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United States Department of Agriculture

Agricultural Research Service

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Location: Animal Genomics and Improvement Laboratory

2013 Annual Report

1a. Objectives (from AD-416):
The objective of this project is to reduce the prevalence of bovine respiratory disease (BRD) through the use of genetic selection and best management practices to improve animal welfare and the economic sustainability of beef and dairy operations.

1b. Approach (from AD-416):
Chromosomal regions will be identified that are associated with BRD by examining 3,000 beef and 3,000 dairy cattle using a multi-tiered genetic approach that includes genotyping arrays and pathway analysis. Economic studies will also be conducted to identify the economic loss associated with BRD in feedlot cattle, replacement dairy heifers, beef bulls and dairy calves. Extension activities will also include outreach and 4-H education.

3. Progress Report:
The major research foci were the ascertainment, processing, and storage of samples from 1,000 feedlot animals (Population C) in Greeley, Colorado and completion of sampling of 763 calves (Population B) at Clovis, New Mexico; completion of genotyping and initiation of genome-wide association analysis (GWAS) of the 2,000 Holstein calves (Population A) collected in Project Year 1; the challenge and animal welfare studies (Population E) at University of California at Davis; the continuation of the metagenomics project to identify novel pathogens associated with bovine respiratory disease (BRD); and the initiation of the gene set enrichment analysis with single nueleotide polymorphism (GSEA-SNP) analysis. Population B (New Mexico dairy heifers) study’s sample collection ended in July and the next phase of following them through production will continue for the next few years. Population B animals were genotyped utilizing the 778,000 Illumina BeadChip assay as was done for genotyping the Population A animals. A case-control GWAS was completed with two different statistical approaches for Population A. The collection of samples from Population C (feedlot cattle) at the JBS-Five Rivers’ Feedlot in Colorado is 76% complete since collection began in September. This was the second year for the challenge study (Population E) as a follow-up to last year’s study where two steers were each infected with one of the seven most common BRD complex pathogens (BVDV, BRSV, IBR [bovine herpes virus], Histophilus somni, Manheimnia hemolytica, Pasteurella multocida, and Mycoplasma bovis). This year, four steers were each infected with one of six administered pathogens. The H. somni was not used as animals were inadvertently vaccinated against this pathogen prior to the trial. Challenged steers were evaluated for clinical signs, blood and nasal swab samples were taken, and necropsies were performed. Four animals served as controls and were not challenged. The analysis of the challenge study animals is ongoing and a manuscript describing the host response to the single pathogen challenges is in preparation. These animals’ tissues were sent to the University of Missouri for nucleic acid extraction and library construction prior to RNA sequencing to identify the host response to the individual pathogens. This information will be used to better understand the host response and will be used in the genomic pathway analysis (GSEA-SNP) to identify genes of modest individual effects underlying susceptibility to each pathogen. The animal welfare study continued in coordination with the challenge study using a single infection model. Clinical signs, nasal swabs, and blood samples were obtained. Measures of behavior were evaluated before and during the infection. Cytokine and prostaglandin E2 levels are being evaluated as well as behavior videos of grooming, licking, lying, and feeding. The metagenomics study to identify novel pathogens has been initiated by collecting deep pharyngeal and mid-nasal swabs from BRD and healthy calves in Tulare, California and BRD-challenged animals from University of California at Davis. Protocols for the isolation of nucleic acids (DNA representing bacterial genomes and RNA representing certain viral genomes) from the swabs were developed and evaluated. At the University of Missouri, next-generation DNA sequencing was performed and is under analysis. RNA extracted at the University of Missouri was sent to Minnesota for 16s rRNA sequencing to determine taxonomy of the organisms. After analyzing these data, a survey of species found in samples collected from BRD and healthy calves across the U.S. will proceed. The GWAS of Population A (2,000 Tulare Holstein calves) was approached by conducting four analyses (EMMAX, GBLUP, PLINK, and SVS7) to identify loci associated with the presence or absence of BRD. Associations of seven significant SNPs were identified that were present in all analyses and many additional SNPs were found to be associated by two or more analyses. Twenty-three chromosomal regions of association were shared when SNPs were ranked and compared across analyses. The GBLUP SNP effects explained 20% of the variation in BRD incidence. Additional analyses using clinical scores and pathogens will be completed by year three. The GSEA-SNP is under development with the 778,000 SNPs and will be conducted following the completion of the RNA-sequencing analysis of the Population E (challenged) animals.

4. Accomplishments

Last Modified: 10/15/2017
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