Gencove_SOW.docx

STATEMENT OF WORK

Background

The project surveys phenotype and genotype of 450 colonies from 30 ND beekeepers to establish a reference data set to use in breeding value estimation through genomic selection methods. The project aims to establish the first such panel for the purposes of developing a genomic selection approach in honey bee breeding. The 30 participant beekeepers constitute a core interest group which will continue to participate by receiving breeding values from the data examined as part of this project and through future collections.

Presently samples are collected but in need of sequencing and processing to arrive at the final variant call set which will be analyzed by Dr. Avalos in HBBGPRL. From the call set we can assess the correlation between target variation and industry-relevant traits (i.e., honey production, viral and varroa tolerance), identifying those mutations that are important for colony success in ND. Resulting information will be used as a selection criterion for participant beekeepers. In addition, the resulting data can be used to provide beekeepers with population-specific information, e.g. genetic ancestry and diversity of their stock, degree of inbreeding, etc. Ultimately, through the use of whole genome sequencing and genomic selection approaches of these samples, we can begin to incorporate cutting-age approaches in bee breeding to the benefit of the industry and towards a healthier, more robust honey bee population in the U.S.

Objectives

1. Identify genetic markers associated with queen quality, low viral and mite levels, and high honey production.

2. Provide genetic and trait information directly to beekeepers in North Dakota.

3. Develop a genotyping service to identify the best queens from derivative breeding value estimations.

Scope Contractor will provide sequencing and imputation services. The contractor has a sequencing approach unique to their company which allows for highly affordable sequencing paired with proprietary imputation services. This has the benefit of providing highly reliable variant calling information for a greatly reduced sequencing cost. Though the sequencing service is broadly available the imputation required to arrive a reliable information is unique to the contractor.

Tasks or Requirements The contractor will extract DNA, sequence samples, conduct variant calling, and impute missing values from a honey-bee specific reference database developed by the contractor for this study. Contractor will provide DNA extraction services for the samples and conduct sequencing with a goal of 10X coverage of each of 450 honey bee genomes. Contractor will also perform variant calling using the honey bee community reference genome. Contractor will also develop a reference data base using publicly available (NCBI) honey bee whole-genome sequencing data. Imputation using said reference will be conducted by the contractor using proprietary methods.

Deliverables or Delivery Schedule Deliverables include raw sequencing reads and an imputed variant call set.

Government-Furnished Equipment and Government-Furnished Information N/A

Reporting Requirements N/A

Travel N/A

Place of Performance Work will be conducted by Contractor at their site.

Homeland Security Presidential Directive (HSPD)-12 (If applicable) N/A

Other Considerations:

N/A