Proestou_Specs_SNPChip Updated.pdf

Specifications for custom Eastern oyster 60K SNP arrays

Background. The USDA ARS Shellfish Genetics Laboratory conducts research to support genetic improvement for commercially important traits, thereby enhancing production and profitability of the East Coast oyster aquaculture industry. Aspects of our research include defining measurable phenotypes for traits such as disease resistance and stress tolerance, investigating the genetic basis of those traits, and more recently establishing a Northeast-specific selective breeding program. Several of our research activities rely on high through-put, high density, genotyping capabilities.

Rationale for procurement. The USDA ARS Shellfish Genetics Laboratory needs to expand its high through-put genotyping capabilities by investing in CUSTOM Eastern oyster high-density 60K SNP arrays and associated reagents and consumables. Each array enables capture of high-quality genotype data for 384 individuals at 60,000 genetic loci simultaneously.

Genotype data will be used to

1) Characterize genetic diversity and differentiation among wild and commercial oyster populations in the Northeast (ME-NY) region

2) Perform genome-wide association studies (GWAS) to identify specific genomic regions/loci underlying traits of interest

3) Facilitate genomic selection methods for genetic improvement of oyster stocks

Scope of work. To genotype 6,000 oyster samples with a high-density 60K SNP array.

Minimum Specifications.

• 16 custom Eastern oyster SNP arrays (enough to genotype 6000 oyster samples)

• Required reagents and consumables to process 16 custom Eastern oyster SNP arrays.

• SNP arrays will be configured as 384-peg arrays.

• SNP arrays will be shipped to Neogen Genomics for genotype processing.