TURKEY GENOMIC RESEARCH AND GENETIC IMPROVEMENT: DEVELOPMENT OF HIGH-DENSITY SNP CONTENT FOR DESIGN OF A GENOME-WIDE ASSAY
Animal Biosciences and Biotechnology Laboratory
2010 Annual Report
1a.Objectives (from AD-416)
Specific Aim 1. Use broad species diversity to identify and select new SNPs that are uniformly distributed across the turkey genome;
Specific Aim 2. Validate and characterize SNPs in relevant commercial populations.
1b.Approach (from AD-416)
For the emerging turkey genome sequence to successfully be applied to gene discovery, there is a need to improve the process of SNP discovery and create high-density SNP genotyping assays. Advances in DNA sequencing technology have increased the capacity to the extent that the reduced representation library model is not the only approach for SNP discovery. Furthermore, aligning contigs containing putative SNPs against a reference genome sequence will enable the detection of contigs that map to a single, unique region of the genome, which increases the chance of obtaining a reliable genotype five times. We hypothesize that deep, shotgun sequencing (24-30X) of turkeys from a broad pedigree range (commercial, historical, heritage and ancestral populations) can be used to rapidly identify and characterize SNPs for creating a high-density (60K) SNP genotyping platform for use by the commercial industry and research communities. This Tools and Resources proposal represents an innovative, integrated approach to rapidly and cost effectively identify and validate SNPs and incorporates second generation sequencing technology to ensure broad genome coverage and the depth to uncover highly probable SNPs, clusters of segregating SNPs based on lines as well as SNPs lost through domestication.
The goal of this project is to provide the content for development of a SNP chip for use by the commercial turkey industry similar to the highly successful Illumina BovineSNP50 SNP chip. We expect to generate a minimum of 500,000 SNPs that are uniformly distributed across the turkey genome. Progress to date includes obtaining representative blood samples from the eight relevant populations (four commercial pure lines, Beltsville Small White, two Heritage breeds, wild turkey) for DNA extraction and cDNA library construction. The ADODR has organized four conference calls with collaborating partners to facilitate sample transfer to BARC. Additionally, email communication with Co-Investigators at Wageningen University has been used to develop and modify timelines for project goals. Finally, in-house meetings with ARS Co-Investigators have been held to develop timelines for library construction and sequencing.