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United States Department of Agriculture

Agricultural Research Service

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Research Project: Pooled Genotyping and Sequencing for Development of Molecular Breeding Values for Resistance to Bovine Respiratory Disease

Location: Genetics, Breeding, & Animal Health

Project Number: 3040-31320-012-06
Project Type: Reimbursable

Start Date: Oct 01, 2013
End Date: Aug 31, 2017

Objective:
1) Identify chromosomal regions associated with incidence of BRDC in commercial feedlots, using a large-scale case/control strategy in conjunction with pooled hi-density SNP genotyping. 2) Develop SNP markers with consistent predictive merit for resistance/susceptibility in regions with significant association, using targeted resequencing of chromosomal regions from the pooled samples.

Approach:
Due to the low heritability, large numbers of animals are required to achieve sufficient power to detect genomic associations with disease incidence. In addition, the disease itself is ill-defined and diagnosis is normally based only on symptoms since laboratory confirmation is too expensive. We propose to use treatment records as a proxy for disease incidence, and a case/control approach to dividing individual animals into pools for genotyping. Commercial cattle (N=100,000) will be sampled, with the expectation based on previous observations that at least 5% (5,000) will experience BRDC treatment while in the feedlot and form the “case” group. An equal number of untreated animals will be matched on feedlot locations and producer source, and the two groups will be divided into 50 pools of 100 animals each for genotyping with the Bovine HD array (~780K SNP). Genome-wide significant SNP will be identified using signal intensity data and comparing estimated allele frequencies for each SNP between pools of case and control groups. Chromosomal regions that appear in 2 or more independent sets of data will be targeted for resequencing using hybridization oligonucleotide bait-based methodology and high-throughput sequencing technology. New markers identified in this step will be tested in phenotyped animals not in the initial discovery pools to replicate their predictive merit, and develop an equation to estimate molecular breeding value (MBV) for this trait.

Last Modified: 12/19/2014
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