Location: Sustainable Perennial Crops Laboratory
Project Number: 8042-21220-258-001-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 1, 2020
End Date: Jul 1, 2023
The objective of this agreement is to support research through collaborations that provide high throughput next generation sequencing link to novel genome assemblage that can accurately reconstruct the entire genome down to the chromosomal level for cacao pathogens. 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, genome assemblages and SNP data as well as providing access to the raw data. The objectives of the agreement directly relate to specific project Objective 1: Develop genomic tools for assessing pathogen genetic diversity and determining the basis for virulence in support of improved cacao breeding. [NP303, C2, PS2A] 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. Sub-objective 1.C. Combining genotyping by sequencing and whole genome sequencing data to assess the genetic diversity of P. megakarya and evaluate the evolution/selection of virulence-associated genes in NP303 project “Developing Pathogen-and Plant-Based Genetic Tools for Breeding Disease Tolerance in Theobroma cacao.”
The Cooperator will produce appropriate libraries for sequencing and direct high throughput sequencing and assemble genomes/transcriptomes using advanced methods and bioinformatics tools. For full genome assemblage, ARS will provide the Cooperator with nucleic acids from isolated microbes/microbial infected plant material. The Cooperator will conduct alignments and genome assemblage analysis and will share the data with ARS or to a third party designated by ARS.