Location: Subtropical Horticulture Research
2020 Annual Report
Objectives
1. Efficiently and effectively acquire and maintain the safety, genetic integrity, health and viability of priority sugarcane, mango, avocado, and other subtropical and tropical genetic resources, and distribute them and associated information worldwide.
1A. Maintain and improve the physical infrastructure and field usage of the SHRS station.
1B. Maintain, regenerate, back up, and distribute the plant germplasm collections.
2. Develop more effective genetic resource maintenance, evaluation, or characterization methods and apply them to priority sugarcane, mango, avocado, and other subtropical and tropical genetic resources. Record and disseminate evaluation and characterization data via GRIN-Global and other data sources.
2A. Develop a GIS map of all germplasm and research accessions at
SHRS.
2B. Develop a local database that is GRIN-Global compatible to accommodate old and new phenotypic, genetic and genomic data for germplasm accessions and Best Management Practices.
3. With other NPGS genebanks and Crop Germplasm Committees, develop, update, document, and implement best management practices and Crop Vulnerability Statements for sugarcane, mango, avocado, and other subtropical and tropical genetic resource and information management.
3A. Develop with other NPGS stations a set of standard descriptors for germplasm evaluation to standardize phenotypic data in the GRIN-Global database and written standard protocols for the collection of such phenotypic data.
3B. Develop and update Crop Vulnerability Statements for the major germplasm collections.
4. In collaboration with clients and stakeholders, investigate the genetic bases and control of key horticultural traits for mango and avocado, and develop genetic markers and other methods to improve the efficiency of breeding those crops.
4A. Identify associations of important horticultural traits with genetic markers for avocado and mango.
4B. Apply currently available genetic markers to further breeding improvement for our clients and stakeholders for avocado and mango.
Approach
The lead scientist/curator will plan, schedule and direct the improvement of the physical infrastructure of the station by training personnel and repairing, maintaining and upgrading farm equipment and irrigation. In addition, the lead scientist/curator will develop a schedule to efficiently and effectively maintain, regenerate, back up and distribute the plant germplasm collections using Best Management Practices. A GIS map and associated local database will be created to house phenotypic and genotypic data on the major collections (sugarcane, avocado and mango) as well as minor collections when phenotypic data becomes available. The local database will be in the same format as GRIN-Global and will facilitate upload of the phenotypic data into GRIN-Global. Accurate and up-to-date information on all germplasm collections in the local database will allow more rapid identification of requested material on the SHRS 200 acre research facility and improve the speed and accuracy of distribution. In coordination with other NPGS stations and Crop Germplasm Committees, the lead scientist/curator will produce standardized phenotypic descriptors to improve accessibility of phenotypic data for SHRS germplasm collections in GRIN-Global and produce Crop Vulnerability Statements for the major collections to identify areas of greatest concern for successful maintenance. Genetic and genomic data will be applied to identify core collections that encompass the available genetic diversity in the larger collection to make backing up of collections more efficient. Finally, in coordination with collaborators and stakeholders, use all available genetic and genomic data to associate molecular genetic markers with useful horticultural traits to improve breeding of avocado and mango.
Progress Report
Production of many tropical fruit crops and sugarcane is based on a few commercial cultivars and thus genetic vulnerability is potentially a problem. This reliance on select genotypes (e.g. the ‘Hass’ avocado which makes up more than 90% of US production), which are often closely related, has developed because of consumer demands for quality products, limited consumer knowledge of the crop, and the difficulties associated with breeding long-lived crops. Collections maintained by the ARS in Miami, Florida, are currently a major genetic reservoir in the Western Hemisphere for ameliorating potential problems caused by genetic uniformity in farmers' fields. As a service oriented project, the number of germplasm distributions for FY 2020 amounted to 112. Over 528 different accessions with 8,469 propagules (i.e., seeds, budwood, rhizomes, corms) were distributed to 23 states in the U.S and 6 international organizations. To manage and curate our collections, ARS scientists in Miami, Florida, must maintain the physical plants and regenerate important cultivars and clones. We have been maintaining fields with irrigation repair, fertilization, trimming and pruning, mowing, pesticide application, and manual plot cleanouts. ARS scientists in Miami, Florida, are regenerating some of our important collections (mango, avocado, sugarcane) with vegetative cloning and sending backups to other ARS clonal repositories in Mayaguez, Puerto Rico, and Hilo, Hawaii. Updates and data entry to our local database and geographical information system (GIS) map of all germplasm and experimental collections on the station continues. The database is a standalone repository of information that includes plant phenotypic and genotypic data, standard operating procedures, best practices, and a record of field maintenance, mowing and pesticide and herbicide application. ARS scientists, at Miami, Florida, have added phenotypic data, images, and protocols and procedures for at least 24 different species, as well as genetic data for mango and avocado. The phenotypic data has then been incorporated into our Germplasm Resources Information System (GRIN) - Global information for clients. The local database has been designed to be congruent with the GRIN-Global database architecture, allowing upload of phenotypic data and images for the germplasm collections. One outcome from the maintenance of both our germplasm collection and the database information has been multiple collaborations with University of Florida scientists on phenotypic and genetic research projects involving our germplasm and experimental collections.
ARS scientists in Miami, Florida, have genotyped most of the available world mango and avocado germplasm collections to validate identification and determine pedigree and relatedness. Current and new collaborators continue to add samples and new cultivars. This data has enabled the identification of mislabeled individuals in our collection as well as in the collections of collaborators, preventing the distribution of incorrect material. ARS scientists, at Miami, Florida, have also determined the parentage of important hybrid selections. Genetic data from these analyses have provided collaborators with important information about their breeding programs, such as determining self-pollinated progeny and parental candidates, which increases the efficiency of selection at the seedling stage and dramatically lowers the field costs of raising the plants to maturity by only planting seedlings that may represent improved cultivars.
Accomplishments
1. Application of ASBVd detection assay. Avocado Sun Blotch Viriod (ASBVd) is a highly contagious RNA viroid that affects avocado trees. Phenotypic expression on the trees includes bleached craters on the fruit, bleached variegation on the leaves, loss of yield and death. This viroid can cross contaminate trees easily through cutting and pruning, root grafting, and pollen. ARS researchers in Miami, Florida, have developed and published a highly sensitive detection assay to test for ASBVd. All avocado trees at the SHRS were previously tested and infected trees were removed. ARS scientists, at Miami, Florida, are in the process of re-testing all avocado fields to ensure the collection is still free of the viroid. Avocado trees from the ARS Laboratory in Ft. Pierce, Florida, have also been assayed to determine that the Ft. Pierce, Florida, avocado collection is free of the virus, allowing research and distribution of material.
2. Creation of crop descriptors in GRIN-Global. Crop descriptors for mamey sapote, avocado, mango, jaboticaba, sapodilla, tamarind, white sapote, custard apple, litchi, jackfruit, canistel, and carambola were developed by ARS scientists at Miami, Florida. With the creation of these crop descriptors, phenotypic data can be uploaded to the crops for the first time ever. Phenotypic data stored in the local database has been uploaded accordingly onto GRIN for these crops as well.
Review Publications
Kuhn, D.N., Groh, A.M., Rahaman, J., Freeman, B.L., Arpaia, M., Van Den Berg, N., Abeysecara, N., Manosalva, P., Chambers, A.H. 2019. Creation of an avocado unambiguous genotype SNP database for germplasm curation and as an aid to breeders. Tree Genetics and Genomes. 15: 71. https://doi.org/10.1007/s11295-019-1374-1.
Ashworth, V., Chen, H., Calderon-Vazquez, C.L., Arpaia, M.L., Kuhn, D.N., Durbin, M.L., Tommasini, L., Deyett, E., Jia, Z., Clegg, M.T., Rolshausen, P.E. 2019. Quantitative trait locus analysis in avocado: The challenge of a slow-maturing horticultural tree crop. Journal of the American Society for Horticultural Science. 144(5):352–362. https://doi.org/10.21273/JASHS04729-19.
Dautt-Castro, M., Lopez-Virgen, A.G., Ochoa-Leyva, A., Contreras-Vergara, C.A., Sortillon-Sortillon, A.P., Martinez-Tellez, M.A., Gonzalez-Aguilar, G.A., Casas-Flores, S., Sañudo-Barajas, A., Kuhn, D.N., Islas-Osuna, M.A. 2018. Genome-wide identification of mango (Mangifera indica L.) polygalacturonases: Expression analysis of family members and total enzyme activity during fruit ripening. Frontiers in Plant Science. 10: 969. https://doi.org/10.3389/fpls.2019.00969.
