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