Location: Subtropical Horticulture Research
2021 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
Tropical fruits and sugarcane are important sources of our daily calorie intake and essential vitamins, minerals, and numerous health-promoting compounds that are effective against cancers, diabetes, and infectious diseases. Additionally, these crops are a source of income for millions of people in the USA and around the world. Currently, only a few commercial varieties of these crops with limited genetic diversity are grown in farmers` fields, which make them prone to diseases and environmental stresses. The National Germplasm Repository of USDA ARS in Miami, Florida, maintains more than more than 2100 genetically diverse tropical fruits and sugarcane germplasm collected from different climatic conditions from around the world, which contain distinct genes for solving problems caused by lack of genetic diversity. To serve researchers who deal with improving productivity, nutritional value and environmental resilience of these crops, ARS scientists in Miami, Florida, in this repository perform four major critical functions: acquisition, maintenance, characterization and distribution of germplasm. As a service-oriented project, over 241 different accessions with 3,967 propagules (i.e., seeds, budwood, rhizomes, corms) were distributed to 12 different states in the U.S and 5 international organizations. To manage and curate our collections, ARS scientists maintain and regenerate important cultivars and clones. ARS scientists 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. To genetically characterize and establish a core collection of sugarcane and its wild relatives representing most of the genetic diversity, ARS scientists in Miami, Florida, have established collaborations with ARS scientists in Beltsville, Maryland. A set of 182 sugarcane accessions have been sampled, which are currently being genotyped using DNA markers.
In FY2021, phenotypic data was collected on 17 species, two of which had no previous data in the database. The phenotypic data have then been incorporated into our Germplasm Resources Information System (GRIN) – Global for clients. One outcome from the improvement and maintenance of our germplasm collection has been the establishment of multiple collaborations with external customers on phenotypic and genetic research projects involving our germplasm and experimental collections. Using latest technologies, ARS scientists 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. These data have 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 have also determined the parentage of important hybrid selections. Genetic data from these analyses have provided stakeholders 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 were previously tested and infected trees were removed. All avocado fields at the SHRS have recently been re-tested to ensure the collection is still free of the viroid. In addition, SHRS avocado trees chosen for distribution to Honduras and Puerto Rico were tested again to ensure a disease-free shipment. Avocado trees needed for a collaborative rootstock research project from the UF/IFAS Tropical Research and Education Center (TREC) in Homestead, Florida, have been assayed to determine that trees are free of the virus before shipment to California.
2. Creation of crop descriptors in GRIN-Global. An important role of the germplasm repository is the collection and dissemination of information about Crop descriptors, which is critical information for stakeholders when they select and order different kinds of germplasm. Crop descriptors of 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 GRIN-Global for the first time ever. Phenotypic data stored in the local database have been uploaded accordingly to GRIN-Global for all these crops as well.
3. Genotyping of world collection of sugarcane and related grasses (WCSRG). The ARS Miami, Florida, germplasm repository maintains one of the world largest collection of sugarcane and related grasses from around the world under field conditions. These collections provide a rich source of genes for tolerance against biotic/abitotic stresses. Maintenance, genetic characterization and establishment of a manageable core collection are critical for finding tolerance. To establish a core collection of sugarcanes, it is critical that the genetic diversity of these accessions is determined using the latest DNA marker technologies. Towards this long-term goal, we have analyzed a set of 2000 SNP molecular markers, which are evenly distributed across the sugarcane genome. Selection, designing and bioinformatics of these markers have been accomplished. In collaboration with ARS scientists in Beltsville, Maryland, ARS scientists in Miami, Florida, are currently analyzing the suitability of these SNP markers for the genetic characterization of a diverse sample of sugarcane core collection. This work has laid a solid foundation for enhancing phenotypic and genetic characterization and safeguarding genetic diversity of sugarcanes. More importantly, this work will assist breeders in selecting parents for developing elite cultivars and will assist geneticists in associating genes with important crop traits such as diseases and pests. All these outcomes will be useful in predicting and optimizing outcomes of genetic crosses.
