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Research Project: Genetic Resource and Information Management and Genetic Improvement of Germplasm for Tropical and Subtropical Fruits, Sugarcane, and Related Grasses

Location: Subtropical Horticulture Research

2023 Annual Report

1. Conduct research to develop genetic resource maintenance, evaluation, or characterization methods and, in alignment with the overall NPGS Plan, apply them to priority tropical and subtropical fruit crops, sugarcane, and related grass genetic resources to avoid backlogs in plant genetic resource and information management. 1.A. Conduct research to develop in vitro maintenance and biotechnology-based germplasm management methods for (sub)tropical fruit crops and sugarcanes. 1.B. Evaluate and characterize germplasm using high-throughput genotyping, phenotyping, and genome-wide association studies. 2. Acquire, distribute, and safely maintain the genetic integrity, health, and viability of priority tropical and subtropical fruit crop, sugarcane, and related grass genetic resources and associated descriptive information. 2.A. Acquire and distribute germplasm and their associated descriptive information for (sub)tropical, sugarcane and related grasses. 2.B. Safely maintain the genetic integrity, health, and viability of priority tropical/subtropical fruits and sugarcanes ex situ in the field. 3. Conduct research to develop genetically-enhanced germplasm that broadens the diversity available for improving avocado and mango by incorporating superior traits from cultivars, landraces, and wild relatives into adapted genetic backgrounds and genepools, and by creating novel breeding populations. 3.A. Develop open-pollinated and targeted pre-breeding populations of avocado and mango. 3.B. Evaluate and characterize novel pre-breeding populations of avocado and mango at the phenotypic and genotypic levels.

The lead scientist/curator will plan, schedule and direct establishment of tissue culture infrastructure and protocols for maintaining germplasm in vitro. In coordination with collaborators, research will also be conducted to develop in vitro regeneration methods for developing cryopreservation methods for germplasm. Effective schedule for maintenance, propagation and regeneration of germplasm will be developed and implemented to better utilize field space at the Subtropical Horticulture Research Station (SHRS). Backing up of germplasm at alternate locations will be coordinated with collaborators. Germplasm and associated data will be distributed to researchers through Germplasm Resources Information Network (GRIN), GRIN-Global. Based on genetics and reproductive biology, germplasm will be planted to maximize outcrossing among genetically diverse germplasm, which will allow closing genetic gaps and facilitate generating open-pollinated populations. Germplasm will be genotyped using latest genotyping methods, which will enable denser molecular markers covering entire genomes. These analyses will also be extended to crop wild relatives of sugarcanes, mangoes and avocadoes when they are acquired. Concurrently, germplasm will be evaluated for agronomic and horticulturally important traits using traditional descriptors as well as new digital evaluation methods such as Normalized Digital Vegetation Index and Normalized Pigments Chlorophyll Ratio Index. Novel molecular phenotyping methods will be developed and implemented for collecting data on lipids, sugars, vitamins, minerals and secondary metabolites, which are expected to enhance value of germplasm for breeding nutrient-enriched and flavorful fruit crop varieties. Genotypic and phenotypic data will be used in genome-wide association studies for linking molecular markers with agronomically and horticulturally important traits. To improve genetic diversity in the germplasm and to provide genetic material for developing varieties, open-pollinated and controlled-pollinated populations of avocadoes and mango accessions will be generated, evaluated and genotyped. In coordination with collaborators and stakeholders, these populations as well as populations developed by stakeholders and collaborators and their associated genetic and phenotypic data will be utilized for developing molecular genetic markers for agronomically and horticulturally important traits for facilitating development of sugarcane, avocado and mango varieties.

Progress Report
This is the first report for the project 6038-21000-026-000D, which began on March 6, 2023 and replaces project 6038-21000-024-000D. Progress was made on several objectives of the project plan, which is summarized 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, 75 orders for sugarcane and related grasses (Saccharum barberi (7), Saccharum edule (3), Saccharum hybr. (13), Saccharum narenga (2), Saccharum officinarum (11), Saccharum robustum (3), Saccharum rufipilum (2), Saccharum sinense (14), Saccharum spontaneum (14) and Saccharum spp. (6)) were processed, reflecting a 10-fold increase over last fiscal year, perhaps due to post-COVID 19 increases in research activities. Information about specific sugarcane germplasm was provided to researchers from USDA, Canal Point, Florida. Lead scientist at USDA, Miami, Florida also assisted the requester of germplasm with sampling sugarcane leaves on-site. In addition to propagules, RNA and DNA samples isolated from sugarcanes and tropical fruit crops (Averrhoa spp.) were provided to collaborators who will use it in generating transcriptomics data for annotating starfruit genomes. In this project, preserving germplasm in tissue culture were introduced for the first time at USDA, Miami, Florida. Towards this goal, a tissue culture technician has been recruited who onboarded in July 2023. Tissue culture infrastructure such as growth chambers and other equipment have been acquired and research on developing tissue culture protocols has been initiated. Metabolite profiling, vitamin, lipids, mineral and sugar analyses of the fruit crops is one of the major objectives in the project 6038-21000-026-000D (2023 – 2028). Accordingly, research has been initiated to develop methods for analyzing these compounds in avocado and mango germplasm. In this respect, a collaborative agreement between the Lead Scientist at USDA, Miami, Florida and investigators at the University of Central Florida who have well-equipped laboratories for these analyses has been established. Part of the Avocado collection has also been grafted on avocado rootstock ‘Walden’ as well as ‘Lula’. For genomics and genotyping germplasm, the entire mango collection and parts of the avocado collection are sequenced. Parts of the open-pollinated populations of avocado have also been genotyped using in-house genotyping platforms. For our collaborators in USDA, TARS, Mayaguez, Puerto Rico, eighty-five mango cultivars including historic samples were genotyped and identifies. Some of these samples turned out to be not present in the mango collection at Subtropical Horticulture Research Station (SHRS). Budwood from some of these mango samples were obtained from USDA, TARS, Mayaguez, Puerto Rico and grafted on ‘Turpentine’ rootstock at SHRS. These mango samples will be evaluated by USDA, ARS scientists at SHRS and TARS and added to the national plant germplasm repository in Miami, Florida. For increasing genic diversity and closing genetic gaps in the collection, several open-pollinated populations of avocado and mango have been generated and planted in pots. In addition, several locations in the fields have been prepared for planting open-pollinated avocado and mango seedlings. various fields at SHRS, Miami, Florida.

1. Generating and genotyping open-pollinated populations of avocados. The avocado production area is currently dominated by only one cultivar ‘Hass’, which accounts for approximately 80% percent of world production. Prevalence of only one type of cultivar with a narrow genetic background makes the avocado trees prone to attack by diseases and pests. In addition, consumers are deprived of the numerous flavors and tastes of other types of avocados. To improve genetics and to introduce new avocado varieties, crossing and creating pre-breeding populations are needed. Availability of mature avocado trees with varying traits – such as canopy architecture, maturity times, salt and cold tolerance, oil contents, and fruit quality traits – offer excellent opportunities to use them as parents in creating novel breeding populations. Towards this goal, 12 open-pollinated populations representing different ecotypes of avocado have been raised in pots, which are being evaluated for seedling growth traits. One of these populations with segregating canopy structure has been genotyped. In addition, another four open-pollinated populations have also been generated and planted in the field at Subtropical Horticulture Research Station (SHRS) in Miami, Florida. These populations provide valuable foundation for studying genetics of canopy structure and growth traits, which will potential be useful in applying genomic selection methods in breeding avocadoes.