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United States Department of Agriculture

Agricultural Research Service

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Research Project: TURKEY GENOMIC RESEARCH AND GENETIC IMPROVEMENT: DEVELOPMENT OF HIGH-DENSITY SNP CONTENT FOR DESIGN OF A GENOME-WIDE ASSAY

Location: Animal Biosciences and Biotechnology Laboratory

Project Number: 1245-31000-105-01
Project Type: Reimbursable

Start Date: Feb 01, 2010
End Date: Jan 03, 2014

Objective:
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.

Approach:
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.

Last Modified: 9/29/2014
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