Source: TEXAS A&M UNIVERSITY submitted to NRP
INTEGRATED PROGRAM FOR REDUCING BOVINE RESPIRATORY DISEASE COMPLEX IN BEEF AND DAIRY CATTLE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0224994
Grant No.
2011-68004-30367
Cumulative Award Amt.
$9,750,000.00
Proposal No.
2015-03333
Multistate No.
(N/A)
Project Start Date
Apr 15, 2011
Project End Date
Apr 14, 2017
Grant Year
2015
Program Code
[A5111]- Global Food Security: Minimizing Losses from Dairy Diseases with Major Impact on Production, Marketing, and/or Trade
Recipient Organization
TEXAS A&M UNIVERSITY
750 AGRONOMY RD STE 2701
COLLEGE STATION,TX 77843-0001
Performing Department
Veterinary Pathobiology
Non Technical Summary
Bovine respiratory disease (BRD) is the leading natural cause of death in beef and dairy cattle, causing annual losses of more than one million animals and $692 million. The objective of this multi-institutional CAP is to fully capitalize on recent advances in genomics to reduce the prevalence of BRD in beef and dairy cattle. The research component of this proposal will identify genetic loci and genomic rearrangements associated with BRD, and use these data to develop BRD diagnostic tests and SNP-based selection tools to identify BRD-resistant animals. Incorporating BRD into genetic evaluations and selection decisions offers a sustainable approach to reduce disease incidence. Selection for resistant animals will ultimately result in improved welfare, reduced antibiotic use and handling costs, superior production efficiency, and improved profitability. The extension component will employ Advisory panel guidance to develop a sustained effort to disseminate, demonstrate, evaluate and document the impact of a range of educational outreach materials and best management practices for beef and dairy cattle producers, and feedlot personnel. The education component will develop undergraduate courses, and offer educational and research internships to cultivate a future human resource for continued reduction in BRD prevalence. 4-H youth will be exposed to approaches to minimize BRD though participation in educational games and instruction. All educational and outreach materials will be integrated into eXtension to ensure their continued accessibility. Newly-available genomics tools offer an innovative approach to reduce BRD incidence which is much-needed given increasing public concern regarding animal welfare and traditional therapeutic treatments of disease.
Animal Health Component
10%
Research Effort Categories
Basic
90%
Applied
10%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3033310108015%
3033410108015%
3043310108010%
3043410108010%
3113310108025%
3113410108025%
Knowledge Area
303 - Genetic Improvement of Animals; 311 - Animal Diseases; 304 - Animal Genome;

Subject Of Investigation
3310 - Beef cattle, live animal; 3410 - Dairy cattle, live animal;

Field Of Science
1080 - Genetics;
Goals / Objectives
The long-term goal is to reduce the prevalence of BRD in beef and dairy cattle while improving the welfare of the animals and the profitability of the industry. The research objective of this proposal is to identify genetic loci associated with BRD and use these to develop SNP-based selection tools and diagnostic tests which, in combination with changes in disease management, will decrease the economic and animal welfare problems caused by BRD. The extension objectives of this CAP are to develop, demonstrate, disseminate and document the impact of a range of educational materials and programs for beef and dairy cattle producers and feedlot personnel outlining practical methods to reduce the prevalence of BRD by implementing best management practices. The education objectives are to develop and offer distance and experiential multidisciplinary learning opportunities for undergraduate, graduate and veterinary students in approaches to reduce the prevalence of BRD.
Project Methods
Molecular genotyping and clinical diagnostics will be used to identify genomic regions (loci) associated with BRD resistance/susceptibility in beef and dairy cattle. Genome-wide association studies using single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) will be employed to identify loci associated with BRD resistance. These studies will be in parallel with RNA sequnecing to determine transcriptional profiles of animals with specific pathogens and metagenomic studies to identify pathogens associated with different SNPs and biological pathways specific to the host animals. Genomic estimates of breeding values for resistance to BRD will be developed, along with a genetic screening panel to identify animals with high values. A BRD diagnostic chip will be developed based on identifier sequences from all known pathogens. Our extension goals will be achieved through integrated networks of producers, industry, veterinarians, resarchers, and students involved in the research trials. We will contribute new content to the eXtension Beef Cattle Community of Practice. The economic cost of BRD to dairies and feedlots will be determined along with the development of stochastic bio-economic models for comparisons among alternative strategies. The GAMS modeling tool will be used. Education goals will be achieved through the development of a nationally accessible distance-learning course on the integration of animal health management with genomic and animal breeding approaches to reduce livestock disease. Veterinary feedlot and dairy internship programs will be developed at the Texas and California instutions in collaboration with feedlot and dairy operations in those states. Graduate and undergraduate students will be supported to attend extension and research activities and a 4-H curriculum built around BRD will be developed.

Progress 04/15/11 to 04/14/17

Outputs
Target Audience:The RESEARCH component targets the scientific community involved in genomics and animal health in general and Bovine Respiratory Disease in particular. The EXTENSION component targets all aspects of the beef and dairy industries in which BRD is an issue. The EDUCATION component targets students and idustry trainees in genomics and animal healtlh. Changes/Problems:Objective 2 in RESEARCH was dropped in order to put more emphasis on discovery of genetic variation underlying host resistance/susceptibility to BRD. This was done on advisement of the Advisory Board. The online host of courses in Objective 2 of EDUCATION was changed, also on advice of the Advisory Board. What opportunities for training and professional development has the project provided?In addition to the specific trainees reported under EDUCATION above, 12 graduate students and 4 postdocs have worked with PI's in the RESEARCH component. One postdoc has worked extensively in EXTENSION along with other part-time postdoctoral and graduate trainees. Large numbers of industry personnel have been trained in both the EDUCATION and EXTENSION programs as described under accomplishments above. How have the results been disseminated to communities of interest?Results have been disseminated to the scientific community through peer reviewed publications and conference presentations. Dissemination to industry personnel and other stake holders has been through numerous presentations using a variety of media sources as described under accomplishments above. The website developed at UC Davis, brdcomplex.org, contains a complete file of materials that have been produced through this CAP, including high quality videos, brochures, pamphlets, posters and scientific publications. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? RESEARCH Objective 1. We identified genomic regions associated with BRD resistance/susceptibility in beef and dairy cattle. Genome-wide association analysis (GWAA) was used to identify regions with major effects on BRD susceptibility using case-control and health score phenotypes in beef and dairy cattle. Gene set enrichment analyses using SNPs(GSEA-SNP) were used to identify genes that work together for a major effect. Whole genome sequencing (WGS) was used to identify putative causal DNA variants underlying QTL and dense SNP assays were used to further identify SNPs predictive of BRD susceptibility. We challenged cattle withpathogens to determine which genes responded by differential expression. Dairy cattle used were pre-weaned calves from CA and NMand beef animals were from feedlotss in CO and WA. GWAA was done with both case-control and health score phenotypes and genotyping with Illumina BovineHD chips. Four statistical approaches were employed. Heritability estimates for BRD were from .21 in single populations to .13 in combined populations. Both beef and dairy studies identified >300 BRD associated SNPs representing > 100 genomic regions. Several dozen strong QTL overlapping animal populations and statistical approaches were identified.Lung score QTL were also identified. GSEA-SNP revealed more than 100leading edge genes associated with BRD in the enriched gene sets. Six leading edge gene sets were shared between dairy and beef populations. RNA sequencing of bronchial lymph node transcriptomes of challenged cattle identified 142 differentially expressed genes previously identified in the dairy GWAA. Whole genome sequencingincluded 59 animals to identify DNA sequence variants underlying QTL identified by GWAA,GSEA and the challenge study. More than 28,000 SNPsfrom the dairy study were put on the GeneSeek GGP F250 BeadChip. GWAA data from both the dairy and beef populations are currently being used on a refined chip with 7000 SNPs and indels to produce a more robust marker panel. Objective 2. Identify novel pathogens present in animals with BRD and development of a diagnostic test. Abandoned on the advice of the AB. Objective 3. We assessed how animal welfare is affected by BRD in cattle. Morbidity response was quantified using animals challenged with BRD pathogens. Behavioral phenotypes were compared and reported. A study using naturally occurring BRD was done ina feed yard. This allowed comparison to the challenge-based models and addresses the feasibility/efficacy of using behavioral as an early indicator of BRD. Objective 4. We developed genomic estimates of breeding values for susceptibility to BRDC. These genomic predictions will provide a means for selection to enhance host resistance at the herd level for BRD. TheCDCB is considering including BRD into the Lifetime Net Merit prediction. EXTENSION Objective 1. We organized annual Advisory Board face-to-face meetings and BRD research conferences. The extension team organized 5 face-to-face advisory board meetings and 4 progress meetings. A BRD research conference was held in 2014 in Denver, involving more than 300 participants from 35 states and 10 countries. A BRD Symposium was held in 2015 in New Orleans and another symposium was held in 2016 in Salt Lake City. Objective 2. We utilized existing extension networks to integrate producers, industry, veterinarians, researchers, graduate and veterinary students into the conducting and interpreting of the research trials. A BRD pathogen challenge trial provided hands on research opportunities for graduate, undergraduate and veterinary students and interns. A website, brdcomplex.org, was developed to house BRD-related materials produced by this grant. Objective 3. We enhanced the eXtension Beef Cattle Community of Practice (CoP) by contributing new content, increasing membership in the CoP, and creating a cross-disciplinary partnership with DAIReXNET in the area of BRD research and outreach. In 2015, eBEEF.org was launched as part of the Beef Genetics and Genomics CoP in eXtension.This group has produced 32 FAQ videos, 27 fact sheets and 4 newsletters.This will serve as a repository for materials createdby beef-related CAP grants at conclusion. A Beef Improvement Federation (BIF) task force evaluated aset of guidelines for BRD scoring that can be used in industryto accomodate genetic evaluation. Objective 4. We developed community-based programming and work with county-based local extension agents (farm advisors) to identify farms/ranches/managers (beef, dairy, and feedlot) interested in participating in an evaluation of their BRD management practices. A WSU team developed a modular curriculum addressing best management practices (BMPs) for the prevention of BRD as part of a grant that leveraged BRD-CAP funding. These efforts produced a series of 11 fact sheets and SOP development and SPA worksheets. On-farm risk assessments were completed and an interactive online risk assessment tool was developed and is available on the BRD CAP website. Objective 5. We determined the economic cost of BRD to dairies and feedlots and develop stochastic bio-economic models for the net cost-benefit of implementing strategies for reducing the prevalence and severity of BRD. The economic cost of BRDC prevalence was estimated in the study's test populations for dairy calves and feedlot animals. BRDC losses included mortality, treatment, and lost productivity. This analysis identified that dairy calf production net margins could be increased by up to 16% by reducing BRDC incidence to 0.05. The average loss in value of a BRDC case in feed yards compared to controls was determined to be $253.97. Objective 6. We developed and delivered educational programs on best management practices for integrated and economically sustainable animal health management, genomic, and animal breeding approaches to reduce BRD. Six video episodes of NCBA's Cattlemen to Cattlemen have aired. Outcomes from the BRD CAP have resulted in 33 journal publications, 76 presentations, 33 abstracts, 16 posters, and 72 media articles. Team members and collaborators have given presentations at meetings and conferences throughout the US and internationally. EDUCATION Objective 1. We developed a nationally accessible distance-learning course on the integration of animal health management with genomic and animal breeding approaches to reduce livestock disease (i.e., two courses; 1) Genetic improvement of BRD resistance, and 2) Animal health and genetic approaches to disease). Courses were offered as partial semester courses for 1-hour of graduate level credit and through the CSU Online program (https://www.online.colostate.edu) (approved by the A.B.) Objective 2. We developed an undergraduate summer research internship program, with an emphasis on students from minority-serving institutions, to expose and train them in multidisciplinary integrated research to reduce BRD prevalence.This objective was accomplished by : 1) participation of students at the research locations and 2) participation of students that extended beyond the initial activities of the Southern Great Plains Dairy Consortium for Teaching. Objective 3. We developed a veterinary feedlot and dairy internship program (3 month and 12 month opportunities). Two students participated in these activities and produced publications. Objective 4. We sponsored graduate and undergraduate students to attend the Southern Great Plains Dairy Consortium where extension and research activities was ongoing. Eight students were funded to attend this undergraduate educational program of large dairy herd management in each year of the CAP. Objective 5. A 4-H curriculum will be developed to expose and train youth on animal disease using BRD as an example application. Fact sheets were developed on biosecurity practices and on BRD as a contagious disease to help youth and 4-H leaders understand BRD and its treatment protocol.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Love, W.J., Lehenbauer, T.W., Karle, B.M., Hulbert, L.E., Anderson, R.J., Van Eenennaam, A.L., Farver, T.B., Aly, S.S. 2016. Survey of management practices related to bovine respiratory disease in preweaned calves on California dairies, Journal of Dairy Science, 99(2): 1483-1494.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Love, W.J., Lehenbauer, T.W., Van Eenennaam, A.L., Drake, C.M., Kass, P.H., Farver, T.B., Aly, S.S. 2016. Sensitivity and Specificity of On-Farm Scoring Systems and Nasal Culture to Detect Bovine Respiratory Disease Complex in Pre-weaned Dairy Calves. Journal of Veterinary Diagnostic Investigation 28(2): 119-128.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Toaff-Rosenstein, R., Gershwin, L.J., Zanella, A.J., Tucker, C.B. 2016. The sickness response in steers with induced bovine respiratory disease before and after treatment with a non-steroidal anti-inflammatory drug. Applied Animal Behavior 181:49-62.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Toaff-Rosenstein, R.L., Gershwin, L.J., Tucker, C.B. 2016. Fever, feeding and grooming behaviour around peak clinical signs in bovine respiratory disease. Journal of Animal Science 94(9):3918-3932.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Buchanan, J.W., MacNeil, M.D., Raymond, R.C., McClain, A.R., Van Eenennaam, A.L. 2016. Variance component estimates for Charolais-sired fed cattle and relative economic impact of bovine respiratory disease. Journal of Animal Science 94:5456-5460.
  • Type: Journal Articles Status: Accepted Year Published: 2017 Citation: Toaff-Rosenstein, R.L., M. Velez and C.B. Tucker. 2017. Heifer use of an automated grooming brush and potential for radiofrequency identification-based measurements of this behaviour. Journal of Dairy Science. Accepted.


Progress 04/15/14 to 04/14/15

Outputs
Target Audience:This project has a diverse target audience, including scientists interested in host response to pathogens and bovine respiratory disease and dairy and beef producers interested in genetic predictions and marker assisted selection. Animal health professionals will be educated in the use of genetics to improve heard health and the relationship of host genetics to infectious diseases. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?In addition to undergrads, graduate students and post-docs directly funded by this CAP, a large number of trainees have been exposed to the principles of genetics and disease and the data generated by this project. Presentations and posters at scientific meetings touch a large number of young scientists. Our database, housed at UC Davis is accessed by a large number of students, in addition to members at all levels of the beef and dairy industries. How have the results been disseminated to communities of interest?This is addressed in our Extension and Education accomplishments above. What do you plan to do during the next reporting period to accomplish the goals?Our goal for the final year is to facilitate the translation of our research to the dairy and beef industries. This will be accomplished through the production of genetic tools revealing important genotypes and the distribution of information to our target audiences.

Impacts
What was accomplished under these goals? Research Accomplishments. We completed the binary GWAS for dairy cattle and identified candidate genes as described in a publication cited in this report. We have also completed GWAS with the additive phenotype of clinical scores. There is considerable overlap between QTL signals across the two BRDC phenotypes. The new analyses uncover many moderate to large effect QTL and several new biologically meaningful candidate genes known to be involved in pathogen entry or immune related functions. We have made strides on the imputation of dairy genotypes to whole genome sequening with the 1000 bull project and provided evidence of our ability to impute genotypes. Imputation of genotypic data for beef cattle from beef cattle sequence has accuracies of approximately 85%. However, the use of beef and dairy breeds for imputation of 778K data to genomic SNPs for Holstein falls to 78%. This drop in accuracy is the result of incoirporating genome level diversity from variants in beef breeds that is not present in Holstein cattle. We analyzed GWAS in a Mixed Linear Model on imputed genomic SNPs for our CA preweaned Holstein calves using the binary phenotype. The analysis confirms most of the 778K results including the identification of PVRL1 on chromosome 15 as a strong candidate gene but also identified a second large-effect immune-related locus on chromosome 27. As mentioned in the last report, beef cattle were experimentally challenged with individual BRDC pathogens and lymph nodes were obtained and used with RNAseq. These expression analyses provided validation for many of the candidate genes identificed in our GWAS results. BRDC pathogen profiles revealed differences in geography and dairy management practices. Inclusion of diagnostic pathogen data in our mixed model analyses nearly always resulted in larger heritability estimates. Extension Accomplishments. In addition to peer-reviewed papers cited in this report, 11 oral presentations and 6 posters were presented at scientific, producer, and practicioner gatherings, most of them resulting in published abstracts. A major focus of the extension program was in media where 39 programs were produced and presented. Examples include an AgWeb eBEEF site dedicated to beef cattle genetics and other eBEEF YouTube videos. Dr. Van Eenennaam has become an internationally recognized spokesperson for genetics and BRD at all levels, from feedlot and dairy managers to research scientists. We held a BRD symposium in conjuction with the AABP annual meeting in September, 2015. A BIF task force was created to evaluate a standardized set of practical guidelines for BRD scoring that could be used in industry herds with the data to be used for genetic evalustion. This committee includes four members from this CAP. We have made progress in determining the economic cost of BRD to dairies and feedlots and developing models for implementing strategies for reducing the prevalence and severity of the disease. Dr. Shannon Neibergs has headed this effort and presented data and several meetings and conferences. Education Accomplishments. We continue to participate in the Southern Great Plains Dairy Consortium and have developed two on-line graduate courses in breeding and genetics at Colorado State University and are continuing efforts to geographically expand the use of these courses.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Love WJ, Lehenbauer TW, Karle BM, Lindsey E, Hulbert LE, Randall AJ, Van Eenennaam AL, Farver TB and Aly SS (2015). Survey of management practices related to bovine respiratory disease in preweaned calves on California dairies, Journal of Dairy Science, http://dx.doi.org/10.3168/jds.2015-9394
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ng TF, Kondov N, Deng X, Van Eenennaam A, Neibergs HL, Delwart E. (2015). Viruses associated with bovine respiratory disease identified using metagenomics and a case-control study. Journal Virology, doi:10.1128/JVI.00064-15.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Tizioto PC, Coutinho LL, Decker JE, Schnabel RD, Rosa KO, Oliveira PSN, Souza MM, Mour�o GB, Tullio RR, Chaves AS, Lanna DPD, Zerlotini Neto A, Mudadu MA, Taylor JF and Regitano LCA (2015). Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes. BMC Genomics, 16:242.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bickhart DM, Hutchison JL, Xu L, Schnabel RD, Taylor JF, Reecy JM, Schroeder S, Van Tassell CP, Sonstegard TS, and Liu GE (2015). RAPTR-SV: a hybrid method for the detection of structural variants. Bioinformatics, 31:2084-90.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Chen J, Huddleston J, Buckley RM, Malig M, Lawhon SD, Skow LC, Lee MO, Eichler EE, Andersson L and Womack JE. Bovine NK-lysin (2015). Copy number variation and functional diversification. PNAS;112(52):E7223-7229.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bickhart DM, Xu L, Hutchison JL, Cole JB, Null DJ, Schroeder SG, Song J, Garcia JF, Sonstegard TS, Van Tassell CP, Schnabel RD, Taylor JF, Lewin HA, and Liu GE (2016). Diversity and population-genetic properties of copy number variations and multicopy genes in cattle. DNA Res 2016:1-10.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Decker JE, Taylor JF, Kantanen J, Millbrooke A, Schnabel RD, Alexander LA and MacNeil MD (2016). Origins of cattle on Chirikof Island, Alaska, elucidated from genome-wide SNP genotypes. Heredity Feb 10. doi: 10.1038/hdy.2016.7.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Whitacre LK, Tizioto PC, Kim JW, Sonstegard TS, Schroeder SG, Alexander LJ, Medrano JF, Schnabel RD, Taylor JF and Decker JE (2015). Whats in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual. BMC Genomics 16:1114.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Gershwin LJ, Van Eenennaam AL, Anderson ML, McEligot HA, Shao MX, Toaff-Rosenstein R, Taylor JF, Neibergs HL, Womack J and the Bovine Respiratory Disease Complex Coordinated Agricultural Project Research Team (2015). Single pathogen challenge with agents of the Bovine Respiratory Disease Complex. PLoS One 10:e0142479.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Tizioto PC, Kim JW, Seabury CM, Schnabel RD, Gershwin LJ, Van Eenennaam AL, Toaff-Rosenstein R, Neibergs HL, Bovine Respiratory Disease Complex Coordinated Agricultural Project Research Team and Taylor JF (2015). Immunological Response to Single Pathogen Challenge with Agents of the Bovine Respiratory Disease Complex: An RNA-sequence analysis of the bronchial lymph node transcriptome. PLoS One 10:e0131459.


Progress 04/15/13 to 04/14/14

Outputs
Target Audience: This project has a diverse target audience. Scientists interested in genetics of host response to pathogens, particularly those involved in the BRD complex, will be informed of specific chromosomal locations of genes influencing the sensitivity of individual animals to BRD. Both dairy and beef producers will be given access to Marker Assisted Selection technology to identify animals with combinations of genes for resistance or susceptibility to the disease. Animal health professionals will be educated in the use of genetic markers to improve heard health and in the relationship of host genetics to other factors influencing this and other infectious diseases. Changes/Problems: No problems or challenges were encountered. What opportunities for training and professional development has the project provided? Five abstracts submitted; three posters and a 40 minute oral presentation given at 2014 International Plant and Animal Genome and a poster presentation at the Impact of Large-Scale Genomic Data on Statistical and Quantitative Genetics Conference. Repository and databases are available for the research community and have been accessed by researchers outside of the BRD consortium. Integration of disciplines (microbiology, virology, veterinary epidemiology, genetics, dairy industry, extension) to successfully conduct the study have been established. Biweekly research conference calls have facilitated the interaction of the PDs. We obtained a $10,000 NIFA conference grant for Bovine Respiratory Disease Symposium (BRDS) 2014: New Approaches to Bovine Respiratory Disease Prevention, Management and Diagnosis to be held at the Renaissance Denver Hotel in Denver, Colorado, USA from July 30th to July 31st, 2014. Washington State University Beef Team leveraged BRD CAP educational materials to obtain a $51,954 grant from the Western Center for Risk Management Education at Washington State University grant program entitled "Delivery and Evaluation of the BRD Curriculum and On?farm assessments of BRD Risks". Impacts of the Education component included developing infrastructure and materials for delivery of BRD research findings to students and making the course accessible to the public. Students from URM demographics were provided opportunities for learning about agricultural research. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? GWAS: The initial case-control genome-wide association analysis study (GWAS) has been completed by three labs (Jerry Taylor, University of Missouri (MU); Chris Seabury, Texas A&M University (TAMU); and Zeping Wang, Andrzej Wojtowicz, and Holly Neibergs, Washington State University (WSU)) using four analytical approaches. These approaches included: Efficient Mixed-Model Association eXpedited (EMMAX, Kang et al. 2007), full versus reduced model logistic (FvR) regression using principle component analysis-corrected input data within SNP & Variation Suite 7 (Golden Helix, Bozeman, MT), genomic best linear unbiased prediction (GBLUP) and PLINK (Purcell et al. 2007). Many overlapping regions of association were identified with the four analyses and the results have been presented at the Plant and Animal Genome meeting (January 2014) and the Brown Bagger Webinar series through the National Beef Cattle Evaluation Consortium. In summary, 324 significant SNPs and 116 significant regions were shared (1 to 20 SNPs defined each region) across all four analyses when the top 2000 SNPs were compared from each of the four analyses in the combined populations. When only the New Mexico population was evaluated with the top 2000 SNPs across all four analyses, 370 significant SNPs and 138 significant regions were shared with 1 to 18 SNPs defining each region. When only the California population was evaluated, 373 significant SNPs and 126 significant regions were shared with 1 to 29 SNPs defining each region. The consistency of the results across these analyses provides strong evidence of the reliability and repeatability of the approaches. Several candidate genes underlie the genomic regions associated with BRDC that are shared across all analyses and across all populations. These include receptors for known pathogens of BRDC, genes responsible for severe acute respiratory syndrome and acute respiratory distress syndrome in humans and genes involved in the immune response. Heritabilities for BRDC susceptibility were consistently estimated at 19-21% for the individual populations and 13% when the California and New Mexico populations were combined. The differences in these heritability estimates is postulated to be due to the differences in pathogens present in California and in New Mexico (Table 1). When the populations are combined, the divergence in pathogens along with the disparity in numbers between California and New Mexico reduced the additive genetic variance that was explained. As more non-genetic (environmental) variance is present, less variance will be explained by additive genetic variation or heritability of BRDC. GSEA: Several databases were evaluated as a source of pathways to analyze for the GSEA. Bos taurus gene sets sourced from GO, KEGG, Panther, Reactome, and Metacyc were chosen. Gene sets with fewer than 10 and greater than 200 SNPs were excluded from the analysis as well as gene sets that contained at least 80% redundancy. A total of 19,598 bovine genes were mapped within gene sets. The null distribution of the GSEA test statistic was approximated using 10,000 permutations. Results for the case-control analysis identified four gene sets (GO:0045637 - regulation of myeloid cell differentiation, BTA00620 - pyruvate metabolism, GO:0002761 - regulation of myeloid leukocyte differentiation, BTA00010 - glycolysis/gluconeogenesis) that were found to be associated with susceptibility to BRDC (FDR<0.25). These pathways include 249 unique genes; 89 of which contributed to an increase in the GSEA test statistic and represent putative functional candidate genes involved in BRD susceptibility. Beef Study. The initial study conducted at JBS Five Rivers feed yard in Greeley, Colorado was completed in August of 2013. Closeout data became available in November 2013. All samples have been processed, data entered and stored (Holly Neibergs, WSU). Carcass data were collected by Ty Lawrence (West Texas A&M) and by camera at the processing plant. The 1000 beef animals will be genotyped upon entry of fiscal year 4 when additional funds are available. Economic analysis is underway (Shannon Neibergs, WSU) from the data provided by both JBS and Cactus Feeders to identify the cost of BRDC in finishing operations. JBS had originally agreed to provide 2000 samples to the project but the study collection became a hardship for them and so it was curtailed at 1000 samples. A second feed yard was immediately recruited for sample ascertainment by WSU. This operation is in Warden, Washington and is owned by AgriBeef. The cattle in the yard are all Bos taurus and many originate from Canada. As with JBS, AgriBeef is vertically integrated and has a processing facility not far from their finishing facility. This will allow us to identify differences (if any) of carcass yield or quality in cattle that were affected with BRDC. To date, only about 20 samples have been received. The extension component of the BRD CAP progress included delivering two episodes of Cattlemen-to-Cattlemen which aired on September 24th and October 15th, 2013, coordinating the development of a committee to plan a conference entitled Bovine Respiratory Disease Symposium (BRDS) 2014: New Approaches to Bovine Respiratory Disease Prevention, Management and Diagnosis to be held in collaboration with NC1192 and AVC at the Renaissance Denver Hotel in Denver, Colorado, USA from July 30th to July 31st, 2014 in conjunction with the 2014 Summer Academy of Veterinary Consultants (AVC) meeting, the continued refinement of the BRD CAP website (http://BRDComplex.org), the initiation of efforts to develop an extension team to overhaul the beef cattle CoP site on breeding and genetics to include extension and producer decision support tools from AFRI-sponsored cattle genetics grants (http://www.extension.org/category/beef_breeding_and_genetics), posting of 10 fact sheets on reducing the incidence of BRD for beef cow-calf operators by WSU beef team on the beef eXtension CoP and successful leveraging by the WSU team to obtain a $51,954 grant entitled "Delivery and Evaluation of the BRD Curriculum and On?farm assessments of BRD Risks" from the Western Center for Risk Management Education, continuing collaboration with California researchers on the "Risk Assessment, welfare analysis, and extension education for dairy calf respiratory disease management in California" to develop a novel clinical scoring system for on-farm diagnosis of bovine respiratory disease in pre-weaned dairy calves, the establishment of a collaborative research agreement with a large integrated cattle firm to analyze phenotypes and DNA samples on 9,000 animals in its feedlot for a three year period as part of community-based programing demonstrating how genomic information might be integrated into a beef cattle operation; team members have given presentations at meetings and conferences including American Society of Animal Science (ASAS), Plant and Animal Genome (PAG) Conference, and the National Institute for Animal Agriculture Annual (NIAA) Conference. A full listing of presentations, papers, abstracts, papers and press is included at the end of this section and is also available at http://www.brdcomplex.org). The educational component of this CAP is greatly assisted because its' activities are organized with infrastructure collaborating programs. Specifically: Teaching component of the Southern Great Plains Dairy Consortium-Teaching (SGPDC-T; http://sgpdct.tamu.edu/), and Breeding and Genetics Graduate Education Online, (http://enbgeo.iddl.vt.edu). Program has new title of: Engaging the New Biology, Breeding and Genetics Education On-line.

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Taylor, J.F. (2013). Implementation and accuracy of genomic selection. Aquaculture http://dx.doi.org/10.1016/j.aquaculture.2013.02.017
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Chapple, R.H. Tizioto, P.C., Wells, K.D., Givan, S.A., Kim, J., McKay, S.D., Schnabel, R.D., Taylor, J.F. (2013). Characterization of rat developmental liver transcriptome. Physiological Genomics 45(8): 301-311.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Van Eenennaam, A.L. (2013). GMOs in animal agriculture: time to consider both costs and benefits of regulatory evaluations. Journal of Animal Science and Biotechnology 4:37.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Van Eenennaam, A.L., K. A. Weigel, A. E. Young, M. A. Cleveland, and J. C. M. Dekkers (2014). Applied Animal Genomics: Results from the Field. Annual Review of Animal Biosciences. 2:105-139.


Progress 04/15/12 to 04/14/13

Outputs
Target Audience: This project has a diverse target audience. Scientists interested in genetics of host response to pathogens, particularly those involved in the BRD complex, will be informed of specific chromosomal locations of genes influencing the sensitivity of individual animals to BRD. Both dairy and beef producers will be given access to Marker Assisted Selection technology to identify animals with combinations of genes for resistance or susceptibility to the disease. Animal health professionals will be educated in the use of genetic markers to improve heard health and in the relationship of host genetics to other factors influencing this and other infectious diseases. Changes/Problems: Slower collection of calves at Clovis than expected resulted in less samples collected (763 rather than 1000) than planned. Due to the economic environment of the dairy industry, some of the 763 replacement heifers that comprise Population B have been sold to raise funds for these dairies to remain solvent. The number of heifers lost is not yet known, but all three dairies are still in operation. The loss of these heifers will impact the production data we will be able to collect on these heifers in the future. A decision was made to use feedlot cattle that were solely Bos taurus rather than Bos taurus x Bos indicus cattle. The feedlot study was then moved from Graham Cattle Company’s feedlot at Gonzalez, Texas to JBS-Five Rivers Feedlot at Greeley, Colorado. This study began in September and is ongoing. We have experienced a slower collection of feedlot animals at Colorado than expected. JBS-Five Rivers is only enrolling cattle that are source verified to assure their Bos taurus ancestry. They have also had inconsistent uploading of data collected at Colorado, so data were being entered manually at WSU from hard copy records. Solutions to move record uploading away from manual entering has been successful and will reduce the possibility for data entry errors in the future. Histophilus somni was not used as a challenge organism in 2012 due to the unanticipated inclusion of a bacterin against this organism in a clostridial vaccine that the calves received at branding. However, two animals were challenged with this pathogen in 2011 and their data will be used for the RNA-sequencing. Dr. Gershwin also has additional tissues from H. somni challenges from other studies that could be used if needed. Collection of samples across the US has not occurred pending initial metagenomics study results. Samples will be collected and processed after results are evaluated in keeping with recommendations by the Advisory Board. Population D animals (purebred feedlot bulls) were all treated with antibiotics for BRD prior to arrival in the feedlot, eliminating them from the BRD study. A second population of crossbred Bos taurus cattle has been located to replace the purebred bulls lost this year. These cattle (approximately 240) are being fed in a GrowSafe system at the University of Missouri and another lot of approximately 200 will follow after these animals have gone off test. A second source of GrowSafe cattle will also be investigated. To address geographic diversity in pathogens, the use of swabs to facilitate collection of pathogens in many locations has been suggested. The use of swabs is currently being tested through a test trial from swabs taken at Tulare and the challenge study at UCD. Small portion (8%) of nucleic acid recovered from swabs is of non-bovine origin. Optimization of extraction to obtain high quality nucleic acids has proved a challenge from the swabs but the nucleic acid has been of high quality and will be useful to identify novel pathogens. H. somni was inadvertently vaccinated for in the challenged calves thus eliminating this as a potential challenge Collection of the economic data from Population A was delayed as the producer participant was initially reluctant to provide their economic data. Issues of confidentiality and financial disclosure of an individual operation are valid concerns and were addressed with continual communication with the producer participant. The data was collected but the timing was delayed. This has delayed completing the economic reports analyzing BRD economic effects from being completed in August, 2012 to April 2013. The economic data production cost data from Population A is in hand and is being supplemented and cross validated with additional dairy calf rearing enterprise budgets currently being developed for Idaho dairies. Budget variation will be used in the sensitivity analysis to examine the economic effects of production cost and market value variance on estimating the value of improving disease resistance. Collecting dairy economic information has become increasingly sensitive as dairy profitability has been and continues to be challenged with record high feed costs and low milk prices. This sensitivity has not only be realized in this particular data collection effort but has also been encountered in other studies, for example the study Economic Impact of Washington Dairy Farms that had a reduced survey response rate to economic data questions and even in collecting financial data for the Western Region Intercollegiate Dairy Challenge competition. Data collection for Population B has been challenged. It is not known how many heifers in Population B have been sold. The number of animals sold cannot be determined until the heifers return from the growing lots to the dairies for their first lactation over the next year. It is hoped that a sufficient number have been maintained to evaluate the impact on reproductive efficiency and first lactation of positive BRD incidence versus controls. As we learn of the number impact additional cross validation data can be collected from collaborative producer herds but we will need to be careful to not confound the analysis with production records that we do not have information on disease incidence and treatment. What opportunities for training and professional development has the project provided? Undergraduate student Luis Gamboa plans to present his work on the BRD project to the UC Davis 24th Annual Undergraduate Research, Scholarship & Creative Activities Conference on April 26, 2013. The conference is designed to acquaint undergraduates with the process and academic rigors of presenting scholarly research. It enables intellectual exchange between students and faculty, while encouraging undergraduates to pursue advanced degrees and careers in research. Luis will be presenting a poster entitled “Evaluation of Serum Cortisol Levels as a Biomarker for the Early Diagnosis of Bovine Respiratory Disease” The annual program of SGPDC-T, for large herd dairy management, was held May to June, 2012. Forty students from 13 universities attended. Eight students were funded through the BRD-CAP and overall 12.5% of the students enrolled in the entire program were under-represented minority (URM; demographic other than non-hispanic white). The program was advertised in January and February through the program’s website and social media addresses. Also, e-announcements were sent to minority serving institutions sent via assistance of the American Society of Animal Science. Review and selection of students was conducted by faculty from members of the consortium. Since this program is modular, BRD information was included in the content of herd health module. This module was translational in this CAP as two veterinarians took an active role in teaching herd health as it relates to BRD. Specifically, Dr. Chris Chase (DVM/Ph.D.) from South Dakota State University taught herd health management and Dr. Gavin Kuykendall (DVM) with USDA-APHIS took an active role in teaching labs using on-farm necropsy to show the effects of BRD on calves. Dr. Kuykendall is also involved in data collection in NM. A similar approach is being applied to the module for Dairy Cattle Breeding as Dr. Chad Dechow will learn about the BRD genomics research and incorporate into module content in 2013. The SGPDC-T was enhanced in 2011 and 2012 because Eric Chavez, a program alum, was instrumental in coordinating teaching activities as well as calf sampling for research. Syllabus was developed for the first course of the On-line graduate “Genetic improvement of BRD resistance.” An M.S. student, Natalie Berge, was hired to help start the crafting of the course materials. Many trainees (n ≥ 39; undergraduate interns, graduate students, DVM student interns, postdocs and interns from high school programs) were involved in research programs in both year 1 and 2. Twenty-three percent of these trainees were URM and 8% were international. Results of the undergraduate internship program revealed great leverage for the BRD-CAP; specifically, there was funding for 6 interns in 2011 and 2012; yet 17 additional students participated through other university mechanisms. Also, those working with this educational program are strategically improving the program as per feedback from the advisory board. Specifically, they are focusing the program as per development and documentation of expected outcomes and to find ways to expand the program into curriculum of teaching students of veterinary medicine. Masters student Bryan Welly is going to work developing script and materials for the two episodes for Cattlemen to Cattlemen How have the results been disseminated to communities of interest? First Cattlemen-to-Cattlemen episode “BRD Coordinated Agricultural Project” – aired 16th October, 2012. See how the BRD Coordinated Agricultural Project is looking at new methods for fighting BRD in herds http://tinyurl.com/C2CBRDCAP All publications, presentation, abstracts, posters and press associated with this project are being compiled and made available at brdcomplex.org. Collaborators have given presentations at meetings and conferences throughout the US and internationally including American Society of Animal Science (ASAS), Animal American Association of Bovine Practitioners (AABP), Conference of Research Workers in Animal Diseases (CRWAD), Plant and Animal Genome (PAG), National Beef Cattle Evaluation Consortium (NBCEC), National Association of Animal Breeders (NAAB), AAVLD/United States Animal Health Association (USAHA), and the International Committee for Animal Recording (ICAR) meetings. What do you plan to do during the next reporting period to accomplish the goals? The initial GWAS studies have begun for both Populations A and B. Results from the two populations show some overlap in regions associated with susceptibility to BRD and some novel regions which could reflect the differences in pathogens identified between the two populations. The use of three analytical approaches has shown regions associated with BRD that are common to all of the analyses and is encouraging. Manuscripts will be submitted for publication early in year three. Complete collection of Populations C and D. Submit manuscript on: 1) challenge study, and 2) description of pathogen prevalence in Populations A and B. RNA sequencing from challenge study animals to be completed. GSEA-SNP analysis to be completed for Populations A and B. Nucleic acid extraction to be completed on all beef and dairy samples collected for the metagenomics study from NAHLN and NC1027 sources. Sequencing complete of pooled samples. Begin development of diagnostic test to identify novel pathogens. Complete analysis on behavior traits. Complete prostaglandins and cytokines analysis. Complete analysis of viral shedding. Undergraduate student Luis Gamboa plans to present his work on the BRD project to the UC Davis 24th Annual Undergraduate Research, Scholarship & Creative Activities Conference on April 26, 2013. The conference is designed to acquaint undergraduates with the process and academic rigors of presenting scholarly research. It enables intellectual exchange between students and faculty, while encouraging undergraduates to pursue advanced degrees and careers in research. Luis will be presenting a poster entitled “Evaluation of Serum Cortisol Levels as a Biomarker for the Early Diagnosis of Bovine Respiratory Disease” Masters student Bryan Welly is going to work developing script and materials for the two episodes for Cattlemen to Cattlemen The WSU beef team modular curriculum will be delivered to and evaluated by Washington cattle producers. The final curriculum will be available nationwide through the BRD CAP program. These will be made available at http://extension.wsu.edu/vetextension/brd/Pages/default.aspx and the BRD CAP website. The WSU subcontract project team has submitted a Risk Management Education Proposal to deliver the BRD curriculum to Washington cow-calf producers. A proposal task is to develop on-farm/ranch economic case evaluations of implementing BRD management actions using the NCBA Standardized Production Analysis method for cow-calf production and economic analysis. This is work that is leveraging BRD CAP Extension Aims outputs with additional efforts concerning BRD management. The WSU project team Risk Management Education proposal will be reviewed in April The AB suggested that “Commercial sequencing companies (Illumina and GeneSeek) are interested in a beef demonstration project – think of a multiuse chip, not just BRD, but incorporating information from other nationally funded genomics projects” In year 3 will refine the Simplot project and consider options for developing a multiuse chip that uses information from other nationally funded genomics projects. In response to an Advisory Board recommendations we will plan to look at the opportunity to use behavioral measures (e.g. through use of the GrowSafe system) on some of these calves as an additional phenotype to be examined to increase the accuracy of diagnosis under industry conditions. Obtaining access to this data will need to be negotiated and agreed to by all of the parties involved in this demonstration project. The dairy calf rearing budget model will be made available and BRD dairy calf economic fact sheets and Extension Bulletins will be completed April, 2013. These will be extensions and applications of the budget model. A peer review paper will be developed analyzing the effects of BRD incidence on dairy calf rearing operations using the collective data obtained. The WSU BEEF Team was selected to submit a full proposal to the Western Center for Risk Management Education for 2013 for outreach on their BRD Rick Curriculum through workshops and on-farm assessments of BRD. The project title is BRD Risk Reduction from “Bloodlines to Fencelines”. Develop the budget model and complete the initial analysis of the economic effects on Feedlot Cattle Population C. The cattle from this population are beginning to be sent to slaughter in February 2013 and will continue until all project animals are completed. The economic model will be developed with initial data and finalized upon data completion. The data collection from population C was designed to collect economic effect data from the feedlot finishing phase. That data will be used to estimate the economic cost of BRD incidence at the feedlot and in-turn the economic value of reducing BRD incidence. Proposed under Extension Aims number 5 is a bio-economic model that will include a cow-calf production phase as modeled to implement selection for BRD disease resistance. The proposed modeling framework is time dynamic to simulate BRD disease resistance selection over time and the resulting decrease in BRD incidence and improved economic return at the feedlot. The model will have to account for both calves that are weaned that go directly into a feedlot system and calves that are weaned and are placed in a stocker operation. While we don’t have direct data collection of BRD incidence impacts at the cow-calf and stocker phases in this proposed project the proposed bio-economic model can be adapted to incorporate this information as future efforts and secondary data observations are obtained. Episodes 2 and 3 of Cattlemen to Cattlemen are scheduled for Year 3. We have tentatively booked airdates of September 24 and October 15, 2013. Episode 2 will be on DNA collection and how genotyping is done, episode 3 is tentatively on low stress cattle handling in collaboration with Tom Noffsinger Continue maintaining and enhancing BRD CAP website. Develop presentations, literature and press releases about results of BRD CAP research projects and incorporate results into extension and teaching materials. Upon the advice of the advisory board, plan to meet with diagnostic lab researchers from a major cattle state to recruit them as a collaborator for the diagnostic assay component of the BRD CAP Use the calendar for organizing the SGPDC-T (May to June 22, 2013) to recruit and advertise. Advertisements posted January and February of 2013. March select the pool of candidates (i.e., ~70 applicants for 2013. A panel of 3 faculty review the applicants (Robert Hagevoort-NMSU; Bob Collier-UA, and Mike Tomaszewski-TAMU). A priority is given to students with interest large dairy herd management, upper-class status, and membership in the consortium). Submit another abstract to ASAS-ADSA teaching section regarding translation of research to teaching. Incorporate research findings into teaching program (Herd Health and Breeding modules). Trainees continue gaining experience studying BRD and genetic regulation of susceptibility. Presentations at international meetings; these will eventually lead to publications (theses/dissertations and manuscripts). Hold a forum in summer of 2013 to discuss incorporating genomics into veterinary teaching curriculum, especially as it relates to BRD. Expand direct communication for URM participation to departments of the alumni as this has proven successful in previous years.

Impacts
What was accomplished under these goals? Population A (Holstein calves at Tulare, CA) consisted of data from a total of 2015 calves that were identified as either cases (1003) or controls (1012) based on the diagnostic criteria of Sheila McGuire. The calves ranged in age from 31 days of age to approximately 63 days of age and were all housed and managed at a single 80,000 animal capacity calf ranch. Of the calves, 1260 were male and 755 were female and there were no differences in the proportion of males and females among the cases or controls. The sample collection was completed in January of 2012 and all blood samples have been processed and the DNA extracted, quantified and stored at Washington State University. An identical set of processed samples is stored at the University of Missouri. Bacteriology and virology diagnostics have been completed and a manuscript describing the study and the prevalence of the pathogens is being written by Dr. Terry Lehenbauer and colleagues at the University of California at Davis (UCD). High density Illumina genotyping was conducted at GeneSeek (Lincoln, NE) and genotype and phenotype files were merged at Washington State University (WSU). The initial case-control genome-wide association analysis study (GWAS) has been completed by three labs at the University of Missouri (MU), Texas A&M University (TAMU) and WSU using different approaches (GBLUP, SVS7 and PLINK, respectively). Many overlapping regions of association were identified with the three analyses and the results have been presented at the American Society of Animal Science meeting (July 2012), the International Plant and Animal Genome meeting (January 2013) and the Gordon Research Conference (February 2013). The GWAS will be used with alternative BRD phenotypes as well; as a quantitative trait using the clinical scores from Sheila McGuirk’s diagnostic system, and by pathogen. Common pathogens for this population include BRSV, M. hemolytica and P. multocida. Similar to Population A, samples were collected on pre-weaned Holstein heifer calves in Clovis, New Mexico and evaluated for symptoms of bovine respiratory disease. Three adjacent dairies were used for collection of samples from July of 2011 to July 1 of 2012. A total of 763 samples were collected consisting of 379 BRD cases and 384 controls based on Sheila McGuirk’s diagnostic criteria. (The objective had originally been to collect 1000 samples, but due to a slower acquisition of samples than anticipated, the collection of samples was ended after a year’s time to accommodate the following of these heifers through two lactations). All blood and diagnostic samples were processed at WSU and storage of samples has been mirrored at WSU and MU. High density Illumina genotyping has been conducted at GeneSeek. Case and control GWAS have been conducted by WSU and TAMU and is under analysis at MU. Additional GWAS will be conducted as described for Population A. Common pathogens for this population included bovine corona virus (280 calves positive), M. bovis (404), and P. multocida (442). Only 7 animals were positive for bovine viral diarrhea virus (BVDV), 28 with bovine respiratory syncytial virus (BRSV), 14 with H. somni, 58 with A. pyogenes, and 33 with M. hemolytica. The pathogens present in New Mexico were more diverse than those present in California where the only viral pathogen identified was from BRSV. GSEA-SNP combined with the RNA-sequencing gene expression data will be completed when the RNA-sequencing data is available from Population E. The extension component of the BRD CAP has achieved a number of milestones this year including the delivery of the first episode of Cattlemen-to-Cattlemen which aired on the 16th October, 2012 (http://tinyurl.com/C2CBRDCAP), the continued development and refinement of the BRD CAP website (http://BRDComplex.org), successful leveraging of the data collected in the Tulare dairy calf study to secure an additional $600,000 grant from the University of California, the development of 10 fact sheets on reducing the incidence of BRD for beef cow-calf operators, the development of an agreement with a large integrated cattle firm to collect BRD phenotypes on animals in its feedlot for a three year period as part of community based programing, the submission of a $50,000 BRD conference proposal for a 2014 BRD research symposium - written in collaboration with members from USDA CSREES Multistate Research Project NC-1192, “An Integrated Approach to the Control of Bovine Respiratory Disease”, the completion of a survey of veterinary diagnostic laboratories in the US and presentation of this information to the American Association of Veterinary Laboratory Diagnosticians (AAVLD) laboratory directors, the presence of a BRD CAP booth at the National Cattlemen’s Beef Association (NCBA) convention trade show in February 2013, and team members have given presentations at meetings and conferences throughout the US and internationally including American Society of Animal Science (ASAS), Animal American Association of Bovine Practitioners (AABP), Conference of Research Workers in Animal Diseases (CRWAD), Plant and Animal Genome (PAG), National Beef Cattle Evaluation Consortium (NBCEC), National Association of Animal Breeders (NAAB), AAVLD/United States Animal Health Association (USAHA), and the International Committee for Animal Recording (ICAR) meetings. A full listing of presentations, papers, abstracts, papers and press is included at the end of this report. and is also available at http://www.brdcomplex.org). Economic cost, revenue and production data was collected from dairy calf rearing Population A and used to develop a base budget model to analyze BRD economic effects for the dairy calf rearing production phase. Dairy calf rearing production data and budgets were developed from other sources to valid the production costs data from Population A. Data collected from the Washington State Dairy Federation Economic Impact and collaborating with the University of Idaho dairy calf rearing budget for large dairies in Southern Idaho provide comparative data on production costs and calf rates of gain in hutches were obtained. In collaboration with Dale Moore, Andy Allen and the rest of the WSU Beef Team a set BRD cow-calf curriculum fact sheets are being developed. One of the fact sheets in the set addresses the economic value of preconditioning calves on reducing BRD incidence. Washington State University Team led by Dr. Dale Moore/Andy Allen developed a modular curriculum (see 10 topics below) and a cow-calf BRD Risk Assessment tool. The value of preconditioning on reducing the incidence of BRD Nutritional Management of the Pregnant Cow for Optimal Calf Health Weaning Procedures to Reduce Stress and Minimize the Risk of BRD Feedback from Feeders on BRD Risk Effective use of Vaccinations on Cow/Calf operations to reduce the incidence of BRD Documenting BRD incidence and animal health costs associated with BRD in your herd Cattle Handling To Minimize the Incidence of Bovine Respiratory Disease Calving Management and Its Influence on Calf Health Management approaches to reduce transportation stress risk for BRD Biosecurity on the ranch to reduce risks for Bovine Respiratory Disease

Publications

  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2013 Citation: " Van Eenennaam, A. L. 2012. The Potential Value of DNA-based Tests for Bovine Respiratory Disease (BRD) Resistance to the Beef Cattle Supply Chain The American Association of Bovine Practitioners (AABP) Proceedings 45
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2013 Citation: " Van Eenennaam, A. L. 2012. Whats Happening in Beef Genomics? 24th National Association of Animal Breeders (NAAB) Technical Conference, Milwaukee, WI, 9/20/2012.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: " M. G. Thomas, G. R. Hagevoort, T. T. Ross, R. M. Enns, H. Van Campen, A. L. Van Eenennaam, H. L. Neibergs, C. Chase, S. V. Dindot, N. D. Cohen, and J. E. Womack. 2012. Integrated program for reducing bovine respiratory disease complex (BRDC) in beef and dairy cattle, coordinated agricultural project (CAP): overview of the teaching program. American Society of Animal Science Annual Meeting, Phoenix, AZ. J. Anim. Sci. Vol. 90, Suppl. 3: 498.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: " Toaff-Rosenstein R, Gershwin L, Zanella AJ, Tucker CB. 2012. Physiological and behavioral responses to Bovine Respiratory Disease. American Society of Animal Science Annual Meeting, Phoenix, AZ. J. Anim. Sci. Vol. 90, Suppl. 3:209.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: " Womack, J.E. and the BRDC Project Team. 2012. Integrated Program For Reducing Bovine Respiratory Disease Complex In Beef And Dairy Cattle. USDA Animal Health Investigators Meeting, December 1, 2012 Chicago, IL
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: " T.W. Lehenbauer, S.S. Aly, J.H. Davis, P.C. Blanchard, B.M. Crossley, P.V. Rossitto, H.L. Neibergs, A.L. Van Eenennaam. 2012 Prevalence of viral and bacterial pathogens in nasopharyngeal and pharyngeal recess regions of Holstein calves with and without signs of clinical bovine respiratory disease. Conference of Research Workers in Animal Diseases (CRWAD). Chicago, IL, December 2-4.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: H.L. Neibergs, C.M. Seabury, J.F. Taylor, Z. Wang, E. Scraggs, R.D. Schnabel, J. Decker, A. Wojtowicz, J.H. Davis, T. W. Lehenbauer, A. L. Van Eenennaam, S. S. Aly, P. C. Blanchard, B. M. Crossley, Bovine Respiratory Disease Consortium. Identification of Loci Associated with Bovine Respiratory Disease in Holstein Calves. 2013. Plant & Animal Genome XXI, San Diego, California
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Bovine Respiratory Disease Consortium, H.L. Neibergs presenting. 2012. Identification of loci associated with bovine respiratory disease in Holstein Cattle. Presidential Pick at the Joint American Dairy Science Association-American Society of Animal Science Annual Meeting, Phoenix, Arizona.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2013 Citation: " Van Eenennaam, A. L. 2012. Integrated program for reducing bovine respiratory disease complex in beef and dairy cattle coordinated agricultural project (BRD CAP). The American Association of Bovine Practitioners (AABP) Proceedings 45


Progress 04/15/11 to 04/14/12

Outputs
OUTPUTS: The research component of this project was focused on the ascertainment, processing and storage of samples from the 2000 dairy calves at Tulare, California and 1000 calves at Clovis, New Mexico; the challenge and animal welfare studies at UC Davis; and the initiation of the metagenomics study to identify novel pathogens associated with BRD. The collection, processing, diagnostics and storage of all Tulare dairy calves' samples are complete. The collection of the samples from 2000 animals that met our diagnostic criteria was the result of screening 100,000 animals. A database was developed for the phenotypes and for tracking samples. For the challenge study, two steers were infected with each of the 7 most common BRDC pathogens, clinical signs were evaluated, cultures and blood samples taken, and necropsies performed. The analysis is ongoing. The animal welfare study was initiated using a BRSV- H. somni dual infection model with three replicates of steers. Clinical signs, nasal swabs, and blood samples were obtained. Animals were treated with either meloxicam or placebo and measures of behavior were evaluated before and during the infection. The metagenomics study has been initiated by collecting deep pharyngeal and mid nasal swabs from BRD and healthy calves in Tulare. The extension component of the BRD CAP has achieved the development of a website (http://BRDComplex.org) and a dairy risk assessment tool prototype, (http://dcbsp.ucdavis.edu/t2). We have worked to develop linkages with personnel from regional project NC1027 and personnel at the National Animal Health Monitoring System (NAHMS), and have started to leverage the BRD CAP effort in an attempt to secure additional funding for projects with complementary aims. Presentations and publications were presented at various scientific, veterinary, and producer venues (Plant and Animal Genome, 5th BVDV Symposium, American Association of Bovine Practitioners, Academy of Veterinary Consultants, Beef Improvement Federation, National Beef Cattlemen's Association Cattlemen's College, National Beef Cattle Evaluation Consortium webinar, county-based animal health extension meetings) to introduce the concept of the BRD CAP and discuss the value proposition of including BRD as a trait in selection indexes. The educational component of this CAP was greatly assisted by organization of its activities with infrastructure of strong and logical collaborating programs. These are: the teaching component of the Southern Great Plains Dairy Consortium-Teaching (SGPDC-T; http://sgpdct.tamu.edu/), and Breeding and Genetics Graduate Education Online, (BGGEO; http://bggeo.iddl.vt.edu/). More than 50 students from 12 universities attended the annual program of SGPDC. The internship program of this CAP was initiated by involving students in animal handling and sample collection activities during research trials at UC Davis. A veterinary intern was hired at the UC Davis Veterinary Medicine Teaching & Research Center in Tulare. Also, university faculty involved in developing the distance graduate education modules met in Colorado to discuss the writing of the new modules to be incorporated into BGGEO. PARTICIPANTS: Individuals: Sharif Aly, Assistant Professor, School of Veterinary Medicine, University of California Davis Noah Cohen, Professor, Department of Large Animal Medicine and Surgery, Texas A&M University. Alan Dabney, Assistant Professor, Department of Statistics, Texas A&M University. Scott Dindot, Assistant Professor, Department of Veterinary Pathobiology, Texas A&M University Mark Enns, Associate Professor, Department of Animal Sciences, Colorado State University Lawrence Falconer, Professor and Extension Economist, Texas AgriLife Extension Service, Texas A&M University Laurel Gershwin, Professor, School of Veterinary Medicine, University of California Davis Robert Hagevoort, Extension Dairy Specialist, Extension Animal Sciences and Natural Resources, New Mexico State University. Terry Lehenbauer, Associate Professor and Director for Food Systems and Health Sciences, School of Veterinary Medicine, University of California Davis Holly Neibergs, Assistant Professor, Department of Animal Sciences, Washington State University. J. Shannon Neibergs, Associate Professor, Extension Economist, Washington State University. Tim Ross, Professor and Interim Department Head, Department of Animal and Range Sciences, New Mexico State University Christopher Seabury, Assistant Professor, Department of Veterinary Pathobiology, Texas A&M University Loren Skow, Professor, Veterinary Integrated Biosciences, Texas A&M University Jeremy Taylor, Professor and Wurdack Chair in Animal Genomics, Department of Animal Sciences, University of Missouri Milton Thomas, Professor. J.E. Rouse Chair, Department of Animal Science, Colorado State University Cassandra Tucker, Assistant Professor, Department of Animal Sciences, University of California at Davis Alison Van Eenennaam, Animal Genomics and Biotechnology Extension Specialist, Department of Animal Sciences, University of California at Davis Curtis Van Tassell, Research Geneticist, USDA, ARS, Beltsville Adroaldo Zenella, Associate Professor, Animal Behavior and Welfare Group, Michigan State University Partner Organizations: Washington State University University of California, Davis Universtiy of Missouri New Mexico State University Colorado State University USDA-ARS Beltsville Training: Junfeng Chen, Graduate Student, Texas A&M University TARGET AUDIENCES: Target audiences are the beef and feedlot industries in the US and animal health professionals working within them. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Although only one year of a five year program is completed, a modicum of outcomes/impacts can be reported. Within the research component, videos made during the collection and diagnostics procedures at Tulare are being used effectively to provide consistency in data collection at the other animal facilities. An intern who participated in the Tulare collections is providing training to individuals involved in collections at other sites. The challenge study was determined to be operating with insufficient sample size and was upgraded accordingly. Alternative strategies have been developed, accepted and implemented in the behavioral/animal welfare studies focusing on subclinical indicators of BRD. Within extension, an effective BRD CAP extension advisory board was established which includes members of the NC1027 multistate project. Interactions have resulted in team members being invited to give two presentations at the AABP 2012 meeting. Grant leveraging has been accomplished. The extension advisory group interactions produced a 5 year grant to the University of California Agriculture and Natural Resources 2012 competitive grants program, and a BRD CAP companion grant was developed for the UC Laboratory Fees Research Program. Outcomes of the education program include implementation of internship and teaching programs that have raised awareness of BRD challenges to the ruminant livestock industries. More than 50 students were exposed to integrated heard health practices through SGPDC-T, hosted by New Mexico State University, a Hispanic serving institution.

Publications

  • Van Eenennaam, A.L, and MacNeil, M.D. 2011. What weighting should be given to BRD resistance in selection decisions In Proceedings of the Beef Improvement Federation Research Symposium and Annual Meeting, 1-4 June 2011. Bozeman, MT. pp. 61-68.
  • Abstracts - Davis, J.H., Blanchard, P.C., Crossley, B.M., Aly, S.S, Rossitto, P.V., Neibergs, H.L., VanEenennaam, A.L, and Lehenbauer, T.W. (November 11, 2011). Prevalence of viral and bacterial pathogen in nasopharyngeal recess regions of Holstein calves with and without signs of clinical bovine respiratory disease. 5th BVDV Symposium. San Diego, CA.
  • Van Eenennaam, A.L (January 14, 2012) The Genetic Basis of Host Susceptibility to Bovine Respiratory Disease. Abstract W142. Plant and Animal Genome Conference, San Diego, CA.
  • Neibergs, H. 2011. Invited Review: Feeding the world through improved animal health and genetic selection. Proceedings of the American Association of Bovine Practitioners. pp 1-7.
  • Van Eenennaam, A.L. 2011. Battling Bovine Respiratory Disease. California Cattlemen's Magazine. May. 43-44.