Location: Tropical Crops and Germplasm Research
2024 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: Evaluate germplasm for important agronomical/horticultural characteristics. The following research was conducted by ARS scientists at Mayaguez, Puerto Rico: 1) Cacao population study was established with crosses made using Ecuadorian selections with disease resistance (witches’ broom and frosty pod) and high-yielding TARS selections involves seedlings obtained from six cacao families. Trees started bearing pods for the first time in 2024; 2) A replicated experiment using 7 breadfruit accessions grafted onto breadnut rootstock established at two locations for evaluation of yield, disease and insect response, canopy volume, and organoleptic quality traits. Data is being analyzed; 3) In collaboration with ARS researchers in Fort Pierce, Florida, an experiment with 7 mandarin cultivars grafted onto three rootstocks and evaluated for yield, fruit quality traits, and citrus greening (CG) incidence was completed and data is being analyzed; 4) An experiment to evaluate 10 jaboticaba selections for yield, fruit quality traits, and canopy volume was established at Isabela. Trees started bearing fruit for the first time in 2024; 5) An experiment to evaluate 8 Fiji coconut selections for yield, juice quality traits, disease and insect incidence, and canopy volume was established at Isabela, Puerto Rico. Selections started bearing fruit for the first time in 2024; 6) An experiment to evaluate 12 mango selections for yield, fruit quality traits, disease and insect incidence, and canopy volume was established at Isabela, PR. Trees of some selections started bearing fruit for the first time in 2024; 7) an experiment with 4 avocado cultivars grafted onto four Phytophthora root rot (Prr) resistant rootstocks and two seedlings selections was established at Isabela to be evaluated for yield, fruit quality traits, and Prr resistance. Accessions started bearing fruit for the first time in 2024. Regardless of rootstock, treatments in which the scion was ‘Hass’ became very susceptible to Botryosphaeriaceae and Diaporthe fungi; and 8) Eight disease-resistant cacao and two high-yielding selections grafted onto EET-400 rootstock were established in 2021 in a replicated experiment in Corozal, PR for evaluation of yield, pod index, organoleptic quality traits, and black pod and virus incidence. These accessions have never been evaluated in a replicated experiment. Accessions started bearing pods for the first time in 2024; 9) Nineteen cacao accessions from 10 genetic groups have been evaluated for drought tolerance in a greenhouse setting. Preliminary results using relative water content and plant height identified TARS14, UF36 and PA70 exhibiting superior drought resilience.
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 12 Mangifera spp. were successful grafted on M. indica cv. Mayaguezano, and at least 20 accessions of mango from an old orchard at Mayaguez were backed up for addition to the Miami SHRS collection to secure critical germplasm and current germplasm inventory from tropical storms and hurricanes; 2) Fifty six cacao accessions are being propagated by somatic embryogenesis in an attempt to eliminate viruses; 3) Five Annona accessions from Miami SHRS were added to the Anonna collection in Isabela.
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) Final data (year 5) on yield and fruit quality traits were collected from 30 Spanish lime accessions established in a replicated experiment. Data will be statistically analyzed and published; 2) Passport information has been updated and descriptors from characterizations as well as voucher images have been loaded into Bioversity databases (MGIS); 3) Final data was collected for 80 Musa spp. accessions in Field Verification (FV) V as part of a collaborative project with Bioversity International’s Musa International Transit Center; 4) Fifty accessions of Theobroma cacao have been phenotypically characterized and entered in GRIN-Global 5) Taxonomic nomenclature as well as links provided on QR codes leading to GRIN-Global database information were reviewed and all paper labels glued to metal stakes replaced with significantly more permanent labels where information is engraved on metal labels which are nailed to trees. This effort will continue in FY24.
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) Coordination have been made with other repositories (SHRS, PBARC), universities and private industry to acquire new or missing accessions for several crops; 2) Twenty IMLVT (International Multilocation Variety Trial) coffee varieties from the World Coffee Research (WCR) organization were introduced to TARS, nine have been planted for field evaluations and 11 will be planted in the field during 2024; 3) Eleven CLR coffee differential plants have been introduced to TARS for identification of CLR races locally; 4) 167 Musa spp. accessions were re-established in December 2023, and four new accessions were added to the collection.
Progress was made on Sub-Objective 2.B: Distribute pathogen-tested genetic resources. The following research was conducted by ARS scientists in Mayaguez, PR: 1) Anthracnose is the most important post-harvest disease that affects shelf life in mango. Five species of Colletotrichum were found in 18 of the 40 M. indica cultivars evaluated at the USDA-ARS mango germplasm backup collection in Isabela. Colletotrichum asianum was the most predominant species and it caused anthracnose disease on 30 M. indica cultivars. 2) Forty-one seedlings of M. indica x M. casturi crosses have been inoculated with C. asianum for evaluation of anthracnose resistance. So far, from 41 crosses evaluated, two have shown high tolerance and two moderate tolerance to C. asianum 20 days after inoculation; 3) Several pests have been reported affecting mango inflorescences. A pest survey was conducted in a commercial mango farm in Puerto Rico. Phidotricha erigens, Elaphria chalcedonia and Synchlora frondaria were identified as new pests of mango inflorescences. Associated new parasitoids of these pests included Bracon sp., Phanerotoma sp. (both Braconidae), and Brachymeria sp. (Chalcididae). P. erigans was the most common pest found on proliferated “malformed” inflorescences (more than one panicle emerging from the central axis). Field experiments also revealed higher concentrations of P. erigens and S. frondaria in unmowed plots and in plots treated with insecticides at night; 4) The effectiveness of insecticides for mango inflorescence pests was tested in laboratory bioassays. Pyrethrin-based combinations reduced P. erigens adults by 95.8%. Spirotetramat with azadirachtin reduced S. frondaria adults by 91.7%. Acetamiprid reduced Bracon sp. adults by 92%. 5) Coffee fruit rot (CFR) is a major production problem worldwide. The literature focuses almost exclusively on fungi in the genus Colletotrichum. However, recent work by ARS scientists in Mayaguez showed that five Fusarium spp. were pathogenic to coffee and also caused CFR disease in Puerto Rico. A CFR manuscript describing results is available online since February 2024; 6) Coffee leaf rust (CLR) caused by the fungus Hemileia vastatrix is the most limiting coffee disease worldwide. Fifty physiological races have been reported making its control difficult. To determine genetic variability of CLR in Puerto Rico, 20 coffee varieties (15 IMLVT varieties and 5 commercial varieties) have been inoculated in the laboratory. Diversity of infection was found in Puerto Rican CLR isolates, some isolates infect ‘Sarchimor’ coffee while others infect ‘Catimor’ and arabica coffee. 7) Six species of mycoparasites of CLR have been found and evaluated under field conditions in Puerto Rico. Simplicillium lanosoniveum, S. lamellicola, Lecanicillium aranearum, L. uredinophilum, Akanthomyces lecanii and Akanthomyces sp. novo were able to reduce incidence of CLR in orchards in Puerto Rico; data is being analyzed and will be published in 2024; 8) The number of germplasm distributions in this amounted to approximately 60 orders. Nearly 500 different accessions with ~3,500 propagules. Tropical germplasm was distributed in the form of scionwood, cuttings, rhizomes, corms, seed, pollen, seeds, DNA, and fruit and were made available and distributed to researchers, educators and cooperators at the local, national and international level.
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, PR: 1) Collaborative efforts between several USDA-ARS (SHRS, PBARC and SPCL) laboratories and private industry were undertaken to develop and utilize SNP’s markers to fingerprint Musa and sapotaceae genetic resources. These efforts will focus on utilizing the fingerprint profiles developed as references for establishing trueness-to-type for clonally propagated germplasm, estimating genetic diversity, and identification of potential gaps in the germplasm collections; 2) An invaluable USDA-ARS TARS coffee collection dating from the 1900’s was discovered in a secluded E2 plot in Mayaguez. DNA sequence data of those plants are being analyzed. So far, we have found three different species of Coffea (C. arabica, C. canephora and C. liberica).
Accomplishments
1. Yield and fruit quality traits of rambutan cultivars grafted onto three rootstocks and grown in a Mollisol soil in Puerto Rico. The globalization of the economy, increased ethnic diversity and a greater demand for healthy and more diverse food products have opened a window of opportunity for the commercial production and marketing of tropical fruit, including rambutan. Little is known about the performance using various scion/rootstock combinations in the tropics and subtropics. A study conducted by ARS scientists in Mayaguez, Puerto Rico evaluated yield performance and fruit quality traits of three cultivars (‘Gula Batu’, ‘Jitlee’, ‘R-162’) grafted onto three rootstocks (‘Binjai’, ‘Gula Batu’, ‘R-134’) in an alkaline Mollisol soil in Santa Isabel, Puerto Rico. Overall, scion/rootstock treatments exhibited an increase in fruit number and yield from 2011 to 2015. Cultivar ‘R-162’ grafted onto ‘Gula Batu’, had the highest 5-year mean for number (289,911 fruits) and yield (8,260 kg/ha) of fruit. Regardless of rootstock, ‘R-162’ had higher number of fruit and yield. All cultivars produced more fruit and had higher yield when ‘Gula Batu’ was used as a rootstock. Scion/rootstock treatments did not have a significant effect on individual fruit weight. Cultivar ‘R-162’ grafted onto ‘Gula Batu’ had higher soluble solids concentration but it was not significantly different than the rest of the treatments except for ‘Gula Batu’ grafted onto ‘Binjai’ and ‘Gula Batu’ grafted onto ‘R-134’ which had significantly lower soluble solids concentration. This study provides for the first time useful information to Extension Agents and growers about yield and fruit quality traits of various scion/rootstock combinations and specifically demonstrating cultivar ‘R-162’ being a highly productive cultivar and ‘Gula Batu’ a superior rootstock by performing very well under alkaline soil conditions.
2. Coffee fruit rot distribution, ecology and associated fungi. Coffee fruit rot (CFR) is one of the most important diseases affecting coffee worldwide. This disease is well known in Africa as coffee berry disease (CBD). The disease is characterized by external necrosis and sunken dark brown spots on green or mature coffee fruits that eventually become mummified. In Puerto Rico, coffee fruit rot has been present for many years, but has yet to be quantified. This study conducted by ARS researchers at Mayaguez, Puerto Rico and University of Puerto Rico scientists surveyed the incidence and severity of CFR, and correlated these to environmental parameters, cultivation methods (sun vs shade), presence of the coffee berry borer (CBB), and fruit rot-causing fungi. This study showed that CFR is present throughout Puerto Rico at varying altitudes and environmental and cultivation factors are associated with its incidence and severity. Specifically, increased altitude and shade significantly correlated with lower CFR disease incidence. In addition, fruits damaged by the CBB were found to have higher disease incidence than undamaged fruits. Coffee fruit rot was associated with seven fungal genera with Colletotrichum spp. and Fusarium spp. being the most prevalent suggesting that there is a microecosystem complex on the fruit surface and pulp of coffee fruits. This study is important because planting coffee at higher altitude under shade and controlling CBB can potentially reduce CFR incidence.
3. Coffee fruit rot in Puerto Rico: New associations with Colletotrichum spp., Fusarium spp. and the coffee berry borer. Coffee fruit rot (CFR) is an important disease that affects coffee production and quality. Several Colletotrichum species have been reported causing CFR worldwide. In Puerto Rico, four species of this pathogen were detrimental to coffee fruits. However, the role of Fusarium species affecting coffee was also suggested but pathogenicity tests were not conducted. A study conducted by ARS scientists in Mayaguez, Puerto Rico demonstrated the following: 1) Fusarium spp. cause CFR in Puerto Rico; 2) the coffee berry borer (CBB) has Fusarium spp. as part of its microbiota; 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 diseases 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 worldwide.
4. The Sigatoka Disease Complex Caused by Pseudocercospora spp. and Other Fungal Pathogens Associated with Musa spp. in Puerto Rico. Bananas and plantains (Musa spp.) production worldwide is being limited by fungal diseases. The identification and characterization of these fungi is imperative for the establishment of specific management approaches. Therefore, sixty-one leaf samples of Musa spp. showing fungi diseases symptoms were collected throughout different regions of Puerto Rico by ARS scientists and University of Puerto Rico scientists for diagnosis analysis. Molecular and morphological characterization found that Black Sigatoka, caused by Pseudocercospora fijiensis, is the most frequent disease. However, other fungi such as Cladosporium spp., Corynespora spp., Neocordana spp., Zasmidium spp., and Zygophiala spp. were also found in lower frequency. The identification of these fungal pathogens associated with Musa spp. provides basic information to establish quarantine regulations and an effective and specific management approach for its control in Puerto Rico.
Review Publications
Aviles-Noriega, A., Serrato Diaz, L.M., Giraldo-Zapata, M.C., Cuevas, H.E., Rivera-Vargas, L.I. 2024. The Sigatoka disease complex caused by Pseudocercospora spp. and other fungal pathogens associated with Musa spp. in Puerto Rico. Plant Disease. https://doi.org/10.1094/PDIS-03-23-0433-RE.
Carrasquillo, M.Y., Mariño, Y.A., Medina, A.G., Serrato Diaz, L.M., Bayman, P. 2023. Coffee fruit rot in Puerto Rico: distribution, ecology and associated fungi. European Journal of Plant Pathology. 168: 527-540. https://doi.org/10.1007/s10658-023-02781-1.
Serrato Diaz, L.M., Simbaña-Carrera, L., Velez-Negron, Y., Rivera-Vargas, L.I. 2023. Detection and incidence of pineapple heart rot disease caused by Phytophthora nicotianae in commercial farms in Puerto Rico. Journal of Agriculture of the University of Puerto Rico. 106(2):233-246. https://doi.org/10.46429/jaupr.v106i2.21155.
Goenaga, R.J., Marrero Soto, A.R. 2024. Yield and fruit quality traits of rambutan cultivars grafted onto three rootstocks and grown in a Mollisol soil in Puerto Rico. Journal of Agriculture of the University of Puerto Rico. 108(1):1-11. https://doi.org/10.46429/jaupr.v108i1.21409.
Serrato Diaz, L.M., Mariño-Cardenas, Y.A., Gonzalez De Jesus, J., Goenaga, R.J., Bayman, P. 2024. Coffee fruit rot: the previously unrecognized role of fusarium and its interactions with the coffee berry borer (Hypothenemus hampei). Phytopathology. https://doi.org/10.1094/PHYTO-02-24-0046-R.
