Location: Subtropical Horticulture Research
2023 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
This is the final annual report for the project 6038-21000-024-000D, which ended in March 2023 and is replaced by 6038-21000-026-000D. A five-year summary of the life of the project 6038-21000-024-000D is provided below. Tropical fruits and sugarcanes 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 2100 genetically diverse tropical fruits, and sugarcane and related grasses germplasm collected from different climatic conditions around the world. These precious resources are expected to contain genes for improving horticultural and agronomic traits and for solving issues caused by diseases, pests and adverse climate change factors. To serve researchers who deal with improving productivity, nutritional value and environmental resilience of these crops, ARS scientists in Miami, Florida perform several major critical functions focused on the acquisition, maintenance, characterization, distribution and research of germplasm. As a service-oriented project, over 240 orders for the germplasm of mangoes, avocadoes, sugarcanes, Tripsacum, Miscanthus, and several other minor tropical and subtropical fruit crops were processed and distributed through GRIN-Global. Overall, 11,229 items representing propagules (i.e., seeds, canes, budwood, rhizomes, corms, leaves, flowers, and fruits) were distributed to 30 different states in the U.S and international organizations in 9 different countries. An important role of germplasm repository is the collection and dissemination of information about crop descriptors, which is critical for stakeholders to select and order different kinds of germplasm through GRIN-Global. Crop descriptors for avocado, canistel, carambola, custard apple, jaboticaba, jackfruit, litchi, mamey-sapote, mango, sapodilla, tamarind, and white sapote were developed and created in GRIN-Global. With the creation of these crop descriptors, phenotypic data have been uploaded to GRIN-Global, and updating plant passport information and images, plant phenotypic and genotypic data, standard operating procedures, best practices, and a record of field maintenance, mowing and pesticide and herbicide application continues. Descriptor definitions as well as data collection protocols and manuals have also been added to the GRIN for these crops to facilitate the standardization of phenotypic data. Standard phenotypic data collection protocols have been written for all 29 species used for data collection at SHRS, some after consultation with other NPGS stations that share the same or similar crops. Descriptors and supporting information along with phenotypic data for more crops continue to be added as they are developed.
Fourteen new mango accessions were added to the Subtropical Horticulture Research Station (SHRS) germplasm collection from the private collection. Crop Wild Relatives are an important source of useful genes for climate adaptation, disease resistance and horticultural traits and as such are increasingly getting more attention to be preserved and safeguarded from irreparable loss. Two crop wild relatives of mangos, Mangifera altissima (commonly known as Paho) and Mangifera rubropetela (commonly known as Red Petaled Mango), were obtained from private donors and were sequenced, which revealed their genetic diversity and relationship with cultivated cultivars.
Fields and germplasm collections at SHRS have been maintained using efficient agronomic and horticultural methods and construction of new nurseries. Critical repairs and improvements to the irrigation systems, fertilization, trimming and pruning, mowing, pesticide application, ground covers, and manual plot cleanouts have been routinely performed. Many trees at SHRS including rare and historic cultivars that may not be found anywhere else were saved after hurricane Irma. In addition to many avocados and other species, over 65 mango trees, some over a century old and 50 feet tall, were successfully re-erected and the few that could not be saved were grafted. All trees re-erected are healthy with new growth and mostly with fruit. The sugarcane collection was cleaned, and a major portion rotated to a new field. Most Fruit collections have been tagged with metallic durable tags with QR codes for access to GRIN-global and a local database. A local database and GIS map of all germplasm and experimental collections on the station has been developed with web interface. Detection and control of diseases and pests including exotic diseases is important for maintaining health of the germplasm. Avocado Sun Blotch Viriod (ASBVd) is a highly contagious RNA viroid that affects avocado trees. ARS researchers in Miami, Florida have developed a highly sensitive detection for ASBVd, which was used in testing all avocado germplasm at SHRS. 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. Similarly, prophylactic fungicides were applied for protecting avocado trees from the laurel wilt, a devastating avocado disease. ARS scientists in Miami, Florida 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. Although the COVID-19 pandemic slowed and at some points halted the progress of germplasm backup, close to 70% of the avocado germplasm collection is backed up in Hilo, Hawaii at PBARC. A portion of the avocado collection has been grafted and the rest are being grafted.
On the genomics and genetic characterization front, genome of a commercially important mango cultivar ‘Tommy Atkins’ was sequenced and published. In addition, the genomes of 267 mango cultivars that are maintained at National Germplasm Repository of USDA ARS in Miami, Florida were also sequenced, which led to genome-wide identification of genetic differences among these mango cultivars. Assessing the genetic diversity and relatedness of germplasm is essential for identifying genetically distant parents with favorable agronomic traits to produce hybrid population enabling selection of improved cultivars. Genotype analysis can also validate cultivar identity and infer parental candidates. ARS researchers in Miami, Florida have developed molecular genotyping methods for mango, avocado and the sugarcane germplasm. Avocado and mango germplasm collections and research populations at SHRS were genotyped along with most of the available world mango and avocado germplasm collections to validate identification, determine pedigree and relatedness, and estimate genetic diversity in the collections. 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. The ARS Miami germplasm repository maintains the World Collection of Sugarcanes and Related Grasses, which has been utilized in breeding and research projects throughout the world. This collection was genotyped with molecular markers, genetically characterized and was rotated to a new field for rejuvenation. In addition to curating the main germplasm, SYs at SHRS have characterized mapping and research populations of avocadoes and mangoes populations. Over thirty avocado selections were made from a population that resulted from a cross of cultivar ‘Hass’ and ‘Bacon’. These selections have been established in the field at SHRS. Similarly, mango research populations were evaluated and genotyped. A seedling from polycross of mango cultivar ‘Nam Doc Mai’ with potentially desirable fruit qualities has been selected and established at SHRS for long-term evaluations. To take advantage of available fruit trees, a majority of which date back to early 1900s, 12 open-pollinated populations of avocadoes have been generated for closing genetic gaps and for generating novel genetic combinations of different ecotypes of avocadoes.
Scientists at SHRS have collaborated with national and international researchers in genotyping various accessions of mangoes, avocadoes and sugarcanes and related grasses, which has led to elucidating genetic diversity of these crops on a global scale. This project plan has generated 13 peer-reviewed articles and numerous abstracts and presentations which have been cited by other scientists and researchers and have provided valuable information for germplasm characterization and management. Under this project, numerous interns, students, and post-doctoral researchers have received mentorship and training in horticulture, genomics, genetics and agricultural sciences and thus has indirectly added to the technical workforce on national and international levels.
Accomplishments
1. Identification of molecular markers for the polyembryony trait in mangos. A majority of fruit trees are highly heterozygous and are propagated by cuttings and grafting, which maintain their gene combinations for horticulturally important traits. Polyembryony in mangoes and other clonally propagated fruit trees usually result in producing embryos that are genetically identical to the mother plant and is therefore important for clonally propagating elite cultivars through seeds thus bypassing grafting. Introduction of polyembryony in elite cultivars through breeding will need several years for the offspring to set fruits and to select the polyembryonic trait. Developing molecular markers that are associated with polyembryony will enable selecting polyembryonic seedlings very early in the breeding cycle. In a subordinate project of the parent project 6038-21000-024-000D, scientists at USDA, Miami, Florida, using whole-genome resequencing and genome-wide association studies, identified molecular markers for the polyembryony trait in mangoes, which will be useful in accelerating selection of the polyembryony trait, which in turn will have positive impact in clonally propagating germplasm and elite varieties with fixed desirable genes, and the potential application of the polyembryony trait in other crops.
2. Genotyping of world collection of sugarcane and related grasses (WCSRG). The ARS Miami, Florida, 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. For this purpose, ARS scientists in Miami, Florida, in collaboration with scientists at USDA-ARS, Beltsville, Maryland, investigated clonal redundancy in the sugarcane collection, which resulted in identifying a unique list of sugarcanes. Identifying unique list of sugarcane accessions enabled better germplasm resource management and designing future characterization and evaluations studies. 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, Flordia.
