Location: Sustainable Perennial Crops Laboratory
Project Number: 8042-21000-281-013-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Aug 20, 2018
End Date: Aug 19, 2023
Objective:
The objective of this agreement is to support research through collaborations that provide high throughput next generation sequencing link to novel genome assemblages that can accurately reconstruct the entire genome down to the chromosomal level 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 genetic diversity analysis. ARS desires the Cooperator to provide goods and services necessary to develop appropriate DNA libraries from ARS provided materials for next generation sequencing. The Cooperator will provide sequence data analysis to ARS in the form of usable sequence and genome assemblages as well as providing the raw data.
The objectives of the agreement directly relate to specific project Objectives 3: “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 NP301 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”. The agreement will also relate to specific project Sub-objective 1.A. Identify the genome structure of established and emerging pathogens of cacao to determine the genetic basis for their virulence in cacao in NP303 project “Developing Pathogen-and Plant-Based Genetic Tools for Breeding Disease Tolerance in Theobroma Cacao.”
Approach:
The Cooperator under ARS direction will produce appropriate sequencing libraries for sequencing and conduct high throughput sequencing and assemble the genome using proprietary methods and bioinformatics tools. When needed, the Cooperator may be asked to reassemble a previously sequenced genome and in that case ARS will provide the Cooperator with raw sequence reads. For full genome assemblage, ARS will provide the Cooperator with isolated plant and/or fungal material. The Cooperators will conduct alignments and genome assemblage analysis and will send the data to ARS or to a third party designated by ARS.
