Location: Sustainable Perennial Crops Laboratory
Project Number: 8042-21220-258-002-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 1, 2019
End Date: Oct 8, 2023
Objective:
The objective of this agreement is to support research through collaborations that provide high throughput next generation sequencing and genotyping by sequencing services for tropical and semitropical plants; phytopathogenic fungi and bacteria; plant insect pests and their associated host plants. The data generated through the collaboration will be used in genomic and transcriptome analysis and genetic diversity analysis. ARS desires the Cooperator to provide goods and services necessary to develop appropriate RNA, DNA, and cDNA libraries from ARS provided materials. The Cooperator will provide sequencing and data processing to ARS in the form of usable sequencing data as well as providing the raw data.
The objectives of the agreement directly relate to specific project objectives: “Develop genomic tools for assessing pathogen genetic diversity and determining the basis for virulence in support of improved cacao breeding” and “Identify cacao defense genes through transcriptome analysis and develop tools to exploit these genes for the improvement of cacao breeding” in the project “Developing Pathogen- and Plant-Based Genetic Tools for Breeding Disease Tolerance in Theobroma cacao and “Elucidate geospatial patterns of genetic diversity for the primary gene pool of cacao” and “Develop and apply genomic tools for improving the efficiency and effectiveness of managing and utilizing genetic resources of other priority tropical crops, such as tea, guava, longan, rambutan, pitaya, star fruit, mangosteen, peach palm and macadamia nut” in the project “Characterizing and Evaluating the Genetic Diversity and Horticultural Value of Genetic Resources for Cacao and Other Tropical Tree Crops Economically Important to the United States”
Approach:
The Cooperator under ARS direction will produce appropriate sequencing libraries for genotyping by sequencing or from infected and noninfected control material and conduct high throughput sequencing. ARS will provide the Cooperator with isolated DNA and or RNA. The Cooperators will conduct initial alignment and comparison analysis and will send the data to ARS or to a third party designated by ARS.
