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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

2021 Annual Report

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.

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
Progress was made this year on most objectives and sub-objectives which fall under National Program 301. Under Sub-objective 1A, new accessions were added to the collection including one avocado, from the University of Hawaii; one cacao accession for rootstock from ARS, Puerto Rico; six macadamia accessions from a commercial orchard; 38 accessions of coffee from a project cooperator; five papaya relatives from a requestor; and one papaya from a local farm. Rootstocks of mango, macadamia, breadfruit, longan, avocado, and durian are growing in the greenhouse, ready for grafting new introductions and repropagating duplicate accessions. Duplicates of each accession are being propagated. Currently, 15 litchi trees have been air-layered, bringing total duplicates for the collection to 90 of the 95 accessions. Other duplicates propagated were six starfruit plants (air-layer), five breadfruit plants(cuttings), 17 guava plants (air-layer), 17 macadamia plants (cutting), eight longan plants (air-layer), and four passion fruit plants (cutting). Sixty-one avocados in the greenhouse collection and 14 dragon fruit were rejuvenated. Eighteen accessions of Carica (10,676g of seed), three Vasconcellea (1,636g of seed), and one Jarilla (49g of seed) were harvested and put into storage. Eight Vasconcellea from the greenhouse and Volcano field were increased for seed (151g). Distributions included 16 requests for 100 items. Five requests for 19 items for research, one request for two items were sent to North Carolina State University, 10 items to University of Florida, and five requests for 19 items were sent to cooperators. Foreign distributions included 36 guavas to ICAR-NBPGR in India and five to Belize. In support of Sub-objective 1B, cacao and avocado rootstock are ready for new accessions to arrive for grafting. New avocado accessions were delayed due to the rejuvenation of the rootstock plants in Fort Detrick and to the pandemic. In support of Sub-objective 1C, pineapple germplasm continues to be screened to ensure the collection is free of Pineapple Mealy Bug Wilt Viruses (PMWV); however, due to the COVID pandemic, lab testing for the viruses and multiplication of extra plant material were paused and work focused on the maintenance of the germplasm. In support of Objective 2, more effective genetic resource maintenance, evaluation, and characterization methods were developed and applied to Pacific tropical and subtropical fruit and nut genetic resources. Evaluation and characterization data was recorded and disseminated via GRIN-Global and other data sources. Descriptor data was entered into Germplasm Resources Information Network (GRIN): five accessions of pineapple plants (90 observations), 17 fruit (459 observations), 51 flower (306 observations), 220 observations for 10 accessions of breadfruit (fruit), 30 observations for two peach palm accessions, 46 observations for three pili nut accessions, 457 observations for 16 accessions of papaya, 33 observations for one litchi accession, and 23 observations for one rambutan accession. In support of Sub-objective 2A, data collection on breadfruit production is ongoing across multiple seasons. Preliminary data on cacao yield, pod disease, and bean data were collected from a cooperator field trial. In addition to data collection, scion wood from this field is being utilized to prepare plants for two additional field trials. The cacao accessions have been grafted and are awaiting planting at two locations on Hawaii island. In support of Sub-objective 2B, five breadfruit accessions have been propagated using a new technique for propagation via cuttings. Seventeen accessions of macadamia have been propagated through a new method of rooting shoot tips. In support of Sub-objective 2C, fifteen leaf samples of macadamia were sent to the University of Hawaii cooperator for molecular analysis. Seeds of papaya 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 polymorphisms (SNP) markers for Coffea arabica accessions. In support of Sub-objective 2D, macadamia research of re-emerging fungal pathogens continued, and the disease severity and field distribution study of Macadamia Quick Decline (MQD) in Kona was completed. Incidence and severity were calculated for a variety trial containing 37 trees and eight varieties. Overall incidence was determined to be greater than 60%. A disease rating scale for macadamia germplasm was developed. Certain varieties (ie. HAES 800, 900) were very susceptible to MQD, and 90% were infected with the pathogen. Other varieties (ie. HAES 879, 932) were more tolerant to MQD; however, the symptomology of most trees suggested that fungicide treatments would be ineffective at the current stage of disease, and all trees were removed from the field. Phytophthora populations from MQD-infected trees from Hawaii Island were compared and found to be identical. A major macadamia grower in Ka’u, Hawaii, recently discovered dying trees in mature and newly planted orchards. Samples were collected from trees with symptoms (partial or full brown canopy that died rapidly), and fungal cultures were identified by morphology and molecular identification. Phytophthora tropicalis, the causal agent of MQD, was identified. A different species of Phytophthora was identified in the newly planted field. The fungal pathogen was associated with cankers approximately one to two feet above the soil line. Trunk canker is the most widespread disease in all macadamia-producing countries. We are currently working with the macadamia field manager to assess the impact of Phytophthora diseases in mature and newly planted orchards. Additional samples are being collected and analyzed to determine if the seedlings were infected in the nursery or after planting. Recommendations for improved management practices to minimize tree loss in the mature orchards are being provided. Phytophthora sp. isolates from papaya were collected and purified for morphological and molecular population studies and to be used as inoculum for germplasm screening. The effectiveness of using papaya seedlings and Albizia leaflets to bait Phytophthora sp. from infected field-collected soil was determined. Both worked well for P. palmivora and provided an additional option for baiting from the soil. A potential emerging pathogen causing gummy stem blight symptoms in the field of mature papaya was isolated and identified (Stagonosporopsis sp.). Additional research is needed to identify the species to determine if it is a new Hawaii pathogen record or a new host record. In response to a newly emerging disease detected in late October 2020 that has the potential to devastate the Hawaii coffee industry, research commenced on Hemileia vastatrix, the causal agent of coffee leaf rust. All germplasm-related pathology results were submitted to Germplasm Resources Information Network (GRIN). In support of Objective 3, National Plant Germplasm System (NPGS) genebanks and Crop Germplasm Committees developed, updated, documented, and implemented 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. The Cacao and Coffee Crop Germplasm Committee, composed of researchers and industry representatives, published the Crop Vulnerability Statements for coffee and is currently developing the vulnerability statement for cacao.

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. Over the last year, additions included 38 coffee, six papaya and papaya relatives, six macadamia, one cacao, and one avocado accessions to the respective collections. Sixteen requests for 100 items were filled, including foreign distributions of guava to India and Belize. This project contributes to positive economic and environmental impact worldwide by providing a reliable and sustainable source of plant germplasm for research and crop production. It provides critical plant genetic resources for fundamental knowledge in plant science.

2. Confirmation of pathogenicity of coffee leaf rust in Hawaii. Coffee leaf rust, caused by Hemelia vastatrix, is the most devastating disease in coffee production and was recently discovered in Hawaii on the island of Maui in October 2020. ARS researchers in Hilo, Hawaii, have proven that the pathogenicity of H. vastatrix is present on coffee and is now leading pathology efforts since its discovery in Hawaii. Educating coffee growers on the proper identification of coffee leaf rust provides a valuable new tool for early detection to implement control methods for this potentially devastating disease.

3. Identification of threats to coffee conservation in the United States. Coffee is one of the most important agricultural commodities in the world. Although demand for coffee is expected to increase, challenges posed by climate change and associated impacts such as higher incidence of insect pests and plant pathogens are expected to reduce productivity. To help guide the National Plant Germplasm System (NPGS) coffee genetic resource collection, the Coffee and Cacao Crop Germplasm Committee, including ARS researchers in Hilo, Hawaii, developed a coffee crop vulnerability statement that includes background information about the crop, threats to coffee genetic resources, the current status of coffee genetic resources and capacities, and projected future needs of coffee research, breeding, and production. The crop vulnerability statement will guide the development of the coffee collection and prioritize and address the needs of the coffee industry in the United States.

Review Publications
Luiz, B., Keith, L.M. 2021. Influence of culture media and temperature on growth and sporulation of Ceratocystis lukuohia. Pacific Science. 74(4):389-394.
Luiz, B., Stacy, E.A., Keith, L.M. 2020. Screening of Metrosideros polymorpha ('ohi'a) varieties for resistance to Ceratocystis lukuohia. Forest Pathology. 51(1). Article e12656.
Roy, K., Bjontegard, N., Jaenecke, K., Mikros, D., Dunkle, E., Yanger, C., Sugiyama, L.S., Keith, L.M., Peck, R.W. 2020. Decontamination of ceratocystis pathogens responsible for rapid 'ohi'a death. Plant Health Progress. 21(4):301-305.