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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Research Project #441462

Research Project: Metabolomics and Mineral Analyses of Tropical Crops Germplasm

Location: Subtropical Horticulture Research

Project Number: 6038-21000-026-004-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2023
End Date: Aug 31, 2027

The USDA mandate to produce quality food at a lower environmental impact will require developing sustainable crop varieties that grow sustainably, are adapted to modern orchard management practices and enriched in nutrients. Developing such varieties are heavily dependent on availability of genetically diverse germplasm that is characterized not only for horticultural traits but also for health-promoting traits such as vitamins, minerals, lipids, dietary fibers and calories. The germplasm resources of tropical and subtropical fruits, and sugarcanes and related grasses maintained at the Subtropical Horticulture Research Station (SHRS) in Miami, FL provide a foundation for developing climate-resilient, high-yielding and nutrient-rich crop and fruit varieties. Avocados and mangos are the two major fruit crops maintained at USDA-ARS-SHRS, Miami, FL. The parent project of this cooperative agreement aims to accomplish maintenance, acquisition, characterization, gene-trait association and improvement of these genetic resources using existing and innovative approaches, which will eventually enable breeders, researchers and other stakeholders to use these genetic resources effectively and efficiently. Strengthening collaborations with universities are important for accomplishing these goals efficiently, which fits very well with one of the USDA’s missions of modernizing and utilizing plant genetic resources and their associated information management systems. The overall objective of this cooperative agreement is to build superior germplasm resources and to evaluate and characterize tropical and subtropical fruit germplasm of USDA/ARS Subtropical Horticulture Research Station (SHRS), Miami, FL, which is part of the National Plant Germplasm System (NPGS). The overall objective of this agreement is to support ARS research through collaborations that provide high throughput metabolomics, lipidomics, vitamins and mineral analyses of tropical crops germplasm. The data generated through the collaboration will be used in chemical and nutrient diversity analysis of germplasm. This agreement will focus on the following objectives: 1) to develop GC-MS/MS, LC-MS/MS and ICP-MS methods for chemical and mineral profiling of mangoes and avocadoes. 2) to conduct untargeted metabolomics, lipidomics, vitamin and mineral analyses of mango and avocado germplasm through advanced analytical chemistry methods, and 3) to analyze generated data for classifying germplasm into different chemotype groups.

In his agreement, lipids, vitamins, minerals, untargeted metabolites, and sugar profiling of avocado and mango accessions will be analyzed as follows. Avocado fruits will be collected and stored at 5 0C for seven days to allow for uniform maturity. Avocado lipid profiling will be conducted essentially as reported in literature with modifications as needed. In the initial phase of the agreement, focus will be developing analytical methods on five genetically diverse avocado and mango accessions. Once developed, these methods will be applied to the entire avocado and mango collection. When needed these methods will be updated to leverage latest developments in chemical analytics such as Direct Analysis in Real Time-AccuTOF™ mass spectrometry (DART-ToF-MS). Briefly, extracted avocado oil will be methylated with sodium methoxide and (trimethylsilyl)diazomethane and analyzed using GC-MS/MS. For vitamins, initially published extraction methods will be tested and standardized on five genetically diverse mango and avocado accessions using GC-MS/MS. Minerals analyses will be conducted using Inductively Coupled Plasma Spectrometry, which are routinely performed by the cooperators. Other numerous phytochemicals contribute to the nutritional value of these fruits. For example, the avocado-eating quality is associated with aroma compounds such as 1-octen-3-one, hexanal, (Z)-4-decenal and perhaps others. To capture metabolite profiles of avocado and mango fruit, untargeted LC- and/or GC-MS/MS will be conducted on priority accessions. Mass-Spec data will be stored in community-maintained open-source standard formats such as, mzxML, mzML, mzData or others, which could be accessed by the mzAPI by the community, and also for analyses in R packages such as mzR, MALDIquantForeign or open-source analysis sources such as XCMS online. Prominent features from lipid, minerals and vitamin profiles will be analyzed using Principal Component analysis (PCA) and machine learning approaches, which will separate accessions into different groups. Since the quantity of these compounds is dependent on cultivars, growth season, and fruit maturity, analyses will be performed at the mid-fruiting season for each accession separately. In addition, to account for effect of seasonal variability on fruit maturity and nutritional traits, several accessions from each race will also be evaluated at different fruit developmental stages for 2-4 seasons.