Location: Subtropical Horticulture Research
2022 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, FL maintains more than more than 2100 genetically diverse tropical fruits, and sugarcane and related grasses germplasm collected from different climatic conditions from around the world. These precious resources are expected to contain 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, FL perform several major critical functions: acquisition, maintenance, characterization, distribution and research of germplasm. As a service-oriented project, over 135 different accessions with 785 propagules (i.e., seeds, budwood, rhizomes, corms) were distributed to 11 different states in the U.S and 3 international organizations. To manage and curate our collections, ARS scientists in Miami, FL maintain and regenerate important cultivars and clones. Major irrigation repairs have been completed. Germplasms have been maintained using appropriate fertilization, trimming and pruning, mowing, pesticide application, ground covers, and manual plot cleanouts. ARS scientists in Miami, FL have been vegetatively regenerating some of our important collections (mango, avocado, sugarcane) and sending backups to other ARS clonal repositories in Mayaguez, Puerto Rico and Hilo, Hawaii.
The ARS Miami germplasm resource maintains one of the world’s largest collections of sugarcane and related grasses from around the world under field conditions. These collections provide a rich source of genes for meeting current agronomic needs and for coping with the changing climatic conditions. Maintenance, genetic characterization and establishment of a manageable core collection are critical for meeting these needs. To establish a core collection, it is critical that the genetic diversity of these accessions is determined using latest DNA marker technologies. To genetically characterize and establish a core collection of sugarcane and its wild relatives that will cover most of the genetic diversity, ARS scientists in Miami, FL in collaboration with ARS scientists in Bethesda, Maryland, first screened a list of 1200 DNA markers. These markers were analyzed using computer programs and the list was narrowed down to a set of 400 DNA markers. Initial genetic analyses of these DNA markers of 1,400 individual plants have identified individuals that are identical to each other, which after additional in-depth analyses will facilitate establishing a core collection that carries most genetic diversity and is manageable for maintenance in the field as well as off-site at alternate locations. This core collection will also provide a useful and manageable resource for conducting genetic and genomic studies to identify genes for desirable agronomic traits as well as for climate adaptation. In addition, these analytical procedures consisting of molecular markers will facilitate establishing a manageable collection of sugarcanes in tissue culture. These molecular markers may be used by other sugarcane germplasm repositories around the world for cultivar identification, which will assist USDA scientists and private breeders in acquiring only unique sugarcane germplasm that is different from the currently available germplasm at USDA ARS, Miami, FL.
One of the major goals of a germplasm repository is acquisition of genetically diverse germplasm. In order to increase genetic diversity of sugarcanes at the repository at Miami, FL, ARS scientists in Miami, FL have initiated collaborations with researchers at the University of Hawaii. Under this collaboration, we have genotyped 96 sugarcane accessions, maintained at Hawaii, with 400 DNA markers. Analyses are in progress, which will inform on the genetic diversity of these accessions and their potential acquisition and addition to the sugarcane collection at Miami, FL. Wild relatives of mangos are mostly confined to Southeast Asia and are not easily accessible for acquisition. Many of these wild relatives of mango are considered endangered or vulnerable due to loss to climate change and other factors. These wild relatives are potential sources of useful genes for improving disease resistance, nutritional values and other horticultural traits of cultivated mangoes. Two new species of mangos, Mangifera altissima (commonly known as Paho) and Mangifera rubropetela (commonly known as Red Petaled Mango) were donated by private donors to the USDA National Germplasm Repository at Miami, FL. These new additions will be genotyped and evaluated, and eventually made available to researchers for development of new climate-resilient mango varieties and for studying horticultural and nutritional traits.
Avocado Sun Blotch Viroid (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, FL 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. 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 were tested again to ensure a disease-free shipment. This assay was used to ensure that newly grafted avocado germplasm is also free from this viroid. Applying these assays ensures that the avocado germplasm is maintained free from this viroid.
Establishing open-pollinated populations of avocado for enhancing genetic diversity: The avocado collection at USDA-ARS, Miami, FL is represented by three major botanical types that have originated from Mexico, West Indies and Guatemala. To utilize these accessions for generating novel genetic material and for genetic and genomics studies, ARS scientists in Miami, FL have initiated establishing breeding populations that will be characterized in the future for horticultural characteristics. So far, we have accomplished establishing over a dozen populations, which are being maintained in pots. The establishment and availability of these populations will facilitate genetic and horticultural studies of avocados, which will be useful for improving avocado cultivars for adaptation to extreme environmental conditions, and resistance to diseases and pests.
Accomplishments
