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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Research Project #428155

Research Project: Reassembly of Cattle Immune Gene Clusters for Quantitative Analysis

Location: Cell Wall Biology and Utilization Research

Project Number: 5090-31000-026-06-I
Project Type: Interagency Reimbursable Agreement

Start Date: Feb 1, 2015
End Date: Jan 31, 2019

Objective:
ARS researchers will work with scientists at the Pirbright Institute in the UK to sequence and reassemble critical immune system genes in the cattle genome. Many immune gene regions in the current cattle reference assembly are shortened or misassembled and are not currently used in genetic evaluation for health traits. Reassembled contigs will be assessed for quality and aligned with existing high throughput sequence data to identify high frequency SNPs and INDELs. Identified SNPs and INDELs will be used in a genome-wide association study to identify variants associated with bovine tuberculosis resistance in cattle.

Approach:
Collaborators at the Pirbright Institute will extract DNA from a Holstein herd with extensive data on tuberculosis susceptibility and resistance. DNA samples will be taken from bulls that have haplotpes associated with tuberculosis resistance. Fosmid libraries of the DNA extracted from these resistant bulls will be used to create fosmid libraries and collaborators will screen the library for fosmid clones that contain critical immune gene regions. ARS scientists will sequence fosmid clones containing the gene regions using Pacific Biosystems long-read technology and assemble the sequence into contigs. ARS scientists will then align existing high throughput sequence data from 40 Holstein bulls to the assembled contigs to identify high frequency variants on the contigs. Next, ARS scientists will send SNP genotyping assay designs to collaborators at the Pirbright Institute to genotype the Holstein herd selected for tuberculosis susceptibility and resistance. The Pirbright Institute will then genotype the herd and perform an association of tuberculosis resistance with identified SNP markers.