Progress 10/27/16 to 09/30/21
Outputs
Target Audience:Veterinarians, cattle feeders, dairyman, cow-calf producers, allied health professionals, research scientists. Changes/Problems:Covid-19 resulted in the termination of sampling of calves at the commercial dairy we were collaborating with last year. This made it necessary to find a new facility as a source of calves and sampling. This new location was identified and sampling calves began again in November of this year. What opportunities for training and professional development has the project provided?In the last year, a PhD student and four undergraduate students have been trained using the BRD data. In previous years, a second PhD student and numerous undergraduates have been trained using the BRD data. The BRD data has been used to educate undergraduate students in two capstone classes (beef production and dairy production), and in two junior-level classes (Agricultural Animal Health and Animal Breeding and Genetics) for several years. How have the results been disseminated to communities of interest?Results have been presented to an international audience once, a national audience 12 times and for regional audiences 4 times. Eight publications have so far been published in scientific journals. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
This year: We are collecting mid-nasal and deep pharyngeal swabs for diagnostics for BRD pathogens in preweaned Holstein calves. We aim to determine if pathogen profiles differ geographically across the US. This information will be important when producers use genomic selection to choose cattle that may be more resistant to some BRD pathogens than others.In addition, we are collecting blood samples for genotying and for serum analysis in the same calves to validate our previous results of loci associated with BRD susceptibility. Of the calves' samplescollected last year, bacteriology has been completed on all of the calves and virology will be completed soon. DNA has been extracted on all blood samples in preparation for genotyping. Over the period of this project we have developed genotypes anddiagnostic profiles for bacteriology and virology for almost 6,000 cattle that have been clinically scored. We have completed GWAS, gene set and pathway analyses on all of the genotypes we have amassed. Only the samples collected in the past year have yet to be genotyped. We have completed whole genome sequencing on 60 beef and 30 Holstein cattle to identify the DNA variants that are present in the loci associated with disease susceptibility. The DNA variants associated with BRDmay then be used for prediction of cattle that are less likely to get BRD through genotyping. The sequencing data will be used to identify unique and shared DNA variants associated withdisease susceptibility across and within breeds. We have identified loci that are associated with susceptibility to specific pathogens and are more important in some herds or geographic regions than others. We are continuing to investigate how vaccination, climate and management are interacting with the prevalence of certain pathogens and how that may dictate genomic selection in different regions of the countryl New viruses have been identified that are associated with BRD through these studies as well.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Genetics of calf diseases. Health Management of Calves: From intrauterine life to successful weaning. 41st American
Dairy Society Association Discover Conference on Food and Animal Agriculture, Itasca, Illinois.
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Progress 10/01/19 to 09/30/20
Outputs
Target Audience:Veterinarians, cattle feeders, dairyman, cow-calf producers, allied health professionals, research scientists. Changes/Problems:As was previously stated, the covid-19 pandemic has left the dairy we were collecting samples from in Wisconsin with too few personnel to continue with the study. We are actively seeking other alternatives for sample collection. What opportunities for training and professional development has the project provided?A new PhD student has joined the program to study the genetics of disease resistance/susceptibility which will include BRD. The undergraduate students reached by the lectures on BRD have exceeded 300 students. How have the results been disseminated to communities of interest?Undergraduate students in animal science, veterinary science, the honors college and agricultural food systems. Veterinarians, animal scientists and researchers through journal articles. Drovers published an article that reviewed my presentation on the genomics of BRD in late 2019 which reaches dairy professionals and producers throughout the U.S. What do you plan to do during the next reporting period to accomplish the goals?We hope to locate a new dairy that we can conduct sampling at that is less affected by the covid-19 pandemic and proceed with our experiment. We are also writing a manuscript for submission on the role of corona virus on BRD in cattle.
Impacts
What was accomplished under these goals?
A USDA-NIFA funded proposal (PD Seabury and Co-PD Neibergs) was continued (and then interrupted due to covid) to identify pathogen profiles and loci associated with enhanced resistance to BRD in 1000 pre-weaned calves in Wisconsin. Samples on approximately 150 calves were collected prior to cessation of sample collection due to a decrease in cases, and lack of personnel on the dairy.Bacteriology and virology will be used to identify pathogen profiles from mid-nasal and deep pharyngeal swabs and Illumina BovineHD BeadChips will be used for genotyping. Genome-wide association results will be compared with previous results in pre-weaned dairy calves in California and New Mexico. As the dairy is still under siege on keeping sufficientpersonnel to be able conduct the sampling, we are also trying to locate alternatives to the dairy in Wisconsin to continue with the study.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
R.H. Nissly, N. Zaman, P.A.S. Ibrahim, K. McDaniel, L. Lim, J.N. Kiser, I. Bird, S.K. Chothe, G.L. Bhushan, K. Vandegrift, H.L. Neibergs, S.V. Kuchipudi. Influenza C and D viral load in cattle correlates with bovine respiratory disease (BRD): Emerging role of orthomyxoviruses in the pathogenesis of BRD. 2020. Virology 551(December) 10 https://doi.org/10.1016/j.virol.2020.08.014
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2020
Citation:
H.L. Neibergs. Genomics: Host Genotype and Relevance to BRD. Animal Health Research Reviews (in press)
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Progress 10/01/18 to 09/30/19
Outputs
Target Audience:veterinarians, cattle feeders, dairyman, cow-calf producers, allied health professionals, research scientists Changes/Problems:Sampling of calves has been slower than anticipated due to a tornado that hit the ranch which disrupted animal sampling, and that fewer calves than usual are getting sick. We actually began sampling earlier than anticipated, but have now decided to wait until spring when more calves experience disease to continue sampling. What opportunities for training and professional development has the project provided?Results have been provided at two scientific meetings (Midwest Section American Society of Animal Science, and Bovine Respiratory Disease Symposium as part of the Academy of Veterinary Consultants annual meeting) and in the following college courses: Beef Production, Dairy Production, Honors Research, Agricultural Animal Health and Biology. In addition, graduate and undergraduate students have been involved in this project. How have the results been disseminated to communities of interest?See above What do you plan to do during the next reporting period to accomplish the goals?Continue with the funded proposal to genotype 1000 preweaned calves and conduct genomic analyses to validate loci and identify causal mutations for genomic selection.
Impacts
What was accomplished under these goals?
A USDA-NIFA funded proposal (PD Seabury and Co-PD Neibergs) was initiated to identify pathogen profiles and loci associated with enhanced resistance to BRD in 1000 pre-weaned calves in Wisconsin. Bacteriology and virology will be used to identify pathogen profiles from mid-nasal and deep pharyngeal swabs and Illumina BovineHD BeadChips will be used for genotyping. Genome-wide association results will be compared with previous results in pre-weaned dairy calves in California and New Mexico.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
2. J.N. Kiser, M.A. Cornmesser, R. Blackburn, S.M. McGuirk, J.F. Taylor, C.M. Seabury, J.E. Womack, the Bovine Respiratory Disease Complex Coordinated Agricultural Project Research Team, H.L. Neibergs. Validated loci associated with bovine respiratory disease complex in pre-weaned Holstein calves. Animal Genetics https://doi.org/10.1111/age.12878
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
4. J.L. Hoff, J.E. Decker, R.D. Schnabel, C.M. Seabury, H.L. Neibergs, J.F. Taylor. 2019. QTL-mapping and genomic prediction for bovine respiratory disease in U.S. Holsteins using sequence imputation and feature selection. BMC Genomics 20:555 https://doi.org/10.1186/s12864-019-5941-5
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
8. M. Neupane, J.N. Kiser, the Bovine Respiratory Disease Complex Coordinated Agricultural Project Research Team, H.L. Neibergs. 2018. Gene set enrichment analysis of SNP data (GSEA-SNP) in dairy and beef cattle with bovine respiratory disease. Animal Genetics http://dx.doi.org/10.1111/age.12718
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2020
Citation:
H.L. Neibergs. 2019. Genomics: Host Genotype and Relevance to BRD. Animal Health Research Reviews.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
H.L. Neibergs, J.N. Kiser, M. Neupane, C.M. Seabury, J.F. Taylor, M.A. Cornmesser, S. McGuirk, R. Blackburn, BRD Consortium, J.E. Womack. 2018. Genome-wide association analysis identifies QTL associated with clinical and sub-clinical bovine respiratory disease. Midwest Section American Society of Animal Science, Omaha, Nebraska.
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Progress 10/01/17 to 09/30/18
Outputs
Target Audience:Cattle producers, scientists, veterinarians, allied health care professionals. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A graduate student used this as partial completion for his PhD dissertation. How have the results been disseminated to communities of interest?Published in a journal and work was also presented at a regional (midwest section) American Society of Animal Sciene meeting and at the Washington State Cattlemen's Association meeting. What do you plan to do during the next reporting period to accomplish the goals?We hope to secure funding to expand our studies to a new population in the midwest.
Impacts
What was accomplished under these goals?
An Igenuity Pathway Analysis and Gene Set Enrichment Analysis was conducted to identify gene sets, leading edge genes and upstream regulators associated with BRD in pre-weaned dairy calves and beef feedlot cattle. Holstein calves were sampled from commercial calf raising facilities in California (1003 cases and 1011 controls) and New Mexico (376 cases and 372 controls). Commercial feedlot cattle were sampled from Colorado (500 cases and 499 controls) and Washington (504 cases and 497 controls). There were 102 and 237 unique leading edge genes identified in the dairy calf and beef cattle populations respectively. Six leading?edge genes (ADIPOQ, HTR2A, MIF, PDE6G, PRDX3 and SNCA) were associated with BRD in both dairy and beef cattle. Network analysis identified glucose as the most influential upstream regulator in dairy cattle, whereas in beef cattle, TNF was the most influential upstream regulator. The genes, gene sets and upstream regulators associated with BRD have common functions associated with immunity, inflammation and pulmonary disease and provide insights into the mechanisms that are critical to BRD susceptibility in cattle.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
M. Neupane, J.N. Kiser, the Bovine Respiratory Disease Complex Coordinated Agricultural Project Research Team, H.L. Neibergs. 2018. Gene set enrichment analysis of SNP data (GSEA-SNP) in dairy and beef cattle with bovine respiratory disease. Animal Genetics http://dx.doi.org/10.1111/age.12718
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Progress 10/27/16 to 09/30/17
Outputs
Target Audience:Target audiences include beef and dairy producers; veterinarians; associated animal health professionals including companies selling vaccines, BRD treatments and genotyping services; dairy and beef breed associations; artificial insemination companies; and schools of higher education where new approaches to reduce BRD are taught. Changes/Problems:The CAP has now been completed so further work will need to be supported by additional funding. What opportunities for training and professional development has the project provided?To date, three post-docs, two graduate students and numerous undergraduates have completed work on this study. How have the results been disseminated to communities of interest?Yes. Two publications have been published and one is submitted. Several presentations (5)have also been given as outlined in "Products" as well as using this information in two courses that I teach. What do you plan to do during the next reporting period to accomplish the goals?There is currently a proposal submitted to further address the goals of this multi-state project.
Impacts
What was accomplished under these goals?
Change in Knowledge has resulted from our study. It was not anticipated that the prevalence of pathogens would vary so greatly in different geographic regions in the Western United States in pre-weaned dairy calves. These differences then affected the loci associated with BRD susceptibility in the different locations, as the pathogens responsible for BRD differed. In addition, we have recently validated several loci associated with BRD in dairy calves from a new population in Wisconsin. In beef cattle, pathogen frequency was similar across geographic regions in the Western United States and so the loci associated with susceptibility to BRD were more consistent. The loci identified as associated with susceptibility to BRD are all unique and many are responsible for a good portion of the genetic variation seen in BRD. We have also completed an analysis on subclinical BRD by evaluating lung lesions and this work has been published. This knowledge allows the development of genotyping assays for these loci that can be incorporated into selection indexes that will facilitate the selection of cattle that are less likely to succumb to BRD. Selection for loci that reduce the susceptibility to BRD will result in the decline of the disease, a reduction in the use of antibiotics, added food security, and an improvement in animal well-being.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
J.N. Kiser, T.E. Lawrence, M. Neupane, C.M. Seabury, J.F. Taylor, J. E. Womack, the Bovine Respiratory Disease Complex Coordinated Agricultural Project Research Team, H.L. Neibergs. 2017. Rapid Communications: Subclinical bovine respiratory disease loci and pathogens associated with lung lesions in feedlot cattle. Journal Animal Science 95(3):1080-1091. Doi:10.2527/jas.2016.1152
- Type:
Other
Status:
Published
Year Published:
2017
Citation:
Moore, D.A., H.L. Neibergs. 2017. Dairy genomics research update: New aspects of selection for health and fertility Progressive Dairyman August 25, 14:44-45
- Type:
Journal Articles
Status:
Submitted
Year Published:
2017
Citation:
J.N. Kiser, M.A. Cornmesser, R. Blackburn, S.M. McGuirk, J.F. Taylor, C.M. Seabury, J.E. Womack, the Bovine Respiratory Disease Complex Coordinated Agricultural Project Research Team, H.L. Neibergs. Validating loci associated with bovine respiratory disease complex in pre-weaned Holstein calves. Animal Genetics
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