Location: Subtropical Horticulture Research
2018 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 U.S. 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 at 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.
ARS has developed molecular tools for avocado and mango and are applying them to assess the genetic diversity in our germplasm collections and other germplasm collections in the U.S., Australia, Brazil, Senegal, South Africa and Thailand. We have produced high resolution genetic maps for avocado and mango and are applying them to associate important horticultural traits to these maps such as flower type in avocado and polyembryony in mango. Because it takes so long to grow a tree to maturity to test for important horticultural traits, finding molecular markers associated with such traits can accelerate tree breeding, increase the efficiency of selection at the seedling stage and dramatically lower the field costs of raising the plants to maturity by only planting seedlings that may represent improved cultivars.
To manage and curate our collections, ARS has been up-to-date with all the changes to the Germplasm Repository Information Network (GRIN), now GRIN Global system. In addition, we have developed a local database and Geographical Information System (GIS) map of all germplasm collections on the station. We are using this database to improve efficiency of curation and distribution, to create an accurate inventory of all germplasm collections, and to provide a secure transfer of knowledge to incoming staff. 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. An Android app for tablets to allow access to genotypic and phenotypic in the field through quick response code (QR code) labels on the trees has been implemented for the local database. 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. GRIN Global is not yet able to accept genotypic data, so our local database supplies a safe repository for the substantial amount of genetic and genomic data we have and continue to generate.
Accomplishments
