Source: AGRICULTURAL RESEARCH SERVICE submitted to
INTEGRATED PROGRAM FOR REDUCING BRDC IN BEEF AND DAIRY CATTLE
Sponsoring Institution
Agricultural Research Service/USDA
Project Status
NEW
Funding Source
Reporting Frequency
Annual
Accession No.
0421802
Grant No.
(N/A)
Project No.
8042-31000-104-05R
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Apr 15, 2011
Project End Date
Feb 29, 2016
Grant Year
(N/A)
Project Director
VAN TASSELL C P
Recipient Organization
AGRICULTURAL RESEARCH SERVICE
RM 331, BLDG 003, BARC-W
BELTSVILLE,MD 20705-2351
Performing Department
(N/A)
Non Technical Summary
(N/A)
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3033310104050%
3043410108050%
Goals / Objectives
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.
Project Methods
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.

Progress 10/01/12 to 09/30/13

Outputs
Progress Report 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. 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. 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.

Impacts
(N/A)

Publications


    Progress 10/01/11 to 09/30/12

    Outputs
    Progress Report Objectives (from AD-416): The objective of this proposal 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. 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. The major research foci were the attainment, processing, and storage of samples from 2,000 dairy calves at Tulare, CA and 1,000 calves at Clovis, NM; challenge and animal welfare studies at UC Davis; and the initiation of a metagenomics study to identify novel pathogens associated with bovine respiratory disease (BRD). The dairy calf studies began in July in Tulare and in August in Clovis. The collection, processing, diagnostics, and storage of all of the 2,000 Tulare dairy calves� samples for Genome- Wide Association Studies (GWAS) were completed. Sample collection from 2, 000 animals that met our diagnostic criteria was the result of screening approximately 100,000 animals (the number of animals born over a six- month period that were evaluated from day 1 to 73 days of age). A database was developed for the phenotypes and to track the samples in storage and when in use. Two thousand samples were sent to GeneSeek for genotyping. An initial analysis on 400 calves showed no evidence for population stratification and several loci with moderate associations with BRD. The ascertainment of the calves at Clovis is 60% complete in the 6 months since collections began. To obtain samples from more than 600 animals meeting our diagnostic criteria, approximately 10,000 calves were screened (the number of animals born during the period that were evaluated from birth to weaning). The three dairies involved had a lower incidence of BRD than anticipated; sample collection is completed. For the challenge study, two steers were each infected, one with each of the seven most common BRD-causing pathogens (i.e., BVDV, BRSV, IBR [bovine herpes virus], Histophilus somni, Manheimnia hemolytica, Pasteurella multocida, and Mycoplasma bovis), clinical signs were evaluated, cultures and blood samples were taken, and necropsies were performed. Two animals served as controls and were not challenged. The analysis of the challenge study animals is ongoing. Tissues from these animals will be used for RNA sequencing to identify the host response to each pathogen. This information will be used to better understand the host response and will be used in the genomic pathway analysis to identify genes of modest effects. A follow-up study is planned for this summer with four animals per treated group to increase the sample size for more meaningful statistical comparisons of the host response. The animal welfare study was initiated using a BRSV- H. somni dual-infection model with three replicates of steers. Steers were either infected with BRSV on day 0 and H. somni on day 5 or were infected with placebo at both time points. Clinical signs, nasal swabs, and blood samples were obtained. Animals were treated with either meloxicam or placebo and all received antibiotics. Measures of behavior were evaluated before and during the infection. Antibody titers to BRSV, shedding of BRSV, and levels of prostaglandin E2 were evaluated from the animals in the behavior study. Cytokine and behavior analyses are ongoing. The metagenomics study to identify novel pathogens was initiated by collecting deep-pharyngeal and mid-nasal swabs from BRD and healthy calves in Tulare. The isolation of nucleic acids from the swabs and sequencing are being performed on these samples in Missouri. Once the sequencing is complete, we will be able to determine if the use of swabs will be sufficient for the metagenomics study. If so, this method will be used to collect samples from BRD and healthy calves across the U.S. If this method is not sufficient, a new design will be investigated. Collection of these samples is to be completed by year 2. This research supports one objective of its related in-house project: 1) to use genotypic data and resulting bovine haplotype map to enhance genetic improvement in dairy cattle through development and implementation of whole-genome selection and enhanced parentage verification approaches (obj. #2).

    Impacts
    (N/A)

    Publications