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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

2013 Annual Report


1a.Objectives (from AD-416):
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.


1b.Approach (from AD-416):
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.


3.Progress Report:

Low coverage DNA sequence data and genotypes from high density genetic marker panels on an additional 174 bulls were supplied to the cooperator. This makes a total of 270 bulls with DNA sequence and high density genotype information. Both sources of data were aligned to a bovine genome assembly. Methods that use pedigrees identifying related animals are being incorporated with the objective of improving imputation of missing and low reliability genotypes. The processes are being expanded to include higher coverage DNA sequence from exomes, the portions of genes that codes for RNA. Identified variants and their genotypes are being studied at U.S. Meat Animal Research Center, Clay Center, Nebraska, as a means of improving genetic predictions across populations.


Last Modified: 10/21/2014
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