Thermofisher statement of work OAG.docx

Statement of work for the development of SNP probes

The USDA-ARS cacao breeding program located at the Subtropical Research Station (SHRS) in Miami, FL currently has a Trust Fund Cooperative Agreement with MARS Inc. titled ‘Genomic Enhancement of Theobroma Cacao’, one of the goals of this project is the identification, mapping, and characterization of genes associated with resistance to cacao diseases, insect pests, and agronomic traits in segregating populations and germplasm collections through the use of DNA markers, as well as linkage and association mapping methodologies. As part of this plan, the extracted DNA from192 cacao accessions will be sequenced in order to conduct SNP discovery, SNP probe design (8,940 probes), and SNP probe validation. This work will be conducted by Thermofisher and must be completed by March 31st. Thermofisher will be using their AgriSeq Targeted Genotyping by Sequencing technology and the SNPs assays generated by this company, will be used by our Ion GeneStudio 5S Plus system to genotype an additional 1,000 cacao accessions. The same SNP assays will be used for future fingerprinting projects.

Thermofisher should provide an analysis results within 30 days to Dr. Osman Gutierrez at SHRS. An invoice must be submitted to the agency for every 96 well DNA plates analyzed and payment for each invoice will be approved by Dr. Osman A. Gutierrez. The 192 cacao accessions are in 2 96 well DNA plates.