Location: Tropical Crops and Germplasm Research
2022 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
Progress was made on Sub-objective 1a: Efficiently and effectively safeguard genetic resources. The following research was conducted by ARS scientist at Mayaguez, Puerto Rico: 1) As a service-oriented project the number of germplasm distributions for FY 2022 amounted to 87 distributions with nearly 2000 accessions and 11500 propagules. Tropical germplasm was distributed in the form of budwood (1000), leaves (8000), rhizomes (100) and fruits (2400) were made available and distributed to researchers, educators and cooperators at the local, national and international level; 2) Important introductions of Musa spp. accessions (4) were selected to be added to the collection to increase genetic diversity and to provide 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 evaluations. Over 80 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 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.
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 will be done by scientists in ARS Miami, Florida and if warranted, accessions will be added to the mango collection in Miami, Florida; 2) A total of 12 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 as we receive new results of accessions being virus free from the collaborating virologist at the University of Arizona.
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. Results showed that a species of Colletotrichum caused anthracnose symptoms on 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. These findings are important because resistance cultivars can be used in mango plant breeding programs for resistance to anthracnose; 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, Kensintong 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 after 20 days after inoculation. These findings are important because crosses of these species/cultivars can be used in mango plant breeding programs for resistance to anthracnose; 3)Coffee is grown in more than 50 countries around the world including Hawaii and Puerto Rico in the U.S. One of the most limiting factors in coffee production is coffee leaf rust (CLR) caused by fungus Hemileia vastatrix. In severe infections, this fungus can defoliate coffee plants reducing quantity and quality of fruit. This fungus is highly variable, and more than 50 coffee leaf rust 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. These findings are important because these species can be potentially used in biological control programs against coffee leaf rust and represent a potential solution to control this disease, particularly for specialty organic coffee production.
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; 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. This was the fourth year of data collection. Data are being organized and reviewed for statistical analysis; 3) Approximately 35 cacao varieties 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. This was the second year of data collection. 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, 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, certified disease-free budwood pieces of seven mandarin cultivars were grafted onto three rootstocks and evaluated for yield, fruit quality traits, and citrus greening incidence. As of FY 2022, determination of citrus greening incidence using enzyme-linked immunosorbent assay (ELISA) tests are confirming that the disease is widespread at the lower elevation site (100% contamination) but not a serious problem at the high-elevation (above 600 meters) site. However, symptoms of citrus greening are starting to appear at this location. During FY2023, polymerase chain reaction (PCR) tests will be conducted on high elevation trees; 6) A 2-year greenhouse study was conducted to determine the effects of various levels of soil Al on dry matter production, plant growth, and nutrient concentration in shoots of three cultivars of lychee. Data is being statistically analyzed for publication of results; 7) Seven breadfruit accessions grafted onto breadnut rootstock were established in a replicated experiment at two locations in August 2015 for evaluation of yield, disease and insect response, canopy volume, and organoleptic quality traits. These accessions have never been evaluated in a replicated experiment. Trees at both locations are fully recovered from damages (defoliation) caused by Hurricane Maria and the 4th year of data was collected in FY2022.
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 30 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 to germplasm requestors with taxonomic nomenclature as well as links or QR codes leading to GRIN-Global database information; 3) Passport information for Tabebuia spp, Syszygium jambos, Poitea punicia, Citrus macrophylla and Sthalia monosperma has been entered and descriptors from characterizations as well as voucher images have been loaded into Bioversity databases for and estimated 30 Musa accessions; 4) A database in Access format was developed for field collection of cacao characterization data.
The genetic resources evaluated by this project under this subobjective are critical for diversifying horticultural production systems. Results from these experiments help to fill the knowledge gaps on cropping management systems for tropical/subtropical fruit crops by assisting to identify promising germplasm for use by growers.
Accomplishments
1. Discovery of new causal agents causing cacao pod rot. Cacao pod rot is a devastating disease worldwide. Infected pods turn black and necrotic causing yield losses of up to 30%. From July 2020 to August 2021, cacao pod rot disease was observed by ARS scientist in Mayaguez, Puerto Rico, in 142 of the 196 accessions (73.9% disease incidence) at the USDA-ARS cacao germplasm collection in Mayaguez, Puerto Rico. This disease was observed at different stages of pod development (small, green, mature, and dry mummified large pods). Four isolates of the fungi Diaporthe tulliensis (Dt) and three isolates of Diaporthe pseudomangiferae (Dp) were identified using taxonomic keys and sequencing of three nuclear genes. Cacao pods were inoculated with Dt and Dp on five healthy detached green, yellow and red pods of the following varieties: TARS27, ICS16, ICS1, GS29, UF601, SIAL56, Amelonado, SIAL98, EET94, ICS129 and GNV58. Eight days after inoculation (DAI) with Dt and Dp, all cacao pods turned dark brown, and 14 DAI white mycelia of Dt and Dp were observed on cacao pods. Untreated controls had no symptoms of pod rot, and no fungi were isolated from tissue. To our knowledge, this is the first report of Dt and Dp causing cacao pod rot. Cacao pod rot disease is caused by a complex of pathogens where Dp and Dt are now included. Knowing the identity and incidence of these new cacao pathogens is the first step for developing specific control measures and potential sources for resistance to cacao pod rot caused by Diaporthe spp.
2. Lasiodiplodia mahajangana as a new pathogen of mango. Mango originated in the the Indo-Burmese region, from where it rapidly expanded worldwide. Since 1948, Puerto Rico, initiated a mango breeding and production program and currently produces considerable quantities of fruit, primarily for exportation to the U.S. mainland and Europe. Dieback caused by fungi in the Botryosphaeriaceae family is an important disease affecting mango production. During 2019 and 2020, symptoms of dieback (progressive death of twigs and branches) were observed by ARS scientists in Mayaguez, Puerto Rico on mango trees of cultivar Keitt planted in the mango germplasm collection of the Agricultural Experiment Station of the University of Puerto Rico located at Juana Díaz, Puerto Rico. Sections of diseased tissue were disinfested and plated on petri dishes containing potato dextrose agar (PDA), a common medium to grow fungi. One representative isolate was selected and identified as Lasidioplodia Mahajangana (Lm) using morphological parameters such as color of colonies, size and shape of the conidia and DNA sequencing of four genes commonly used to identify fungi. Pathogenicity tests were conducted on 6-month-old mango trees of cultivar Keitt. Four healthy seedlings were inoculated on branches with 5 mm fungal disks of Lm grown on PDA. Controls were inoculated with PDA disks only. Twelve days after inoculations, Lm isolates caused stem necrosis and canker, with lesions sizes ranging from 2 to 17 mm2. Untreated controls showed no symptoms of canker and Lm was reisolated from diseased tissue. Lm has been reported causing stem-end rot of mango in Malaysia. Knowing Lm as a new pathogen that causes canker of mango is important to establish an adequate and effective control management of this disease in mango producing countries worldwide.
Review Publications
Puig, A.S., Irish, B.M., Ayala Silva, T., Wurzel, S.B., Gutierrez, O.A. 2022. Effect of cacao black pod rot screening method on disease resistance determination. Chemistry Proceedings. 10(1):71. https://doi.org/10.3390/IOCAG2022-12215.
Zheng, J., Meinhardt, L.W., Goenaga, R.J., Matsumoto Brower, T.K., Zhang, D., Yin, Y. 2022. The chromosome-level rambutan genome reveals a significant role of segmental duplication in the expansion of resistance genes. Horticulture Research. 9:uhac014. https://doi.org/10.1093/hr/uhac014.
Hale, A.L., Todd, J.R., Gravois, K.A., Mollov, D.S., Malapi-Wight, M., Momotaz, A., Laborde, C., Goenaga, R.J., Solis, A., Waguespack, H. 2021. Sugarcane breeding programs in the USA. Sugar Tech. 24(1):97-111. https://doi.org/10.1007/s12355-021-01018-x.
Osuna-Garcia, J.A., Olivares-Figueroa, J.D., Toivonen, P.M., Perez-Barraza, H., Goenaga, R.J., Graciano-Cristobal, M.J. 2021. Novel nondestructive technique to determine optimum harvesting stage of ‘Ataúlfo’ mango fruit. Advances in Agriculture. 12:2349-0837. https://doi.org/10.24297/jaa.v12i.9069.
Goenaga, R.J., Irish, B.M., Marrero Soto, A.R. 2021. Yield and fruit quality traits of two banana cultivars grown at two locations in Puerto Rico under black leaf streak disease pressure. HortTechnology. 31(6):838-845. https://doi.org/10.21273/HORTTECH04914-21.
Quimbita-Reyes, A., Rivera-Vargas, L., Cabrera-Asencio, I., Serrato Diaz, L.M. 2022. First report of lasiodiplodia mahajangana causing canker of mango (mangifera indica) in Puerto Rico. Plant Disease. https://doi.org/10.1094/PDIS-01-22-0149-PDN.
Serrato Diaz, L.M., Ayala Silva, T., Goenaga, R.J. 2022. First report of Diaporthe tulliensis and D. pseudomangiferae causing cacao pod rot. Plant Disease. https://doi.org/10.1094/PDIS-12-21-2634-PDN.
