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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Research Project #443872

Research Project: Genomics and Bioninformatics of Tropical Fruit Crops

Location: Subtropical Horticulture Research

Project Number: 6038-21000-026-007-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: May 1, 2023
End Date: Sep 30, 2025

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. These resources need efficient management, large-scale genetic and phenotypic characterization, and improvement for distribution to diverse stakeholders. 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 and other stakeholders to use these genetic resources effectively and efficiently. Strengthening collaborations with national and international stakeholders and 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 genomic resources 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). This agreement will focus on the following objectives: 1) establish high quality genomic resources of mango and avocado germplasm by developing pan-genomes through advanced genomic and bioinformatics tools, 2) utilize the developed genomic resources for genomic characterization and genome-wide SNP discovery of avocado and mango germplasm collection at USDA, 3) assist in performing marker-trait association mapping of horticultural and fruit quality traits of avocado and mango germplasm, and 4) provide insights and assistance for potential genomic selection and prediction study of mango and avocado.

A trans-disciplinary team of researchers at USDA/ARS and the University of Florida (UF) with expertise in genetics, genomics, bioinformatics, plant physiology, metabolomics, and horticulture will conduct complementary research focused on evaluating and genetically characterizing avocado and mango germplasms. Using genomics, single nucleotide polymorphism (SNP) markers and genome-wide association studies (GWAS), research will be conducted to associate fruit quality and plant growth traits with genetic markers. A Post-Doctoral Research Associate will be recruited by the cooperators at the University of Florida and the USDA ARS PIs. The post-doc will be working on projects that are linked to the parent project. Recruitment of the Post-Doc will be coordinated by the USDA PI and the cooperator at the University of Florida. The ARS PI and the cooperator at UF will participate in experimental design, data collection, analyses, interpretation and writing joint publications. The postdoc will lead the manuscript development with guidance from both PIs. All publications will go through the USDA ARS publication policies and procedures. The postdoc will be primarily mentored by the cooperator at the University of Florida for the cooperator’s expertise in genomics and bioinformatics and coordinate with the USDA research team in utilizing mango and avocado germplasm at SHRS, state-of-the-art laboratory facilities, computing resources and greenhouses for carrying out this research. Major outcomes of these investigations include: 1) high quality, informative genomic resources of both mango and avocados to the general public for research, breeding and conservation purposes, 2) well-characterized avocado and mango germplasm, which will enable our germplasm requesters and other stakeholders to make informed decisions in selecting germplasm for research and breeding purposes, 3) molecular markers associated with horticultural and fruit quality traits, which could be utilize by breeders to accelerate and improve genetic gain in avocado and mango breeding programs, and 4) informative molecular markers for potential genomic selection and prediction in both tropical crops. Overall, the outcomes of this agreement will positively impact the tropical and subtropical fruit industries in the USA and worldwide.