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ARS Home » Pacific West Area » Hilo, Hawaii » Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center » Tropical Plant Genetic Resources and Disease Research » Research » Research Project #434299
Research Project: Management, Characterization, and Evaluation of Pacific Tropical and Subtropical Fruit and Nut Genetic Resources and Associated Information

Location: Tropical Plant Genetic Resources and Disease Research

2023 Annual Report


Objectives
The long-term objective of this project is to provide high quality management and curatorial care of the NPGS tropical/subtropical crop collection at the USDA, ARS, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center (PBARC), Tropical Plant Genetic Resource and Disease Research Unit (TPGRDRU), Hilo, Hawaii. The Hilo repository is physically located on the University of Hawaii, Waiakea Experiment Research Station. Emphasis will be placed on evaluation of the local collection to identify potential gaps and evaluate potential diseases to facilitate transportation/distribution of disease-free plant material; improvement of management practices to advance efficiency of conservation through cooperation with other ARS locations in Beltsville, Fort Collins, Mayagüez, and Miami; and documentation of universal descriptor data and best management practices for U.S. subtropical/tropical fruit and nut genetic resources. Specifically, during the next five years we will focus on the following objectives. Objective 1: Efficiently and effectively acquire Pacific tropical and subtropical fruit and nut genetic resources, maintain their safety, genetic integrity, health and viability, and distribute them and associated information worldwide. Subobjective 1A: Efficiently and effectively conserve and distribute tropical fruit genetic resources and associated information, emphasizing important crop plants and relatives of the primary crops assigned to the Hilo repository. Subobjective 1B: Implement “quarantine-safe” germplasm transfer systems to transfer and back-up the NPGS-Miami avocado and NPGS- Mayagüez cacao collections. Subobjective 1C: Develop long-term storage methods for papaya and pineapple. Objective 2: Develop more effective genetic resource maintenance, evaluation, and characterization methods and apply them to priority Pacific tropical and subtropical fruit and nut genetic resources. Record and disseminate evaluation and characterization data via GRIN-Global and other data sources. Subobjective 2A: Develop and evaluate emerging crops such as cacao, pili nut and breadfruit for increased cultivation in U.S. subtropical and tropical areas. Subobjective 2B: Improve propagation and hybridization of pili nut, breadfruit, guava and macadamia nut. Subobjective 2C: Develop genomic tools for genetic characterization of collection. Subobjective 2D: Identify, mitigate and manage emerging diseases for sub-tropical and tropical fruit and nut crops. Objective 3: With other NPGS genebanks and Crop Germplasm Committees, develop, update, document, and implement best management practices and Crop Vulnerability Statements to efficiently and effectively protect the safety, health, and genetic diversity of the U.S. tropical and subtropical fruit and nut genetic resource collections and associated information.


Approach
Subobjective 1A: 1) improve maintenance procedures for our crops to ensure that accessions are maintained as securely as possible given the resources available; 2) survey existing private and public domestic collections to determine if the germplasm they contain would make a valuable addition to the existing collection; and 3) improve distribution procedures to facilitate access to the collection. Duplication of the living collections and procedures for backup storage of seed are in place or in progress for most species. Subobjective 1B: Create back-up collections for avocado and cacao in Hilo, using a quarantine procedure that will prevent the transfer of pests. Any material found to be infected with pathogens or other pests will be destroyed immediately. Subobjective 1C: Develop protocols for long term storage of the papaya and pineapple collections by assessing the viability and longevity of material stored in liquid nitrogen. If pineapple cryopreservation is unsuccessful, the collection will continue to be maintained in both the greenhouse and tissue culture facilities at Hilo. If papaya cryopreservation does not extend the storage of papaya seeds, papaya seeds will continue to be regenerated at current frequency and stored at locally at two separate locations. Subobjective 2A: Evaluate breadfruit, cacao and pilinut accessions for fruit production and qualities. If any fruit or nut samples for evaluation can’t be collected or processed properly due to weather or other protocol failures, the evaluation will be repeated in future years. Pili nut, breadfruit, guava and macadamia nut are important crops, but basic techniques for propagating and/or hybridizing them still need to be developed. Subobjective 2B: Develop and document clonal propagation techniques for pili nut, breadfruit, and guava, and to develop a technique for making controlled crosses in macadamia. We will modify our propagation techniques in a stepwise process based on which parameters seem to be most important for successful propagation. Subobjective 2C: Develop SNP markers through collaborators for rambutan and pulasan. If markers are not successful in detecting redundancies in the collection or sequencing is sufficient to generate a reference genome, further sequencing or different molecular marker techniques will be explored. Subobjective 2D: Systematically evaluate and characterize emerging disease responses of tropical crops, to understand the host-pathogen interactions, and develop rapid methods for detection of pathogens. If insufficient information is found within our selected crops at the germplasm repository, symptomatic trees will be identified through communication with commercial nurseries, research stations, and private residences. Objective 3: We will work with other repositories, scientists and industry to development of best management practices and develop Crop Vulnerability Statements. If external (national or international) assistance is unavailable, the team will focus upon local stakeholder groups to develop locally applicable methods and statements.


Progress Report
This is the final report for project 2040-21000-016-000D Management, Characterization, and Evaluation of Pacific Tropical and Subtropical Fruit and Nut Genetic Resources and Associated Information, which terminated 3/1/2023. Substantial results were realized over the five years of the project and are continuing in the new project 2040-21000-018-000D, titled "Conservation, Management, and Genetic Improvement of Tropical and Subtropical Fruit, Nut, and Beverage Crop Germplasm for the Pacific Region". In support of Sub-objective 1A, ARS researchers planted a three-acre field of coffee this year with 248 plants, bringing the total to 416 plants of 68 accessions of coffee. Total new introductions over the life of this project are 125 accessions of coffee, one coffee accession for rootstock, four passionfruit, seven papaya, three papaya relatives, 42 avocado, 29 cacao, one litchi, four macadamia, one longan, three guava, and two durian, bringing the field plantings to 1,486 on our 38 acres. A variety trial is being conducted in the Kona district of Hawaii, with 90 coffee plants of 18 accessions. A satellite field in Paauilo (away from commercial papaya production) is used to regenerate papaya seeds. In the 2022-2023 harvest, 6,151 grams of seeds from 18 accessions were placed into 5 degrees C storage. Healthy accessions of Vasconcellea grown in Lalamilo, Volcano, and Waiakea greenhouse produced 285 g of stored seeds. The previous year's seed storage was 13,742 gm of Carica and 1,483 g of related species. Requests filled this year (424 items) included two Vasconcellea to India, 106 to the UK litchi for genetics study, two Carica and seven Vasconcellea and one Jacaratia to Miami University for gene expression studies, one Carica accession to HARC for tissue culture, four Carica for the cooperative extension on Kauai, 243 litchi and longan for ARS genome study, 37 Carica and Vasconcellea were distributed to cooperators for genetic studies. For the previous life of the project, 257 requests were filled for 1,150 items for genomic analysis and virus indexing. Distribution to foreign countries included Nigeria, India, Mexico, Marianas, Malawi, Belize, Guam, Pakistan, India, Micronesia, and Kenya. Duplication of the collection to serve as local backups as air layers were completed for acerola (seven accessions), starfruit (23), avocado (114), and are ongoing for litchi (88/100), longan (20/25), guava (55/65), macadamia (38/43), and rambutan (62/81). Rootstock of macadamia, breadfruit, longan, rambutan and giant rambutan, and pili nut (all six species) are maintained in the nursery for grafting new introductions and repropagating duplicate accessions. Standard operating procedures were written for papaya regeneration, propagation techniques, orchard pruning, and maintenance. Fencing was replaced around all orchards to prevent feral pigs from damaging the field and accessions. Supporting Sub-objective 1B rootstock was established for avocado and cacao and is ready for new introductions to be grafted upon arrival. Thirty-eight avocado from the Miami collection were received and tested for Laurel Wilt and Sun Blotch Viroid. A total number of 114 avocado accessions received from Miami were planted in the field and greenhouse. Cacao (230 plants to date) are being screened for Cacao Mild Mosaic Virus (CMMV) and Cacao yellow vein-banding virus (CYVBV). These viruses are new occurrences, and plants are being tested before planting in cooperator fields in Hilo and Kona. Progress on Sub-objective 1C continues with the pineapple germplasm being screened to ensure the collection is free of Pineapple Mealy Bug Wilt Viruses (PMWV 1, 2, 3, 6). This year 113 accessions have been screened. Virus-free plant materials are being multiplied via tissue culture. Objective 2 progress includes the maintenance of 1,486 field plants with new plantings of 248 coffee, eight macadamia, four breadfruit, and three peach palm. Pineapple is maintained in greenhouses, with 152 harvested and replanted. Tissue culture backup consists of 186 pineapple accessions, ginger (7/10), one papaya, five passionfruit, one starfruit, and nine breadfruit. Germination tests of 5,095 g of old papaya seeds were tested and found unviable, and 1725 g of duplicate seeds were removed from cold storage. Observation data (427) was entered into the Germplasm Resources Information Network (GRIN) this year, with a prior project total of 6,143 fruit, plant, and flower phenotypic data for pineapple, pili nut, breadfruit, peach palm, papaya, longan, and guava. Sub-objective 2A progress includes preliminary data on cacao yield, pod disease, and bean observations. Cacao nibs have been harvested, fermented, dried, and sent for organoleptic analysis. Pili nuts (Canarium sp.) were analyzed for nineteen single plant selections. Dry matter content ranged from 88% to 90%, and oil content ranged from 61.9% to 74.5% on a dry weight basis. Seven selections were identified with oil content greater than 72%. Sub-objective 2B for macadamia hybridization and pollination study has not been pursued due to the presence of Phytophthora in the field. Trees are being proactively treated with injections of fungicides, and a new orchard of macadamia is being established. Seven breadfruit accessions have been propagated with cuttings, nine accessions of macadamia have been propagated through a new method of rooting shoot tips, and thirteen accessions of guava have been rooted successfully from green and semi-mature cuttings. Crosses were made from six plants' stored macadamia pollen and leaves and were sent to a cooperator for sequencing. In support of Sub-objective 2C, 15 leaf samples of macadamia were sent to the University of Hawaii for molecular analysis. Papaya seeds were distributed to researchers at the University of Hawaii to develop breeding projects for seed distribution. Coffee leaves were collected to develop unique single nucleotide polymorphism (SNP) markers for Coffea arabica accessions. Plant samples of macadamia (35), papaya wild relatives (8), rambutan, and pulasan (20) were sent to collaborators for molecular analysis. In support of Sub-objective 2D, research was conducted to develop a rapid bioassay method to determine varietal resistance to Phytophthora species. Minimally invasive tree sampling techniques were refined for macadamia to ensure the reliability of results. A combination of field sampling and qPCR assay for Phytophthora detection has been validated at 8 locations on Hawaii Island. Disease severity and field distribution study of Macadamia Quick Decline (MQD) revealed certain varieties (i.e. HAES 800, 900) were very susceptible and other varieties (i.e. HAES 879, 932) were more tolerant to MQD. Phytophthora populations from MQD-infected trees from Hawaii Island were compared and found to be identical. Samples from macadamia in Ka’u revealed Phytophthora tropicalis as the causal agent of MQD. The fungal pathogen was associated with cankers approximately one to two feet above the soil line. The on-site reliability of the AGDIA ImmunoStrip to detect isolates of Phytophthora cinnamomi, P. heveae, P. tropicalis/capsici, and P. palmivora and the detection of P. heveae, and P. tropicalis/capsici from hardwood samples was completed. Leaf and seedling bioassays were developed to screen and evaluate macadamia accessions for resistance or tolerance to Phytophthora spp. Recommendations for improved management practices to minimize tree loss in mature orchards are being provided. Phytophthora sp. isolates from papaya were collected, purified for morphological and molecular population studies, and used as inoculum to develop a novel screening assay. Papaya seedlings and Albizia leaflets to bait Phytophthora sp. from infected field-collected soil worked well for P. palmivora. A segregating population of papaya seedling resulting from a cross between known susceptible and tolerant cultivars will be used to identify genes expressed in P. palmivora tolerance. A potential emerging pathogen causing gummy stem blight symptoms in mature papaya was isolated and identified (Stagonosporopsis sp.). Papaya field surveys found Colletotrichum spot of papaya fruit was negligible at a commercial field in Keaau, however a post-harvest issue incurred during papaya shipment. Fungal pathogens and a critical control point for disease management were identified to alleviate the problem. Field surveys were also conducted for avocado and cacao, and three new and emerging diseases were discovered. Fungal isolates, including a Pseudocercospora sp. from avocado fruits and a Colletotrichum sp. and Pseudocercospora sp. from cacao pods, were collected, purified. Standard protocols used to isolate Pseudocercospora sp. have been modified to improve isolation efficiency and decrease or eliminate the isolation of secondary pathogens. Finally, in response to a newly emerging disease detected in late 2020, research commenced on Hemileia vastatrix, the causal agent of coffee leaf rust and the most devastating disease of coffee. All germplasm-related pathology results were submitted to GRIN. In support of Objective 3, work continued with repositories in Miami, Florida, and Mayaguez, Puerto Rico, to develop common descriptors for avocado, cacao, coffee, and lychee. The Tropical Fruit Crop Germplasm committee is currently inactive. The Cacao and Coffee Crop Germplasm Committee, composed of researchers and industry representatives, developed, and published a vulnerability statement for coffee and are currently developing the vulnerability statement for cacao. Scientists and technicians from the Hilo repository visited with Mayagüez, Puerto Rico, and Miami, Florida, staff to discuss common crop propagation, cultivation, and pest and pathogen diagnosis and mitigation. Standard operating procedures for data collection of descriptors for shared crops were discussed and will be used to develop common descriptor sets.


Accomplishments
1. Collection and distribution of tropical fruit and nut trees. ARS staff in Hilo, Hawaii, collect, maintain, and distribute 15 designated tropical fruit and nut crop germplasm accessions in fields, greenhouses, and tissue culture with the new addition of coffee germplasm. The repository provided U.S. and foreign researchers with plant material for genomic analysis and virus indexing. In addition, germplasm was distributed to foreign countries included Nigeria, India, Mexico, Marianas, Malawi, Belize, Guam, Pakistan, India, Micronesia, and Kenya. This project contributes to positive economic and environmental impact worldwide by providing a reliable and sustainable source of tropical plant germplasm for research and crop production. It provides critical plant genetic resources for fundamental knowledge in plant science.


Review Publications
Hughes, M.A., Roy, K., Harrington, T.C., Brill, E., Keith, L.M. 2022. Ceratocystis lukuohia-infested ambrosia beetle frass as inoculum for Ceratocystis wilt of 'ohi'a (Metrosideros polymorpha). Plant Pathology. 72(2):232-245. https://doi.org/10.1111/ppa.13653.
 Larrea-Sarmiento, A., Geering, A., Olmedo-Velarde, A., Wang, X., Borth, W., Matsumoto Brower, T.K., Suzuki, J.Y., Wall, M.M., Melzer, M., Moyle, R., Sharman, M., Hu, J., Thomas, J. 2022. Genome sequence of pineapple secovirus B, a second sadwavirus reported infecting Ananas comosus. Archives of Virology. 167:2801-2804. https://doi.org/10.1007/s00705-022-05590-9.
 Larrea-Sarmiento, A., Olmedo-Velarde, A., Wang, X., Borth, W., Domingo, R., Matsumoto Brower, T.K., Suzuki, J.Y., Wall, M.M., Melzer, M., Hu, J. 2022. Genetic diversity of viral populations associated with Ananas germplasm and improvement of virus diagnostic protocols. Pathogens. 11(12). Article 1470. https://doi.org/10.3390/pathogens11121470.
 Wang, X., Larrea-Sarmiento, A., Olmedo-Velarde, A., Kong, A., Borth, W., Suzuki, J.Y., Wall, M.M., Melzer, M., Hu, J. 2023. First detection and complete genome sequence of a new tobamovirus naturally infecting Hibiscus rosa-sinensis in Hawaii. Archives of Virology. 168. Article 40. https://doi.org/10.1007/s00705-022-05634-0.
 Wang, X., Larrea-Sarmiento, A., Olmedo-Velarde, A., Kong, A., Borth, W., Suzuki, J.Y., Wall, M.M., Melzer, M., Hu, J. 2022. First detection and genome characterization of a new RNA virus, Hibiscus betacarmovirus, and a new DNA virus, Hibiscus soymovirus, naturally infecting Hibiscus spp. in Hawaii. Viruses. 15(1). Article 90. https://doi.org/10.3390/v15010090.
 Wraight, S.P., Howes, R.L., Castrillo, L.A., Griggs, M.H., Galaini-Wraight, S., Carruthers, R.I., Matsumoto Brower, T.K., Keith, L.M. 2022. Laboratory studies assessing the microbial biocontrol potential of diverse strains of Beauveria bassiana isolated from coffee berry borer, with emphasis on strains from Hawai'i Island and comparisons to commercial strain GHA. Journal of Invertebrate Pathology. 194. Article 107819. https://doi.org/10.1016/j.jip.2022.107819.
 Zhang, W., Lin, J., Li, J., Zhen, S., Zhang, X., Chen, S., Ma, X., Dong, F., Jia, H., Xu, X., Yang, Z., Ma, P., Deng, F., Deng, B., Huang, Y., Li, Z., Lv, X., Ma, Y., Liao, Z., Lin, Z., Lin, J., Zhang, S., Matsumoto Brower, T.K., Xia, R., Zhang, J., Ming, R. 2021. Rambutan genome revealed gene networks for spine formation and aril development. The Plant Journal. 108(4):1037-1052. https://doi.org/10.1111/tpj.15491.
 Hamim, I., Suzuki, J.Y., Borth, W., Melzer, M., Wall, M.M., Hu, J. 2022. Preserving plant samples from remote locations for detection of RNA and DNA viruses. Frontiers in Microbiology. 13. Article 930329. https://doi.org/10.3389/fmicb.2022.930329.
 Wang, X., Larrea-Sarmiento, A., Olmedo-Velarde, A., Al Rwahnih, M., Borth, W., Suzuki, J.Y., Wall, M.M., Melzer, M., Hu, J. 2022. Survey of viruses infecting Basella alba in Hawaii. Plant Disease. 107(4):1022-1026. https://doi.org/10.1094/PDIS-02-22-0449-SR.
 Keith, L.M., Sugiyama, L.S., Brill, E., Adams, B.L., Fukada, M., Hoffman, K.M., Ocenar, J., Kawabata, A., Kong, A.T., McKemy, J.M., Olmedo-Velarde, A., Melzer, M.J. 2022. First report of coffee leaf rust caused by Hemileia vastatrix on coffee (Coffea arabica) in Hawaii. Plant Disease. 106(2):761. https://doi.org/10.1094/PDIS-05-21-1072-PDN.
 Perroy, R., Sullivan, T., Benitez, D., Hughes, F., Keith, L.M., Brill, E., Kissinger, K.R., Duda, D. 2021. Spatial patterns of 'ohi'a mortality associated with rapid 'ohi'a death and ungulate presence. Forests. 12(8). Article 1035. https://doi.org/10.3390/f12081035.
 Hughes, M.A., Juzwik, J., Chen, Z., Luiz, B.C., Keith, L.M. 2022. Evaluation of kiln-heating as a phytosanitary treatment for Ceratocystis-infested 'ohi'a (Metrosideros polymorpha) wood. European Journal of Wood and Wood Products. 72(3):207-215. https://doi.org/10.13073/FPJ-D-22-00024.
 Perroy, R.L., Meier, P., Collier, E., Hughes, M., Brill, E., Sullivan, T., Baur, T., Buchmann, N., Keith, L.M. 2022. Aerial branch sampling to detect forest pathogens. Drones. 6(10). Article 275. https://doi.org/10.3390/drones6100275.