Organization and Storage of Bovine High Density Genetic Marker Panel and Next Generation Whole Genome DNA Sequence Data
Genetics, Breeding, & Animal Health
2012 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.
Low coverage DNA sequence data and genotypes from high density genetic marker panels on 96 bulls were supplied to the cooperator. Both sources of data were aligned to a bovine genome assembly. Polymorphisms and other variants were identified and can be displayed on a web site. Identified variants and their genotypes are being used at U.S. Meat Animal Research Center, Clay Center, Nebraska, to improve genetic predictions.