research Center (HARC). Established cultures will be sent from the University of Hawaii Hilo facility to HARC in two shipments to ensure plants are not lost to contamination during shipment. The first shipment will be verified to be clean and alive before second shipment is initiated. Objective 1C: Root-knot Nematode Resistance Trials and Enhancement of Resistance Screening Once IMLVT plants are in the greenhouse, screening for nematode resistance will commence. Complete the statewide survey on nematodes in Hawaii. Objective 2: CLR Surveys and Environmental Monitoring Conduct the second year of monitoring at all sites to capture differences in CLR biology, coffee plant phenology, management practices, and weather. Repeat spore viability assays and conduct potted plant experiments to assess additional environmental parameters. Utilize results to develop comprehensive IPM recommendations for Extension activities with growers in both Puerto Rico and Hawaii. Updated Puerto Rico recommendations are expected to go to print by February with field days shortly after. Hawaii IPM recommendations will be narrowed down through an "IPM Summit" with researchers, extension staff, and stakeholders in January with documents and field days shortly after. Objective 3A: Field and laboratory research to identify effective and safe fungicides Continue potted plant bioassays. Conduct second year of field trials to capture variation across multiple seasons. At the Kona Hills field research location, continue to collect monthly efficacy data to complete the first year field trial, analyze data for entire first-year efficacy trial, and repeat the field trial for a second year in order to reach more conclusive conclusions. Objective 3B: Biological Control of CLR Write the first manuscript on biological control of CLR in Puerto Rico; do additional experiments. From the data collected, evaluate the biocontrol potential of Hawaii isolates. Write the first manuscript on biological control of CLR in Hawaii. Objective 3C. Optimizing Field Health for CLR Management in Non-Resistant Varietals Maintain regular farm visitations to document all agronomic practices and CLR management. Support coffee farmers with specific recommendations for improving coffee plant nutrition based on two rounds of soil/leaf tissue sampling, previous fertilization records, elevation, planting density, tree age, and time of year. Conduct comparisons and analysis on the differences in agronomic practices and how this affects CLR. Objective 4A. Genetics of CLR Currently, the Purdue Aime Lab is cleaning the reads and conducting initial QC. With the arrival of a post-doc researcher at Purdue in the spring of 2023, the completed genome will be assembled and annotated and then run through genomic and population analyses.This comprehensive genome will form the scaffold for comparison for additional genomes from other CLR strains, to be generated on a single platform and analyzed. Developed protocols will be used to obtain sufficient infected tissue samples for RNA extraction. RNA will be used to annotate the genome and will form the basis of differential experiments for finding genes associated with virulence and that are specific to different races of CLR. Greenhouse protocols will be used to increase and maintain different races of CLR for subsequent analyses.Hawaii and Puerto Rico staff will continue to collect, store and transfer H. vastatrix spores to Purdue as needed. Objective 4B: Understanding Resistance to CLR Initiate inoculations of CLR on plants to conduct gene expression studies. Objective 5: Economics of CLR Launch the grower survey in January 2023 using the membership list of various coffee organizations active in Hawaii. Data collected from this survey will be used to conduct economic analysis to better understand the costs, benefits, and tradeoffs across different control strategies from the perspective of coffee growers and the larger coffee industry.
Impacts
What was accomplished under these goals?
In 2022, the second full year of Coffee Leaf Rust infection, Kona coffee growers are estimated to have lost 30-75% of their crop. As early research results come in, there is a strong sense of urgency in the scientific and grower communities to address immediate tree health solutions for susceptible trees. First year results point to potential agronomic refinements in the field, as well as proper timing and use of fungicidal sprays, that may reduce infection damage and stabilize crop loss. As we learn more about the fungus' behavior in both Hawaii and Puerto Rico, and see the economic burden of maintaining susceptible trees, growers are increasingly interested in resistant varieties. Stakeholders have taken a proactive role in this project, assisting scientists with identifying varieties currently in the field and communicating their preferences on the taste profile. The work under this grant has broad visibility in the grower community. Objective 1A: Field Trials of CLR Resistant Varieties Hawaii ARS scientists are propagating the World Coffee Research (WCR) International Multi-Location Variety Trial (IMLVT) lines for field trials. To expedite the trials at Mayaguez, WCR granted access to 15 of the IMLVT Puerto Rico lines. All lines were verified by genetic analysis through Dr. Dapeng Zhang at USDA ARS Beltsville. In addition, permits were obtained from APHIS-PPQ and PR Department of Agriculture to introduce seed and in vitro plantlets from Costa Rica and Hawaii. The ARS Mayaguez facility installed growth chambers and bio safety hoods for CLR inoculations and growth of in vitro lines. Objective 1B: Propagation of CLR Resistant Varieties Both regions require a 1-year minimum quarantine period for inbound plant materials. To hasten availability, Hawaii growers identified CLR-resistant varieties already present in the field. Resistance and genotyping were confirmed by ARS scientists, and leaves were obtained for somatic embryogenesis propagation. Callus and direct somatic embryos have been observed in the cultures and are consistent with published literature. Many versions of media were tested as published recipes vary, with success dependent on the coffee variety. Objective 1C: Root-knot Nematode Resistance Trials Resistance screening is underway with faster screening methods under review. Objective 2: CLR Surveys Sampling was conducted every three weeks at 15 sites in Puerto Rico and every four weeks at 15 Hawaii farms. Active and passive spore samplers were installed in Hawaii to characterize pathogen movement. To assess the lifecycle, H. vastatrix spores were collected bi-monthly and compared. CLR infection levels fluctuate in Puerto Rico. Leaves on upper branches have less CLR than middle and lower branches. Highest levels of infection surprisingly appeared in summer but the plots may contain cultivars that differ in susceptibility. Research continues. For Hawaii, average CLR incidence was low early in the season (~4%, Jan-Jun) and increased to ~36% during the harvest (Jul-Dec). Incidence and severity are positively correlated. No significant difference in incidence due to elevation was observed, although farms at mid to high elevations had increased harvest incidence. Severe defoliation was observed from Nov-Mar, followed by a new leaf flush. Results from viability studies ranged from ~20-70% and suggests that spore germination rates vary depending on collection site, time of year, and management practices utilized. Germination was highest in shade and on lower branches and increased during the harvest season. Results from potted assays suggest that low spore density can result in symptom development and relative humidity plays only a minor role. Objective 3A: Field Management Research Fungicide protection experiments were conducted on potted seedlings in a growth chamber. Plants were inoculated with spores on day 0, 7, and 14 days post application (DPA) of the product. Control plants had water applied to the foliage. Trials on three farms tested the efficacy of four commercially available fungicides: Kocide, Badge X2, ProBlad Verde, and Serenade. Another field trial was established for fungicides not yet labeled in Hawaii: 3 systemics and 2 biological control products (Azoxystrobin, Picoxystrobin, Myclobutanil, Extract of Reynoutria sachalinensis, and Pseudomonas chlororaphis strain AFS009). Three replications of each treatment and control were included and organized in a randomized complete block design. For all trials, disease incidence and severity ratings were collected. For potted plant experiments, water-only positive controls sporulated between 14-35 days and had the highest disease incidence ratings. Treated plants had low disease incidence ratings 7 to 14 DPA of the treatment and provided protection against CLR infection when applied proactively. At the first field trial, all products provided protection for 5-6 weeks after the sprays, with variable efficacy levels.Field data suggests that all treated plots are experiencing less spread of CLR in comparison to the untreated control. As of September 2022, the systemics (severity under all 3: <1) are working most effectively. Untreated plots have more than double the amount of disease. No phytotoxicity has been observed. Objective 3B: Biological Control In Puerto Rico, various Lecanicillium-type fungi have been isolated from CLR lesions and inoculated in the field in three locations under two different seasons. Species varied in survival and growth of CLR lesions after application. The experiment will be repeated. In Hawaii, symptomatic leaf samples were collected from various locations, including an organic farm. More than 75 isolates from multiple fungal genera were recovered. The three most common isolates included the following genera: Simplicillium/Cephalosporium, Akanthomyces/Lecanicillium/Verticillium, and Cladosporium. Methods for mycoparasite efficacy were assessed and preliminary biocontrol evaluations of four isolates look promising. Objective 3C. Optimizing Field Health in Non-Resistant Varietals Monthly evaluations of agronomic practices and CLR management were conducted on 11 Hawaii farms. Fields show a high variability in terms of cultivars, elevation, pruning styles, topography, planting density, age of trees, weather conditions and agronomic practices. In cooperation with growers, records of all agronomic practices are documented as well as soil and leaf samples. CLR incidence ranged between 0.1% and 60%. In the early coffee season (April- July), CLR was on average < 3% with slow increases, while during the harvest season (Aug-Dec) CLR increased faster (3-9%). Across the entire season, block pruning systems showed the lowest CLR infection (0.8-2.2%), while traditional Kona style pruning averaged 12.4%. Coffee fields that only applied preventive fungicides had higher infection (12.4%) in comparison to fields in which both fungicides (preventive and systemic) were applied (1.4%). In all farms, recommendations for the improvement of agronomic practices were discussed with growers. Objective 4A. Genetics of CLR To obtain a comprehensive and well assembled genome, the Purdue Aime Lab sequenced the CLR genome using three different platform technologies: Illumina short reads; long-read sequencing at the UC Davis Genome center for PacBio; and long reads using Oxford Nanopore. The Lab have successfully defined protocols for the highly challenging in vivo maintenance of CLR in the greenhouse. Objective 4B: Understanding Resistance Puerto Rico has planted verified true-to-type seeds of susceptible and resistant local varieties to start inoculations of CLR and to conduct gene expression studies. Objective 5: Economics Economists attended the annual meeting of the Hawaii Coffee Association and met with consortium members, industry leaders, and growers to understand the challenges of CLR. Based on this, a questionnaire was developed and is currently being pre-tested.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Aristiz�bal, L.F.; Johnson, M.A. Monitoring Coffee Leaf Rust (Hemileia vastatrix) on Commercial Coffee Farms in Hawaii: Early Insights from the First Year of Disease Incursion. Agronomy 2022, 12, 1134. https://doi.org/10.3390/ agronomy12051134
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Kawabata, A.M., S. Wages, and S.T. Nakamoto. (2022) Pruning methods for the management of coffee leaf rust and coffee berry borer in Hawaii. Honolulu (HI): University of Hawaii. 9 pp. (Plant Disease; PD-126).
- Type:
Other
Status:
Published
Year Published:
2022
Citation:
Baur M.E., Kawabata A.M., Nakamoto S.T., Shriner S., and Elliott S. 2022. National Pest Alert: Coffee leaf rust Hemileia vastatrix. North Central IPM Center.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
1. Kawabata, A.M., M. Miyahira, S.R. Sand, and S.T. Nakamoto. 2022. Managing the Risks from Coffee Leaf Rust, a New and Devastating Disease Affecting Hawaii Coffee Producers presented at the 2022 Extension Risk Management Education National Conference, Omaha, Nebraska. 30 March 2022. (Poster presentation). https://agrisk.umn.edu/Conferences/Presentation/managing_the_risks_from_coffee_leaf_rust_a_ne
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
2. Uyeda, J., A.M. Kawabata, M. Miyahira, S. Sand, and S.T. Nakamoto. 2022. Developing Sprayer Calibration Tools for Coffee and Orchard Crop Farmers that Reduce their Production and Legal Risks presented by Uyeda at the 2022 Extension Risk Management Education National Conference, Omaha, Nebraska. 30 March 2022. (Poster presentation). https://agrisk.umn.edu/Conferences/Presentation/developing_sprayer_calibration_tools_for_coff
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