Location: Subtropical Horticulture Research
Project Number: 6038-21000-026-010-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 1, 2024
End Date: Nov 30, 2025
Objective:
Plants possess immune systems that have evolved to fend off disease and stress. Humans have selectively bred plants with more robust defenses to make crops more disease/stress resistant. However, cultivated crops often lack the genetic diversity of wild relatives. Exploring the diverse germplasm for desirable traits, such as disease/stress resistance, is essential to developing crops that can better withstand current and future threats.
This agreement identifies and characterizes desirable traits in fruit crops and ornamental plants. We will use traditional and innovative tools such as phenomics and genomics to discover the potential values of genetic resources. We propose generating genomics and phenomics data sets at SHRS and UF. The investigation aims to characterize germplasm collections for the desired characteristics such as disease resistance and make them available for use in crop improvement. Transcriptome analysis of subtropical crops and their relatives can identify desirable genes. NACA will use this knowledge to precisely characterize the germplasm collection for its use in developing productive and climate-resilient varieties. The project will also update germplasm preservation strategies, broaden crop diversity, and investigate genetic components for disease and stress protection. The customers are national and international germplasm researchers, breeders, and biologists. The objectives are to identify desirable traits and functional trait-marker associations.
Approach:
This study aims to generate high-quality data on phenomics, genomics, and markers for plant species, including key ones like sugarcane, jamun, cacao, and coconut. The USDA-ARS in Miami and University of Florida scientists will collaborate to generate the data, which will be analyzed using bioinformatics tools and a contemporary analytical pipeline at the University of Florida. The transcriptome will be analyzed to identify conserved and variable regions, differentially expressing genes, functional motifs, regulatory elements, associated pathways, and marker trait associations. The goal is to pinpoint candidate genes linked to important traits.
Statement of mutual interest: The University of Florida (UF) and the SHRS of the U.S. Department of Agriculture's Agricultural Research Service (USDA-ARS) will conduct independent research to characterize the germplasm collection. UF and SHRS are collaborating on a medium-scale SNP panel development in sugarcane. Achieving the goals of this project will strengthen and enhance the research programs of both entities by increasing their understanding of genetic diversity and the role of candidate genes and associated networks linked to desirable traits. This research affirms our mutual interest in cooperative research programs and exchanges, benefiting both parties and the people of the United States.
Roles and responsibilities: PI and Co-PI will be responsible for planning the project and executing this research with team members. PI and Co-PIs,will oversee and supervise the research associate recruited to achieve the project's goal. The research outcome will be shared equally, leading to publication(s). PI and Co-PI will be co-accountable for data generation and quality research.
