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United States Department of Agriculture

Agricultural Research Service

Research Project: Organization and Storage of Bovine High Density Genetic Marker Panel and Next Generation Whole Genome DNA Sequence Data

Location: Genetics, Breeding, & Animal Health

Project Number: 3040-31320-012-04
Project Type: Specific Cooperative Agreement

Start Date: Sep 01, 2011
End Date: Aug 31, 2014

Objective:
Next generation sequencers now make low coverage re-sequencing of individual cattle genomes practical and affordable. Mapping DNA sequencing information and genotypes from well-structured and high-density genetic marker panels would result in a powerful resource for identifying genetic polymorphisms segregating in a population. An interface to visualize and interrogate evidence of DNA polymorphisms would increase the value of the resource. The objective is to produce sequence reads and high-density genetic markers for 96 bulls that have many descendants in the Cycle VII phenotypic resource and develop a genetic polymorphism resource that is accessible and useful.

Approach:
Ninety-six animals with many descendants in the GPE phenotypic resource population will be sequenced with short-length reads from a next generation sequencer. The same animals will be genotyped with high-density 770,000 SNP genetic marker panels. The sequencing information will be processed and stored. Processed sequence and genotypes from the high-density panel will be mapped to the bovine assembly. Results will be made available to subscribed users through a web-based interface that displays the mapped polymorphisms and related information such as the amount of sequence evidence for a genotype, and as a file.

Last Modified: 11/28/2014
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