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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Research Project #445691

Research Project: Characterize the Germplasm Collection of Subtropical Horticulture Fruit Crops and Ornamental Plants Using Genomics/Transcriptomics

Location: Subtropical Horticulture Research

Project Number: 6038-21000-026-006-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Jan 1, 2024
End Date: Dec 31, 2024

Objective:
To characterize and identify the desirable traits in tropical and subtropical fruit crops and ornamental plants and converting the genetic values into economic wealth of the country. Specificially: 1. Characterize and identify genetic variations for desirable traits. 2. Identify potential functional trait-markers associations.

Approach:
High-quality phenomics, genomic, and marker data for a diverse range of plant species proposed in this study, including agriculturally significant species such as sugarcane, jamun, cacao, coconut etc. will be compiled from the USDA-ARS, Miami and other publicly accessible databases. Subsequent bio-informatics analyses will be conducted by cooperator using contemporary analytical pipeline established at LSU. Conserved and variable regions in the genome or transcriptome will be identified from multiple genome alignment. Phylogenetic Analysis: Build a phylogenetic tree using maximum likelihood or Bayesian inference methods based on the aligned genomic sequences. Infer evolutionary relationships and estimate divergence times. The bioinformatics tools will be used to identify differentially expressing genes between genotypes, identify potential functional motifs, regulatory elements, and associated pathways to understand the functional implications of target genes. Marker-trait associations will be identified for traits of interest using various quantitative genetics tools to pinpoint candidate genes associated with important traits. Statement of mutual interest: Both LSUAC and SHRS, USDA-ARS will be involved with independent research on the characterization of the germplasm collection. LSUAC and SHRS are currently involved in a collaborative grant from the Crop Germplasm Committee for development of a medium-scale SNP panel development. Accomplishing the objectives of the proposed project will strengthen and enhance the research programs of both entities by the outputs in terms of understanding the genetic diversity and role of the candidate genes and associated networks linked to desirable traits. The research work shall affirm to our mutual interest in cooperative research programs and exchanges and shall be for our mutual benefit and the benefit of the people of the United States. Roles and responsibilities: Dr. Sukhwinder Singh and Niranjan Baisakh will be responsible for the project planning and execution in coordination. Dr. Baisakh will supervise the (postdoctoral) research associate proposed to be recruited in the project toward achieving the project goal. The outcome the research will shared equally and postdoctoral will lead the publication(s) and Drs. Singh and Baisakh will be co-accountable for data generations and quality research.