Location: Tropical Crop and Commodity Protection Research
2019 Annual Report
Objectives
The goals of our project plan are to conduct foundational research to create the knowledge base necessary to develop innovative control methods and IPM strategies, and to conduct applied research to produce information and products that improve pest control in tropical agriculture. The four major objectives of our program are:
Objective 1: Model pest invasion pathways, and investigate the genomics/genetics, physiology/behavior, population dynamics, biology/ecology, and natural enemies of tropical and subtropical fruit flies and other invasive pests to develop technologies to control (contain, suppress, and eradicate) these pests in Hawaii and the Pacific, the U.S. mainland, and elsewhere.
1A: Build an analysis of emerging tephritid fruit fly genomes, including linkage mapping, uniform and consistent gene structural and functional annotation, and comparative genomic analysis.
1B: Conduct surveys on coffee berry borer (CBB) distribution and abundance on Hawaii Island to provide a baseline for a predictive model that integrates GIS, pest insect population dynamics, host plant phenology, weather data and grower practices to drive area-wide management of CBB on Hawaii Island.
Objective 2: Determine physiological, genetic, and biological factors limiting the effectiveness of the sterile insect technique (SIT) and natural enemies in control and eradication of fruit flies and other tropical plant pests of quarantine significance.
2A: Improve the effectiveness of mass reared fruit flies for SIT by quantifying the impact of colony infusion on incorporating wild genetics into the SIT colony, and correlating fly performance with genomic markers.
2B: Investigate parasitoid-fruit fly host interactions from the molecular to the field level.
Objective 3: To increase export of tropical fruits and vegetables, improve attractants and trapping systems for surveillance and detection, and develop lures, baits, and reduced risk pesticides for area-wide IPM of fruit flies and/or other tropical plant pests of quarantine significance.
3A: Evaluation of C. capitata, B.dorsalis and B. cucurbitae captures in traps baited with solid trimedlure (TML), methyl eugenol (ME) and raspberry ketone (RK) male lure and insecticide dispensers weathered in Hawaii and California.
3B: Evaluation of mixtures, weathering and chemical degradation of SPLAT-spinosad ME and cue-lure (C-L) for fruit fly control under Hawaii and California conditions.
3C: Evaluation of a new attractant system for detection, monitoring and control of the sweetpotato vine borer, a pest of quarantine significance in Hawaii.
Objective 4: Provide baseline information for development of low prevalence and/or pest-free zones, for implementation in Hawaii and the U.S. mainland, to promote or allow unimpeded movement of fruit and vegetable exports.
4A: Create area of low pest prevalence (ALPP) as an independent measure of systems approaches for melon fly.
4B: Utilize models to evaluate the sensitivity of trapping grids for detection and control of insect pests such as tephritid fruit flies.
4C. Effectiveness of foliar and bait sprays against C. capitata, B.dorsalis, B. cucurbitae and B. latifrons.
Approach
Hypothesis 1A: Tephritid genomes have a core set of genes that are related to their proliferation as pests world-wide. If we have trouble generating crosses from a particular species or have issues generating genomic DNA, other species could be sequenced.
Approach 1B: Collect baseline data on distribution and abundance of Coffee Berry Borer and associated environmental and climatic data. Then use GIS techniques to produce a region-wide assessment of infestation and economic impact. If this does not work, surveys can be replaced with grower-collected data.
Approach 2A: Combine genetic, proteomic and phenotypic data into a synthetic analysis. If portions experiments fail or cannot be integrated, publish portions independently.
Approach 2B: Examine tephritid host-parasitoid biology across levels of biological organization to allow integration of foundational knowledge benefiting classical biological control of tephritids. If international releases are impeded by regulatory issues, field work in Hawaii will be done.
Hypothesis 3A: Solid male lure wafers with solid insecticidal tape are just as effective, but more convenient and safer to handle than current liquid lure-insecticide formulations used for fruit fly detection programs. If data are inconclusive, chemical analyses of weathered dispensers from trials will at least provide “use pattern” and formulation data for future trials.
Hypothesis 3B: Generic combination SPLAT-MAT-spinosad-methyl eugenol/cue-lure mixture will perform as well as Min-U-Gel with naled and ME and C-L separately for fruit fly control/eradication. If the sprayable mixtures are too expensive, recommend addition of small amounts of cue-lure or raspberry ketone to STATIC-spinosad-ME as part of a tank mix.
Hypothesis 3C: A binary male attractant system identified with sweetpotato vine borer populations in Vietnam will provide significantly greater male catch in Hawaii populations than male catch in traps baited with an initially identified single compound lure. In cases where low populations are encountered, trials will be shifted to other fields or other time of year where higher populations are present.
Hypothesis 4A: Mass trapping using a plant-odor lure, male lure and protein baits can create areas of low pest prevalence (ALPP) in commercial crops and reduce the risk of a mating pair in a consignment when combined with a second measure such as a (less than 99.9986% effective) quarantine treatment. Alternatively, investigate the effects of other independent measures such as poor host status and quarantine treatments.
Approach 4B: Develop a biologically-based mathematical model of tephritid traps in a landscape that allows formal quantification of trap network sensitivity. Hypothesis 4C: Current preharvest foliar insecticides being used in IPM systems against other fruit and vegetable pests (e.g., spotted wing drosophila and Asian citrus psyllid) in California and Florida are sufficient to meet quarantine requirements for fruit flies when introduced into Florida and California. Alternatives are to use current practices of either malathion protein bait or GF-120 sprays.
Progress Report
In support of Objective 1, development of foundational genomic resources for tephritid fruit flies has continued, including submission of Tephritid genomes into the National Center for Biotechnology Information (NCBI) and i5k databases. Publications on improved assemblies, such as a draft assembly of the Mexican fruit fly (Anastrepha ludens) and diagnostic tools for the melon fly and Mexican fruit fly have been developed to identify the source and strain of detected flies. These tools are now being tested and implemented at the United States Department of Agriculture, Animal and Plant Health Inspection Service/Plant Protection and Quarantine (USDA-APHIS PPQ), in addition to being applied to new samples as they are collected. Scientists in Hilo, Hawaii, are also improving methods for genome assembly and analysis, including implementation of single insect assemblies using PacBio Sequel system, and integrating HiC chromatin contact data, Bionano optical mapping, and linkage mapping data to develop chromosomal scale assemblies. A subordinate project with the University of Hawaii includes a curated collection of Bactrocera specimens and DNA samples, with taxonomic and genomic information digitized. The collection includes specimens from South Asia, The Philippines and South East Asia, from which samples have been lacking until now. In two genetic sexing lines, the melon fly T1 white pupae line, and the Vienna 8 medfly, colony infusion studies have been completed to evaluate the impact of infusion towards improving fitness traits in the flies. Currently, infused lines are being genotyped for connecting the genetics to the strain fitness. Infusion of the oriental fruit fly genetic sexing line is ongoing. In the genetic sexing line “DTWP”, we are in the process of performing a one-time and two-time uni-directional colony infusion study. By crossing DTWP colony females with readily attainable wild Bactrocera dorsalis males, we are able to create a one-time infused DTWP colony within four generations and a twice infused within eight generations. In coffee berry borer (CBB) research, a third and final year of data collection on about two dozen coffee sites on Hawaii island was completed in December 2018, and life cycle studies conducted under natural conditions have been completed and submitted for publication.
Comprehensive geo-referenced data collected using an electronic system include monitoring of CBB populations, plant phenology, management practices and weather conditions. A second year of monitoring based on this program is underway by collaborators in Puerto Rico. Final datasets are being quality checked before publication and general release. Portions of the data have been shared with the University of Hawaii researchers and published. Additional field experiments have elucidated the developmental timing of CBB in Hawaii to help time insecticidal fungus sprays with the times when the beetle is most vulnerable (out of the coffee bean). Additionally, field research on inter-season refugia for CBB has been completed and submitted for publication. In a subordinate project with the University of Hawaii, the geographic variation in bacterial communities associated with CBB in Hawaii was determined. The microbiome of CBB included a number of species that may affect metabolic function of CBB, including Burkholderia spp.
In support of Objective 2, genomics of parasitoid wasps has continued, including investigation of viral genomes integrated into the wasp genome, and their role of these viruses in control host specificity. With collaborators at California State University Monterey Bay, ARS scientists in Hilo, Hawaii, have effectuated shipments of the oriental fruit fly parasitoid Fopius arisanus to Senegal, West Africa (Crop Protection Directorate, Ministry of Agriculture). This continues several years of shipments supporting the efforts of the ministry to establish this biological control agent in Senegal. A similar project in Brazil has been halted because the regulatory bodies in that country have not given clearance for release of F. arisanus.
In support of Objective 3, the binary male attractant system (with Type 1 and Type 2 components) identified with sweetpotato vine borer populations in Vietnam has been shown to similarly provide significantly greater male catch in Hawaii populations compared to male catch in traps baited only with the initially identified Type 1 compound. Certain variations of the Type 1: Type 2 ratio and doses have provided greater than 10-fold increase in male catch compared to catch in traps baited with only the Type 1 component. A lure weathering trial has been completed, with weathered lures collected. Although field sweetpotato vine borer populations have been low, little drop-off in male sweetpotato vine borer catch was apparent over the course of a three-month weathering period. Overall, results to date document greatly enhanced trap catch effectiveness of a Type 1 + Type 2 lure combination, compared to catch baited with the Type 1 lure only, with good persistence of the effectiveness of the binary attractant system over time. These research results are now in press. For integrated pest management of tephritid fruit flies, field weathering trials of solid trimedlure (TML), methyl eugenol (ME), and raspberry keytone (RK) lure wafers with the insecticide “DDVP” are near completion and all experiments on combination Male annihilation technique (SPLAT-MAT-spinosad-ME/C-L mixture) were completed and reported on in previous years.
In support of Objective 4, results of experimental field studies (“mark-release-recapture”) testing the effectiveness of mass trapping have been published, together with field estimates of oriental fruit fly survival. ARS scientists in Hilo, Hawaii, are collaborating with USDA-APHIS and California Department of Food and Agriculture counterparts to conduct mark-release-recapture experiments with sterile oriental fruit fly in California to validate field results from Hawaii indicating that a lower application density of SPLAT-MAT is more effective than the currently used rate. These experiments are in the planning stage with the first trials expected this year. A model on traps (“TrapGrid”) is being utilized by the APHIS Center for Plant Health Science and Technology (Raleigh, North Carolina) to develop new guidelines on delimitation trapping for tephritids and other invasive pest insects. This simulation-based investigation, in collaboration with ARS researchers in Hilo, Hawaii, is guiding action programs on the size and density of delimitation trapping following incursions by a wide variety of invasive insects.
Accomplishments
1. Demonstration of CRISPR/Cas9 in three economically important genera of Tepritid fruit flies. CRISPR/Cas9 gene editing methods have been demonstrated by ARS researchers in Hilo, Hawaii, in three economically important genera of Tepritid fruit flies (Ceratitis capitata, Bactrocera dorsalis, and Anastrepha ludens). In all three species the white gene was targeted to create a phenotypic mutation (white eyes) as a proof of concept demonstration in these species. For each species, unique techniques and modifications had to be made, such as changes in preparation of embryos or injection parameters to get positive mutations. For A. ludens, the injections were performed in Guatemala, with cooperators at the International Atomic Energy Agency (IAEA) and included protocols for using mobile molecular biology tools and injection instruments. These techniques are currently being used to make novel genetic sexing systems in these species, as well as being used as a tool for foundational molecular biology.
2. Release of The Compendium of Fruit Fly Host Information (CoFFHI), Edition 4.0. The Compendium of Fruit Fly Host Information (CoFFHI), Edition 4.0, has been released online, providing more expanded centralized coverage of what is known worldwide about the status of fruits and vegetables as hosts of fruit flies of economic importance. Fruit flies cause direct damage to fruits and vegetables through oviposition and larval feeding and restrict movement of commodities across national and international borders. Establishment of appropriate regulatory procedures, however, is dependent on the knowledge of the status of commodities as hosts for fruit fly species. The online accessible Compendium of Fruit Fly Host Information (CoFFHI; https://coffhi.cphst.org/), developed through collaborative efforts of ARS scientists in Hilo, Hawaii, Wapato, Washington, and Washington, D.C.; scientists from the Animal and Plant Health Inspection Service (APHIS); and scientists from North Carolina State University's Center for Integrated Pest Management (CIPM), provides some host information for over 1,800 fruit fly species, along with provisional host lists, and more comprehensive host documentation, for 28 fruit fly species of economic importance. As a primary reference on fruit fly host plants, CoFFHI is designed to serve as a tool to help regulatory scientists and regulatory officials of USDA and various state regulatory agencies design and implement effective detection, monitoring, suppression, and eradication programs against fruit fly species that pose significant threats to U.S. agriculture and natural resources.
3. Release of parasitoid for biological control of Medfly in coffee orchards. Mediterranean fruit fly (Medfly) is a serious pest of tropical fruits, including coffee berries. In cooperative research between ARS scientists in Hilo, Hawaii, and the University of Hawaii, the African parasitoid, Fopius ceratitivorous, was successfully imported to Hawaii, quarantined, reared, and released into coffee fields on Kauai. The newly released parasitoids were detected at low levels in the field, along with other natural enemies. Establishment of the parasitoids may add to the overall natural enemy mortality of Medfly infesting coffee and other crops in Hawaii, leading to lower infestation rates and reduced control costs.
Review Publications
Manoukis, N., Vargas, R.I., Carvalho, L.A., Fezza, T., Wilson, S.M., Collier, T.C., Shelly, T.E. 2019. A field test on the effectiveness of male annihilation technique against Bactrocera dorsalis (Diptera: Tephritidae) at varying application densities. PLoS One. 4(3):e0213337. https://doi.org/10.1371/journal.pone.0213337.
McQuate, G.T., Sylva, C.D. 2018. Catch of the green garden looper moth, Chrysodeixis eriosoma (Lepidoptera: Noctuidae), in sweetpotato fields in Hawaii. Hawaiian Entomological Society Proceedings. 50:43-53. Available online at http://hdl.handle.net/10125/59367.
Garzon-Orduna, I.J., Geib, S.M., Barr, N.B. 2019. The genetic diversity of Bactrocera dorsalis (Diptera: Tephritidae) in China and neighboring countries: A review from published studies. Journal of Economic Entomology. 112(4):2001-2006. https://doi.org/10.1093/jee/toz073.
Dupuis, J.R., Peigler, R.S., Geib, S.M., Rubinoff, D. 2018. Phylogenomics supports localized and taxonomically-incongruous ecological specialization in a North American moth clade (the Hemileuca maia species complex). Molecular Ecology. 27:4417-4429. https://doi.org/10.1111/mec.14883.
San Jose, M., Doorenweerd, C., Leblanc, L., Barr, N., Geib, S.M., Rubinoff, D. 2018. Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two genetically intertwined fruit fly species (Bactrocera carambolae and B. dorsalis). Journal of Economic Entomology. 111(6):2914-2926. https://doi.org/10.1093/jee/toy272.
Dupuis, J.R., Bremer, F.T., Kauwe, A.N., San Jose, M., Leblanc, L., Rubinoff, D., Geib, S.M. 2018. HiMAP: robust phylogenomics from highly multiplexed amplicon sequencing. Molecular Ecology Resources. 18:1000-1019. https://doi.org/10.1111/1755-0998.12783.
Sim, S.B., Doellman, M.M., Hood, G.R., Yee, W.L., Powell, T.H., Schwartz, D., Goughnour, R.B., Egan, S.P., St. Jean, G., Smith, J.J., Arcella, T.E., Dzurisin, J.D., Feder, J.L. 2017. Genetic evidence for the introduction of Rhagoletis pomonella (Diptera: Tephritidae) into the northwestern United States. Journal of Economic Entomology. 110(6):2599-2608. https://doi.org/10.1093/jee/tox248.
Sim, S.B., Kauwe, A.N., Ruano, R.E., Rendon, P., Geib, S.M. 2017. The ABC's of CRISPR in Tephritidae: developing methods for inducing heritable mutations in the genera Anastrepha, Bactrocera, and Ceratitis. Insect Molecular Biology. 28(2):277-289. https://doi.org/10.1111/imb.12550.
Geib, S.M., Hall, B., Derego, T., Sim, S.B. 2018. Genome annotation generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission. Gigascience. 7(4):1-5. https://doi.org/10.1093/gigascience/giy018.
Lehman, K.A., Barahona, D.C., Manoukis, N., Carvalho, L.A., De Faveri, S., Auth, J.E., Siderhurst, M.S. 2019. Raspberry Ketone Trifluoroacetate trapping of Zeugodacus cucurbitae (Coquillett) in Hawaii. Journal of Economic Entomology. 112(3):1306-1313. https://doi.org/10.1093/jee/toz006.
Manoukis, N., Collier, T.C. 2019. Computer vision to enhance behavioral research on insects. Annals of the Entomological Society of America. 112(3):227-235. https://doi.org/10.1093/aesa/say062.
