Location: Tropical Crops and Germplasm Research
2025 Annual Report
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 banana, cacao, bamboo, coffee, and tropical and subtropical fruit genetic resources to avoid backlogs in plant genetic resource and information management.
Sub-objective 1.A: Evaluate germplasm for important agronomical/horticultural characteristics.
Sub-objective 1.B: Back up germplasm collections and related information.
Sub-objective 1.C: Maintain and disseminate associated information.
Objective 2: Acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority banana, cacao, bamboo, coffee, and tropical and subtropical fruit genetic resources and associated descriptive information.
Sub-objective 2.A: Effectively acquire and maintain genetic resources.
Sub-Objective 2.B: Distribute pathogen-tested genetic resources.
Sub-objective 2.C: Develop SNPs and assess genetic diversity for cacao and other minor crops within the collections.
Approach
Characterization, evaluation and identification of promising germplasm which may be of use to the tropical fruit industry or improvement programs.
To ensure that no confusion occurs during conservation, regeneration, and distribution, each accession in all the collections is carefully labeled in the screenhouse prior to field planting, identified in field maps as well as labeled during the distribution process. The use of a bar coding system and thermal printers with waterproof and non-photosensitive labels is being implemented for labeling of all plant material and a detailed form with information and instructions for requestors is included with all distributions. Priority tropical genetic resources maintained by TARS consist of 184 of Musa spp., 284 accessions of cacao, 31 of mamey sapote, 23 of sapodilla, 30 of Spanish lime, 13 Annona species, 13 Garcinia species, and 28 genera/species of tropical bamboo. These accessions are clonally propagated and established in field collections. In addition to priority genera, a core backup mango collection consisting of 47 diverse genotypes (primary site is SHRS, Miami, FL) as well as a backup of 64 temperate bamboo accessions (primary site is PGRCU, Griffin, GA) are maintained. Furthermore, a backup core collection of coffee (primary site is PBARC, Hilo, HI will be established during this project life. To limit errors during conservation, regeneration, and distribution, each representative plant within accessions in all the collections, in laboratories, greenhouses, and in the field is carefully labeled. In the field, accessions are identified, with labels, stakes, maps (print and electronic) in databases. The use of a local database, QR code system and thermal printers with waterproof and sunlight resistant labels has been employed and a complete packing list and phytosanitary certificate (if required) is included with all distributions. Embedded information in QR labels contains GRIN database passport and characterization data. As introduction of disease and insect pests is a constant threat to local germplasm collections, standard operating procedures are implemented for visitors. Visitors are informed of the risks and the protocols to follow to avoid introductions, particularly when a visitor originates from a region where disease and insects are prevalent on crops curated at TARS. In addition, signs are clearly posted at both TARS’s research sites warning visitors to follow protocols of registering and being accompanied by TARS employees. Specific acquisition, maintenance and distribution practices for each crop are described below.
Progress Report
Progress was made on Sub-objective 1.A: 1) Field evaluation of exotic and cryopreserved Musa spp. germplasm was initiated. Individuals were characterized by using standard descriptors to identify candidates to enrich the tissue culture (TC) collection. Data was uploaded to Bioversity MGIS and local sites. 2) A cacao population study began 6/3/2021 using crosses between disease-resistant Ecuadorian males and high-yieldingTARS females. The study includes six cacao families. Pod production began in mid-2024; second yield evaluation ongoing in 2025. 3)Anthracnose, the main post-harvest mango disease, was surveyed at the USDA-ARS mango germplasm backup site. Five Colletotrichum species from the C. gloeosporioides complex were found in 18 of 40 M. indica cultivars; C. asianum was predominant and infected 30 cultivars. A manuscript was accepted in Plant Disease. 4) Forty-four M. indica x M. casturi seedlings were inoculated with C. asianum. Two crosses showed strong tolerance and 12 moderate tolerance 25 days post-inoculation. The remaining crosses will be evaluated in summer 2025. 5) A pest survey in a commercial mango farm identified Phidotricha erigens, Elaphria chalcedonia, and Synchlora frondaria as new mango pests. A manuscript on P. erigens was accepted in Florida Entomologist. 6) Laboratory bioassays showed pyrethrin-based treatments significantly reduced P. erigens by 95.8%, spirotetramat + azadirachtin reduced S. frondaria by 91.7%, and acetamiprid reduced Bracon sp. by 92%. A second season of cultural control was conducted in the spring; data analysis and manuscript underway. 7) Flatormenis sp. was confirmed as a mango pest. Zeta-cypermethrin caused 83.4% ovicidal failure and 65% post-eclosion mortality. Only 23.08% of eggs hatched, with 39% producing non-viable nymphs. 8) Five mealybug species were found in USDA-TARS cacao: Planococcus citri, Pseudococcus longispinus, Ps. comstocki, Maconellicoccus hirsutus, Ferrisia
virgata. P. citri transmitted CaMMV. Severe viral symptoms appeared in GNV164, EQXZ, GNV182, and TARS23. Aphid Toxoptera aurantii infested 80% of accessions, especially T533_SHRS24 and GU185. 9) Coffee fruit rot (CFR), mostly linked to Colletotrichum, was also caused by five Fusarium spp. in Puerto Rico and manuscript was published. 10) Coffee leaf rust (CLR) caused by Hemileia vastatrix is the most limiting coffee disease worldwide. Fifty physiological races have been reported making control difficult. To determine genetic variability of CLR in Puerto Rico, 25 coffee varieties have been inoculated in the laboratory. Five IMLVT coffee varieties are germinating at the coffee shade-house, and they will be ready for inoculations in 2026. Diversity of infection was found in Puerto Rican CLR isolates, some isolates infect ‘Sarchimor’ coffee while others infect ‘Catimor’ and arabica coffee. 11) Six species of mycoparasites of CLR were identified and evaluated under field conditions in Puerto Rico: Simplicillium lanosoniveum, S. lamellicola, Lecanicillium aranearum, L. uredinophilum, Akanthomyces lecanii, and Akanthomyces sp. while all species demonstrated the ability to parasitize CLR in coffee fields, molecular analysis revealed that the most frequently recovered was S. lanosoniveum. This finding suggests that S. lanosoniveum is the most environmentally adapted and it is a robust candidate for biological control of CLR in Puerto Rico, and that the use of species mixtures is unnecessary for future field evaluations. 12) Cacao pod rot disease is caused by a complex of pathogens that include Colletotrichum spp., Diaporthe spp., and fungi in the Botryosphaeriaceae family. A total of 11 species in the Botryosphaeriaceae were found in 233 cacao accessions evaluated. Pathogenicity tests with Lasiodiplodia spp. were conducted in FY25 to determine which cacao pathogen is causing cacao pod rot disease; 13) Al-tolerance evaluations in cacao revealed no strong tolerance and as a result no field evaluation will be required; manuscript was submitted. 14) Global TR4 impact estimated at $10B. Material for field evaluation of TR4-tolerant Musa in PR is currently in tissue culture and will be established in the field in late 2025. 15) Eight disease-resistant cacao selections and two high-yielding TARS selections were grafted onto EET-400 and established on 9/2/2021 in Corozal, PR. Yield and pod index evaluations began in 2024; second year data collection is underway in 2025. 16) Nineteen cacao accessions from 10 genetic groups were tested for drought tolerance. Preliminary result showed TARS14, UF36, and PA70 performed best. Root architecture and proline were also assessed in 2025; second replication underway. 17) Ten jaboticaba selections replicated six times were planted on 5/16/2018 in Isabela, fruiting began in 2024; second production year in 2025 was completed. 18) Twelve mango selections were established on 8/26/2021 on Isabela farm. Fruiting began in 2024; all 2025 production data was assessed and completed. 19) Eight Fiji coconut selections established on 6/8/2021 in Isabela showed full production by 2025 with evaluations completed. 20) Characterization and GRIN-Global entry of Theobroma spp. (Ecuador and PR criollos) were delayed to 2026 due to dieback/mortality, putatively from Lasiodiplodia and wet weather. LICOR-based physiological characterization along with previously described traits are scheduled for early 2026. 21) An avocado experiment with four cultivars grafted onto four Prr-resistant rootstocks and two seedlings was established on 12/9/2021 in Isabela. Hass scions showed high susceptibility. 2025 evaluations were completed for yield.
Progress was made on Sub-objective 1.B: Back up germplasm collections and related information. The following research was conducted by ARS scientists in Mayaguez, PR: 1) Approximately 28% of the entire cacao collection has been regrafted and establish in a greenhouse as part of the mission to reestablished, secure and maintain critical germplasm inventory safe from tropical storms and hurricanes; 2) Fifty-six cacao accessions are being propagated by somatic embryogenesis in an attempt to eliminate viruses while five will remain in long term storage at the end of treatments; 3) Two Annona accessions from the collection were successfully grafted and backed up in a greenhouse while currently undergoing initial tissue culture stages for protocol testing and preservation; 4) Air-layering of five mamey sapote accessions were completed for greenhouse backup and are currently at initial rooting stages.
Progress was made on Sub-objective 1.C: Maintain and disseminate associated information. The following research was conducted by ARS scientists in Mayaguez, PR: 1) A complete dataset on yield and fruit quality traits was collected from the Spanish lime collection and uploaded to GRIN; 2) Musa passport information, field descriptors, and voucher images from characterizations have been entered into the MGIS database. Cacao Characterization effort will continue in FY26; 3) Approximately 40% of the entire germplasm site (Miscellaneous and Collection sections) was surveyed to identify missing labels and update taxonomic nomenclature. Tag replacement was initiated, including the installation of QR-coded labels linked to GRIN-Global database entries. These were replaced with engraved metal stake labels. This effort will continue in FY26.
Progress was made on Sub-objective 2.A: Effectively acquire and maintain genetic resources. The following research was conducted by ARS scientists in Mayaguez, PR: 1) Twenty IMLVT (International Multilocation Variety Trial) coffee varieties from the World Coffee Research (WCR) organization were introduced to TARS, 11 have been planted for field evaluations in the field during 2024; while close to 50 accessions are currently deployed in the field during 2025 period including CLR coffee differentials; 2) Labeling effort all field collections and digitalized field map construction continue through all germplasm and miscellaneous collections.
Progress was made on Sub-Objective 2.B: Distribute pathogen-tested genetic resources. The following research was conducted by ARS scientists in Mayaguez, Puerto Rico: Musa spp. collection was planted in the field in late 2023 and evaluated late 2024. True to type accessions phenotypically asymptomatic for virus were reestablished into TC conditions. Currently 98% of collection is backed-up in vitro for indexing; 2) Three cacao R-clones were introduced via quarantine from SHRS and ICQRC and are currently being grafted in greenhouse for backup. These accessions target enrichment of the collection by providing resistant traits against frosty pod and witches’ broom diseases; 3) All germplasm is currently available for distribution as requested by stakeholders.
Progress was made on Sub-objective 2.C: Develop SNPs and assess genetic diversity for cacao and other minor crops within the collections. The following research was conducted by ARS scientists in Mayaguez, Puerto Rico: Partnerships between several USDA-ARS laboratories (SHRS, PBARC, and SPCL) and private industry focused on developing and utilizing SNP markers to fingerprint genetic resources in Musaceae, Annonaceae, and Sapotaceae. These efforts aim to establish fingerprint profiles as reference standards for verifying clonal fidelity (trueness-to-type), assessing genetic diversity, and identifying potential gaps in germplasm collections. All samples have been submitted and are currently progressing through the marker development pipeline.
Accomplishments
1. Coffee fruit rot in Puerto Rico. Coffee fruit rot (CFR) is a significant disease that negatively impacts coffee yield and quality. Several species of Colletotrichum have been associated with CFR worldwide. A study conducted by ARS scientists in Mayaguez, PR demonstrated the following: 1) Fusarium spp. causes CFR in Puerto Rico; 2) the coffee berry borer (CBB) has Fusarium spp. as part of its microbiota; and 3) this insect is responsible for spreading Fusarium spp. in coffee fields. A total of nine Fusarium species in six Fusarium species complexes were identified and collected from CBBs and from rotten coffee fruits in the field. Pathogenicity tests showed that five Fusarium species (F. bostrycoides, F. lateritium, F. nirenbergiae, F. solani-melongenae and F. pseudocircinatum) were pathogens of coffee causing CFR on green coffee 15 days after inoculation. Internal rot was significantly higher than external rot indicating that these pathogens use the hole left by the CBB to penetrate and infect coffee tissue. Fusarium bostrycoides was the most predominant species isolated from the CBB microbiota, coffee fruits with symptoms of CFR, and from isolates recovered from pathogenicity tests suggesting a possible symbiosis between F. bostrycoides and the CBB. To our knowledge, this is the first report of F. botryscoides, F.solani melongenae, F. pseudocircinatum and F. nirenbergiae causing CFR worldwide and the first report of F. lateritium causing CFR in Puerto Rico. Fusarium species can produce mycotoxins and may cause disease in plants. Understanding that CFR is a disease complex that includes Fusarium species and how the CBB is contributing to disperse these fungi in coffee farms is important to address the best management practices of this disease in Puerto Rico and other coffee-producing countries. Due to these findings stakeholders such as World Coffee Research have initiated collaborations with ARS to find possibles sources of resistance to this new disease and thus to assist rural coffee farmers.
Review Publications
Osuna-Garcia, J.A., Gomez-Jaimes, R., Goenaga, R.J., Garciano-Cristobal, M.J. 2025. Ripening degree at harvest and ethylene conditioning facilitate the mango process for frozen cheeks. Acta horticulturae. 1415: 297-304. https://doi.org/10.17660/ActaHortic.2025.1415.35.
Osuna-Garcia, J.A., Graciano-Cristobal, M.J., Goenaga, R.J. 2025. Non-destructive techniques to determine optimal harvesting time in mango fruit. Acta horticulturae. 1415: 155-162. https://doi.org/10.17660/ActaHortic.2025.1415.17.