Location: Subtropical Horticulture Research
2019 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 National Germplasm Repository 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 2019 amounted to 137. Over 3000 different accessions with 10,600 propagules (i.e., seeds, budwood, rhizomes, corms) were distributed to 34 states in the U.S and 8 international organizations.
To manage and curate our collections, ARS researchers 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 researchers 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 for the Subtropical Horticulture Research Station (SHRS) that includes plant phenotypic and genotypic data, standard operating procedures, best practices, and a record of field maintenance, mowing and pesticide and herbicide application. We have added phenotypic data and protocols and procedures for at least 20 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 researchers in Miami, Florida, have genotyped most of the available world mango and avocado germplasm collections to validate identification and determine pedigree and relatedness. 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. We 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. Rescue and recovery of mango germplasm after hurricane Irma. One of the main objectives of a germplasm collection is to preserve and foster biodiversity by maintaining multiple cultivars and genotypes of important species such as mango, thus providing a genetic reservoir for farmers and breeders. Many mango trees at the Subtropical Horticulture Research Station (SHRS) in Miami, Florida, were downed by hurricane Irma, including rare and historic cultivars that may not be found anywhere else. Over 65 mango trees, some over a century old and 50 feet tall, were successfully re-erected by ARS researchers in Miami, Florida, and the few that could not be saved were grafted. All trees re-erected are healthy with new growth, many with fruit. Through germplasm exchange lost germplasm has been recovered, and new mango cultivars are being added to the collection at the SHRS. The augmented biodiversity of the mango germplasm collection at SHRS will continue to provide ample genotypes for clients and researchers.
2. Development of a novel visual method to analyze genotype data. Traditional tree breeding programs face the challenges of long generation times and significant expense in land and personnel resources. Genotyping of progeny at the seedling stage can increase the efficiency and decrease the costs of selection of improved cultivars. Assessing the genetic diversity and relatedness of germplasm is essential for identifying genetically distant parents with favorable agronomic traits to produce hybrid populations enabling selection of improved cultivars. Genotype analysis can also validate cultivar identity and infer parental candidates. ARS researchers in Miami, Florida, have developed a simple visual method using single nucleotide polymorphism (SNP) genotype data from both mango and avocado germplasm and hybrids with an affinity propagation analysis to define related groups of individuals. This method can distinguish a single cultivar of interest from all other cultivars in the dataset enabling the accurate identification of important commercial cultivars, and to identify self-pollinated individuals and infer likely candidates for the paternal parent. Identification of self-pollinated individuals is particularly important as self-pollinated progeny are likely to uncover deleterious recessive alleles. With this method breeders can determine the genetic diversity of their breeding stock at the seedling stage to optimize breeding and selection programs and increase the efficiency of genetic improvement.
Review Publications
Kuhn, D.N., Freeman, B.L., Greering, A., Chambers, A. 2019. A highly sensitive method to detect Avocado Sunblotch viroid (ASBVd) in avocado trees for maintenance of viroid-free avocado germplasm collections. Viruses. 11(6):512. https://doi.org/10.3390/v11060512.
Rendon-Anaya, M., Ibarra-Laclette, E., Mendez-Bravo, A., Lan, T., Zheng, C., Carretero-Paulet, L., Perez-Torres, C., Chacon-Lopez, A., Hernandez-Guzman, G., Chang, T., Farre, K.M., Barbazuk, W., Chamala, S., Mutwil, M., Shivhare, D., Mitter, N., Hayward, A., Fletcher, S., Rozas, J., Sanchez-Gracia, A., Kuhn, D.N., Barrientos-Priego, A.F., Salojarvi, J., Librado, P., Sankoff, D., Herrera-Estrella, A., Albert, V.A., Herrera-Estrella, L. 2019. The avocado genome enlightens deep angiosperm phylogeny and reveals pathogen-influenced gene space. Proceedings of the National Academy of Sciences. https://doi.org/10.1101/654285.
Rubenstein, M., Eched, R., Rozen, A., Zvian, T., Ophir, R., Kuhn, D.N., Sherman, A. 2019. Genetic diversity of avocado (Persea Americana Mill.) germplasm using pooled sequences for SNP discovery. Scientific Reports. 20:379. https://doi.org/10.1186/s12864-019-5672-7.
Kuhn, D.N., Warschefsky, E., Groh, A.M., Rahaman, J., Freeman, B.L., Bally, I., Dillon, N., Innes, D., Chambers, A. 2019. Estimation of genetic diversity and relatedness in a mango germplasm collection using SNP markers and a simplified visual analysis method. Scientia Horticulturae. 252:156-168. https://doi.org/10.1016/j.scienta.2019.03.037.
Kuhn, D.N., Livingstone III, D.S., Richards, J.H., Manosalva, P., Van Den Berg, N., Chambers, A. 2019. Application of genomic tools avocado (Persea americana) breeding: SNP discovery for genotyping and germplasm characterization. Scientia Horticulturae. 246:1-11. https://doi.org/10.1016/j.scienta.2018.10.011.
