Location: Tropical Crops and Germplasm Research
2023 Annual Report
Objectives
1. Efficiently and effectively maintain the safety, genetic integrity, health and viability of priority tropical and subtropical tree fruit, bamboo, and cacao genetic resources and distribute them and associated information worldwide.
1a: Efficiently and effectively safeguard genetic resources.
1b: Back up genetic resource collections.
1c: Distribute pathogen-tested genetic resources.
2. Develop more effective genetic resource maintenance, evaluation, and characterization methods and apply them to priority tropical and subtropical tree fruit, bamboo, and cacao genetic resources. Disseminate evaluation and characterization data via Germplasm Resources Information Network (GRIN)-Global and other data sources.
2a: Characterize and evaluate genetic resources for important horticultural characteristics.
2b: Maintain and enhance access to characterization and evaluation data through GRIN Global, publications, and other databases (MusaNet, ICGD, Bioversity International).
2c: Develop Single nucleotide polymorphisms (SNPs) for cacao and other minor crops within the collections.
3. With other National Plant Germplasm System (NPGS) genebanks and Crop Germplasm Committees, develop, update, document, and implement best management practices and Crop Vulnerability Statements for tropical and subtropical tree fruit, bamboo, and cacao genetic resources and information management.
Approach
Plant genetic resources will be efficiently and effectively conserved, backed-up, regenerated, evaluated, and distributed free of diseases. This will be carried out by implementing latest technologies available for field, lab, and greenhouse plant labeling, by maintaining on and off-site backups of critically important germplasm, by field evaluating for important horticultural traits and by indexing/eliminating plant diseases in stock to be distributed. All information associated with plant genetic resources including passport, characterization, and evaluation data will be incorporated into the publicly available Germplasm Resources Information Network (GRIN)-Global database. Development of molecular marker tools is a collaborative effort with other USDA-ARS laboratories and will be used to genotype accessions within the cacao, Annona, sapodilla, Garcinia, sapote and other tropical fruits in the collections, which will aid in the identification of redundancies, discrepancies, and genetic gaps in the collections. In addition, the marker work will complement morphological characterization and stakeholder community input in the development of guidelines to follow for prioritization of future plant introductions. Best management practices and Crop Vulnerability Statements for tropical and subtropical tree fruit, bamboo, and cacao genetic resources and information management will be developed, updated, documented, and implemented.
Progress Report
This is the final report for the project 6090-21000-057-000D which terminated in February 2023 and was replaced by 6090-21000-061-000D. Substantial results were realized over the 5 years of the project.
Progress was made on Sub-objective 1a: Efficiently and effectively safeguard genetic resources. The following research was conducted by ARS scientists at Mayaguez, Puerto Rico: 1) As a service-oriented project the number distributions during the project’s five-year cycle amounted to 754 orders of 3640 different items with about 36,500 propagules. Propagules consisted of leaves (23,125), seeds (1594), rhizomes (183), cuttings (1275), scionwood (3248), tissue culture (191) and fruits (6884). These were made available and distributed to researchers, educators and cooperators at the local, national and international level; 2) Important introductions of Musa spp. accessions (6) were selected to be added to the germplasm collection to increase genetic diversity and to have clonal stock with improved horticultural traits for further research; 3) Most research efforts in the Musa spp. collection have focused on distributions and selection of material for field evaluation/verification. Over 290 Musa spp. accessions propagated through tissue culture and cryopreserved in liquid nitrogen (LN) were received from Bioversity International. These plants are part of a continued collaborative effort to verify the genetic integrity of banana genetic resources held at the International Transit Center banana collection in Leuven, Belgium. Many of these accessions being field verified have been grown in tissue culture and/or LN for more than ten years and over this period may have developed somaclonal variation or have propagation mistakes; 4) Several accessions resistant to Tropical race 4 (TR4), the fungal strain that causes Fusarium wilt, were requested and received from Bioversity International for evaluation of important horticultural traits. Initial evaluation of these materials will start under the new research project.
Progress was made on Sub-objective 1b: Back up genetic resource collections. The following research was conducted: 1) Fifteen mango accessions from a 75-year-old orchard in a former USDA-ARS site which was donated to the University of Puerto Rico in the 1970s and currently in danger to be lost by development, were grafted for preservation. DNA fingerprinting was carried out by an ARS collaborator in Miami, Florida and results will be available later this FY. If warranted, accessions will be added to the mango collection in Miami, Florida under the new research project; 2) A total of 22 cacao accessions from the Mayaguez field germplasm collection and found to be free of Cacao Mild Mosaic Virus (CAMMV) have been placed in tissue culture to preserve as CAMMV-free plants. These accessions represent the most commonly requested accessions. The process will continue under the new research project as we receive new results of accessions being virus free from the collaborating virologist at the University of Arizona. Concominantly, virus infected accessions are being propagated by somatic embryogenesis as an effort to clean up materials from viruses.
Progress was made on Sub-objective 1c: Distribute pathogen-tested genetic resources. The following research was conducted: 1) Resistance/susceptibility to mango anthracnose was evaluated on Mangifera indica cultivars grown in Isabela, Puerto Rico. Species of Colletotrichum were isolated from symptomatic leaves in 30 of the 40 M. indica cultivars evaluated. This is the first report of this species causing anthracnose of mango in Puerto Rico; 2) ARS scientists at Mayaguez, Puerto Rico in collaboration with a mango industry partner evaluated eight different species of mango (Mangifera casturi, M. indica, M. lalijiwa, M. laurina, M. odorata, M. zeylanica, M. sylvatica and M. rubropetala), seven M. indica cultivars (Suny, Kensingtong Pride, Irwin, Nam Doc Mai, Keitt, Totapuri, Maha Chanok) and 23 M. indica x M. casturi crosses to identify possible sources of resistance to anthracnose. Results showed that the wild mango species M. casturi, two M. indica cultivars (Suny and Keitt) and two M. indica x M. casturi crosses were tolerant to anthracnose 20 days after inoculation. Other 18 M. indica x M. casturi crosses were inoculated this fiscal year and fruit will be evaluated under the new project plan; 3) One of the most limiting factors in coffee production is coffee leaf rust (CLR) caused by the fungus Hemileia vastatrix. This fungus is highly variable, and more than 50 CLR races have been identified, making it very difficult to control with fungicides and resistant plants. ARS scientists in Mayaguez, Puerto Rico and Beltsville, Maryland, in collaboration with the University of Puerto Rico, discovered a new species of Akanthomyces fungi hyperparasitizing CLR and found that five different species of mycoparasites (Simplicillium lanosoniveum, S. lamellicola, Lecanicillium aranearum, L. uredinophilum, Akanthomyces lecanii) were able to reduce coffee leaf rust in coffee orchards in Puerto Rico. Evaluations of these mycoparasites on two different seasons (cold-dry and hot-humid) will be conducted during the new research project plan.
Progress was made on Sub-objective 2a: Characterize and evaluate genetic resources for important horticultural characteristics. The following research was conducted by ARS scientist at Mayaguez, Puerto Rico: 1) A total of 22 Sapodilla varieties were characterized and evaluated. Parameters measured were total weight, number of fruits, size, 20-fruit weight, and Brix. This was the third year of data collection and data are being organized and reviewed for input into GRIN Global; 2) A total of 30 Spanish lime varieties were characterized and evaluated. Parameters measured were total weight, number of fruits, size, weight of 20 individual fruits, Brix, and titratable acidity. A fifth and last year will be collected under the new research project and the data published and entered into GRIN-Global; 3) Approximately 78 cacao clones were characterized and evaluated for number of pods per tree, pods weight, size, color, number of beans, bean color, seed weight, fermentation photos, dry weight of beans. These data will be uploaded to GRIN-Global and the information made available to researchers and stakeholders; 4) In collaboration with ARS scientists at the Sustainable Perennial Crops Laboratory, Beltsville, Maryland, ARS scientists in Mayaguez, Puerto Rico, developed and utilized SNP’s (single nucleotide polymorphism) to fingerprint tropical fruits and coffee genetic resources; 5) In collaboration with ARS researchers in Fort Pierce, Florida, seven mandarin cultivars grafted onto three rootstocks were evaluated for yield, fruit quality traits, and citrus greening (CG) incidence. CG was found to be widespread at the lower elevation site (100% contamination) but not as serious problem at the high-elevation (above 600 meters) site. One variety was found to be highly tolerant to CG when grafted on two of the rootstocks. This experiment will be completed in 2023 and results published under the new research project; 6) A 2-year greenhouse study demonstrated no rootstock differences for dry matter production in lychee trees grown under Al stress and demonstrated that lychee is highly susceptible to acid soils; 7) A breadfruit experiment evaluating 7 breadfruit accessions grafted onto breadnut rootstock at two locations for yield, disease and insect response, canopy volume, and organoleptic quality traits, will be completed in 2023 (5th year production data collection) and results published under the new research project.
Progress was made on Sub-objective 2b: Maintain and enhance access to characterization and evaluation data through GRIN Global, publications, and other databases. The following research was conducted: 1) Final data (plant height, stem diameter, number of leaves, flowering, number of hands and fingers) were collected for 290 Musa spp. accessions in Field Verification site IV and V as part of a collaborative project with Bioversity International’s Musa International Transit Center; 2) Provided germplasm requestors with taxonomic nomenclature as well as links or QR codes leading to GRIN-Global database information; 3) Passport information for approximately 148 germplasm accessions (Cacao, Sapotaceae, Clusioideae (Garcinia), ornamentals, and palms has been entered and descriptors from characterizations as well as voucher images have been loaded into Bioversity database for and estimated 95 Musa accessions: Some examples follow:
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1909076
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1635348
https://npgsweb.ars-grin.gov/gringlobal/ImgDisplay?id=1967527
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1967527
https://npgsweb.ars-grin.gov/gringlobal/ImgDisplay?id=1778929
https://npgsweb.ars-grin.gov/gringlobal/ImgDisplay?id=1676866
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1647310
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1620591
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1656950
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1656978
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1674986
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1901397
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1901415
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1135057
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1112287
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1112287
https://npgsweb.ars-grin.gov/gringlobal/ImgDisplay?id=1679271
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1654384
https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1000900
Accomplishments
1. First report of a polerovirus infecting cacao trees. Cacao production worldwide is severely affected by diseases and pests. The exchange of germplasm across production areas is needed to introduce new sources of disease resistance. However, the detection of pathogens during the germplasm quarantine process is of paramount importance to avoid the introduction of diseases not previously present in production areas. Leaves with virus-like symptoms that consist of leaf discoloration and distortion with downward rolling at leaf edges, and light-yellow speckling or mottling were observed on cacao grafted trees of various genotypes that were undergoing quarantine. ARS scientists from Mayaguez, Puerto Rico, and Miami, Florida, collected leaf samples of symptomatic plants and shipped them to the University of Arizona for analysis. RNA sequencing was conducted, and results compared with plant virus databases. Sequencing results indicated that a Polerovirus was responsible for the observed symptoms, and it was named Cacao Leafroll Virus since it was different from other Poleroviruses that affect other crops. This is the first report of a Polerovirus in cacao and underscores the importance of the development of molecular tools for the detection of viruses before releasing the germplasm from quarantine.
2. Lychee susceptibility to acid soils. The most productive soils of the world are already under cultivation, and those available for agricultural expansion are often strongly acid, possessing toxic levels of soil aluminum and/or manganese. These elements could drastically reduce crop yields when present in the soil at high concentrations. Incorporation of lime to the soil is a common practice to ameliorate acidity but it is not very effective below the plough layer and often lime is not available to farmers with limited resources. The effect of soil acidity factors on dry matter production and leaf nutrient composition of three cultivars of lychee was assessed during a 2-year greenhouse study. High concentrations of soil aluminum (Al) resulted in a 77% reduction in total dry matter production which is indicative that this crop is highly susceptible to acid soils rich in soil Al. Future studies should be directed to the screening of a wider pool of lychee germplasm as an effort to identify Al-tolerant genotypes which could be used as commercial rootstocks in acid soils.
Review Publications
Goenaga, R.J., Marrero Soto, A.R., Perez, D.O. 2022. Growth and nutrient concentration of lychee grown on an acid ultisol. HortTechnology. 32:6. https://doi.org/10.21273/HORTTECH05120-22.
Adegbola, R.O., Keith, C.V., Gutierrez, O.A., Goenaga, R.J., Brown, J.K. 2022. A previously undescribed polerovirus (solemoviridae) infecting theobroma cacao germplasm. Plant Disease. 107(3). https://doi.org/10.1094/PDIS-06-22-1449-PDN.
Yaw, T.A., Merem, E.C., Namwamba, J.B., Annan, J.B., Ayala Silva, T., Asare-Ansah, A.B., Ning, Z., Oppong, J., Loh, P., Frimpong, D.B., Owusu, F., Mjema, J.E., Okwemba, R., Mwakimi, O.S., Petja, B.M., Akinrinwoye, C.O., Mcclendon-Peralta, J., Mosby, H.J. 2021. Land resource areas and spatial analysis of potential location of bioenergy crops production in Mississippi. Journal of Sustainable Bioenergy Systems (JSBS). 11:187-214. https://doi.org/10.4236/jsbs.2021.114013.
