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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 #444088

Research Project: Conservation, Management, and Genetic Improvement of Tropical and Subtropical Fruit, Nut, and Beverage Crop Germplasm for the Pacific Region

Location: Tropical Plant Genetic Resources and Disease Research

Project Number: 2040-21000-018-000-D
Project Type: In-House Appropriated

Start Date: Mar 1, 2023
End Date: Feb 29, 2028

This project aims to address the following objectives. Objective 1: Conduct research to develop genetic resource maintenance, evaluation, or characterization methods and, in alignment with the overall NPGS Plan, apply them to priority tropical and subtropical fruit (e.g., papaya, pineapple), nut (e.g., macadamia), and beverage (e.g., coffee) crop genetic resources to avoid backlogs in genetic resource and information management. Sub-objective 1.A: Develop novel tools and strategies to isolate, identify, characterize, and manage common and emerging plant pathogens of macadamia and other tropical and subtropical crops to maintain optimum health of the current collection and distribute clean germplasm. Sub-objective 1.B: Evaluate genetic diversity and population structure of tropical and subtropical fruit, nut, and beverage germplasm collections and apply genomic tools in germplasm management. Sub-objective 1.C: Conduct research to improve propagation methods, enable safety duplication, increase the number of cryopreserved accessions, and digitize relevant information. Objective 2: Acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority tropical and subtropical fruit (e.g., papaya, pineapple), nut (e.g., macadamia), and beverage (e.g., coffee) crop genetic resources and associated descriptive information. Objective 3: Breed genetically enhanced germplasm that broadens the diversity available for improving selected crops, such as coffee and papaya, by incorporating superior traits from cultivars, landraces, and wild relatives into adapted genetic backgrounds and gene pools. Sub-objective 3.A: Identify and validate genomic regions in the coffee genome harboring coffee leaf rust (CLR) resistance genes and develop and breed CLR-resistant coffee cultivars that maintain high cupping quality. Sub-objective 3.B: Develop molecular tools to identify and breed new P. palmivora tolerant Carica papaya.

This project is responsible for collecting, maintaining, evaluating, and distributing germplasm of tropical and subtropical fruit, nut, and beverage crops. Crops include pineapple (Ananas), breadfruit (Artocarpus), starfruit (Averrhoa), peach palm (Bactris), pili nut (Canarium), papaya (Carica and Vasconcellea), coffee (Coffea), longan (Dimocarpus), lychee (Litchi), macadamia (Macadamia), acerola (Malpighia), rambutan and pulasan (Nephelium), and guava (Psidium). Objective 1 will determine the fungal pathogens and species of Phytophthora that exist on macadamia and other tropical crops through the identification and characterization of host-pathogen interaction. A collection of Phytophthora isolates will be established to understand the diversity of pathogens that may affect the macadamia accessions. In vitro, fungicide tests will be conducted to identify the efficacy of fungicides and will be confirmed in vivo using seedling and field trials. In addition, we will develop high-resolution SNP panels for the designated crops at the Hilo genebank to assess genetic diversity and population structure, identify gaps for future collections, and confirm genotype identity. Also, improve propagation methods for clonal crops to enable accession safety in the Hilo genebank while increasing the storage length of seeds to enable greater regeneration and potential expansion of the Carica and wild relative collections. Objective 2, will manage and operate a clonal germplasm genebank of 15 genetically diverse fruit and nut crops, and provide scientists, domestically and internationally, with high-quality, disease-tested scion, seed, and leaf samples for characterization and research. New germplasm will be acquired through public and private institutions. Clonal crops have a minimum of two plants per accession and, where possible, maintain additional propagules for distribution. We aim to initiate and maintain all clonal accessions in tissue culture and investigate methods for cryopreservation. Plants grown in tissue culture will be acclimatized into the greenhouse every few years to ensure the plant can be successfully regenerated into the field and ensure the phenotype of the accession is unchanged. Germplasm stored as seeds will be maintained in our cold storage facility and also cryopreserved at Fort Collins. We will also serve as backup for the avocado and cacao collections for Miami and Mayagüez repositories, respectively. Objective 3, will identify the genomic regions in coffee linked to or conferring coffee leaf rust (CLR) resistance to improve the effectiveness of the molecular breeding platform for developing new coffee varieties through analysis of an F2 segregating population with SNPs markers to identify quantitative trait loci (QTLs). The Carica collection will be screened for P. palmivora using an inoculated seedling assay. We will also determine if a cross between Phytophthora susceptible ‘SunUp’ and tolerant ‘Waimanalo’ will identify tolerant genes in C. papaya to facilitate the identification of new cultivars for the papaya industry. This will be accomplished through Bulked segregant analysis Ribonucleic Acid-sequencing (BSR-Seq).