Source: UNIVERSITY OF CALIFORNIA, DAVIS submitted to NRP
NATIONAL ANIMAL GENOME RESEARCH PROGRAM
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1002117
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
NRSP-8
Project Start Date
Jan 3, 2014
Project End Date
Sep 30, 2018
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
Animal Science
Non Technical Summary
My interest is in the application of genomic information to the beef cattle industry to improve the accuracy of selection and enable the incorporation of novel traits like fertility and disease resistance into breeding objectives
Animal Health Component
90%
Research Effort Categories
Basic
10%
Applied
90%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3033310108030%
3043410108040%
3083840108030%
Knowledge Area
303 - Genetic Improvement of Animals; 308 - Improved Animal Products (Before Harvest); 304 - Animal Genome;

Subject Of Investigation
3840 - Laboratory animals; 3310 - Beef cattle, live animal; 3410 - Dairy cattle, live animal;

Field Of Science
1080 - Genetics;
Goals / Objectives
Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals. Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species. Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest.
Project Methods
· Next generation sequencing approaches, coupled with well-defined phenotypes will be the key to the development of genomic tools for the beef cattle community · Need to develop large databases of phenotyped, genotyped cattle for development of accurate prediction equations · Facilitate the translation of genomic information through education and extension

Progress 01/03/14 to 09/30/18

Outputs
Target Audience:The target audience reached through my outreach efforts during this period included scientists (academic and industry), educators, veterinarians (academic and private practice), beef and dairy cattle producers and breeders, policy makers, as well as undergraduate, graduate and veterinary students. I have also done a lot of genomics and biotechnology presentations to explain basic plant and animal breeding methods to a more general public audience during the reporting period. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Several graduate students and one postdoctoral researcher are working on the projects described in this report. These include two personnel on the Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP; USDA NIFA grant 2011-68004-30367) Sasha Dubrovsky a Master's student working on risk factors affecting BRD in preweaned dairy calves, and post-doctoral researcher Justin Buchanan who is working on determining the value of using genomics to select against BRD on a vertically-integrated beef cattle enterprise. Master's student Lindsay Upperman is working on the project "Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle" (USDA NIFA grant 2013-68004-20364, and Master's student Maci Lienemann Mueller is working on the grant "Improvement of dairy animal well-being by genetic dehorning" (USDA NIFA grant 2015-67015-23316). And Ph.D. student Joseph Owen is supported on the grant "Genetic containment of livestock via CRISP-mediated gene knock-in" (USDA BRAG Competitive Grant 2015-33522-24106). How have the results been disseminated to communities of interest?I gave 73 outreach presentations to audiences nationally and globally during the final year of this project (10/1/2017-9/30/2018 What do you plan to do during the next reporting period to accomplish the goals?We plan to produce more content for eBEEF and start to merge information from three NIFA-supported grants (Integrated Program for Reducing Bovine Respiratory Disease Complex in Beef and Dairy Cattle; National Program for Genetic Improvement of Feed Efficiency in Beef Cattle; and Identification and Management of Alleles Impairing Heifer Fertility While Optimizing Genetic Gain in Beef Cattle) onto the eBEEF.org site. Work on the BRD CAP will finish and data from the large dairy and beef populations will be migrated to public repositories. Data collected from some of the projects listed above will be used for validation of genetic markers, risk assessment of management factors associated with BRD, and estimation of the value of genomics to the beef industry. The fertility markers identified by genotyping the 10,000 heifers with the F250 chip will be incorporated into MateSel software for modeling of how they impact fertility. Dr. Van Eenennaam will continue to speak to both live audiences and the press nationally and internationally on topics related to animal biotechnology and genomics.

Impacts
What was accomplished under these goals? Development of http://www.ebeef.org website (Collaboration with Darrh Bullock, University of Kentucky; Jared Decker, University of Missouri; Megan Rolf and Bob Weaber, Kansas State University; Matt Spangler, University of Nebraska; and Alison Van Eenennaam, University of California, Davis) As part of the Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP; USDA NIFA grant 2011-68004-30367), the www.ebeef.org website (the beef genetics/genomics community of practice within eXtension) was officially launched. eBEEF.org is part of the national eXtension program with the goal of being a one-stop site for beef cattle genetics and genomics information. Beef cattle specialists from five land grant institutions have joined forces to provide educational materialspertinent to today's beef cattle producers. The site contains factsheets, short FAQvideo clips, relevant conference recordings and webinars, newsletter and links to other useful beef sites.? Another goal of the eBEEF.org website is to archive the information generated from current and future beef genetics integrated grants funded by USDA-NIFA. All eBEEF.org team members are a part of one or more of the three current grants (Integrated Program for Reducing Bovine Respiratory Disease Complex in Beef and Dairy Cattle; National Program for Genetic Improvement of Feed Efficiency in Beef Cattle; and Identification and Management of Alleles Impairing Heifer Fertility While Optimizing Genetic Gain in Beef Cattle). Determine the value of genomics on a vertically-integrated beef cattle enterprise (Collaboration with Michael D. MacNeil, Simplot Land and Livestock, and GeneSeek and Alison Van Eenennaam, University of California) As part of the Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP; USDA NIFA grant 2011-68004-30367), post-doctoral scholar Dr. Justin Buchanan is working to determine the value of genomics on a vertically-integrated beef cattle enterprise. He has data on 12,812 genotyped (19/26K GGP-LD versions 1.1-4) calves, of which 1,167 were treated at least once for BRD. Of those 1,167, 1,108 had a temperature recorded at treatment, 1,031 had a sire identified (285 different sires; Range of # calves 1-114; average = 31), and 65 died. There were 312 sires that had no calves treated for BRD (Range of # calves 1-81; average = 9). He calculated the variance component estimates and relative economic impact of BRD during finishing and determined the relative economic value of BRD in an economic selection index. Risk Assessment, welfare analysis, and extension education for dairy calf respiratory disease management in California(Collaboration with Sharif Aly, UC Davis School of Veterinary Medicine Alison Van Eenennaam, UC Davis) Graduate student Sasha Dubrovsky is working on dairy BRD longitudinal study for her Master's degree at UC Davis on the project "Risk Assessment, welfare analysis, and extension education for dairy calf respiratory disease management in California", PD Dr. Sharif Aly, funded by the University of California. She has over 13,000 enrolled calves including 1,096 cases and 3,061 control Holstein heifers from a single dairy where all of the calves have been 50K genotyped. Each case record includes the date of treatment, a 0/1 for absence/presence of symptoms and the medications administered. The possible symptoms are ocular discharge, nasal discharge, head tilt/ear droop, cough, rapid respiration, and temperature. The general calf data includes the calf ID, date of birth, the type of housing it was in, whether or not it was a twin, if ART was used, its status (sold, dead, alive), and if it was dead or sold on the date that the event happened. She completed her Master's in December 2016 on evaluating risk factors for BRD on dairies and presented the data at the Conference of Research Workers in Animal Diseases (CRWAD). Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle (USDA NIFA grant 2013-68004-20364, Dave Paterson, MO) As part of a collaborative grant entitled "Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle" (USDA NIFA grant 2013-68004-20364), collaborator Dr. Jerry Taylor at University of Missouri is sequencing more than 250 Angus, Hereford, Simmental, Charolais, Gelbvieh, Red Angus, Maine Anjou, Beefmaster and Limousin bulls to identify loss of function alleles. These will then be tested on populations of 10,000 heifers with reproductive and breeding data that are part of the Show-Me-Select heifer replacement program. The ultimate objective of this research project is to identify lethal recessive alleles and develop tools forimplementation of strategic mating. Alison Van Eenennaam has been working with Dr. Brian Kinghorn, at the University of New England in Armidale, Australia, and graduate student Lindsay Upperman (UC Davis) to develop a computer program to optimize mating between animals carrying multiple loss of function alleles. Mating programs can help to simplify the use of DNA information to ensure that carriers are mated strategically to minimize the incidence of affected offspring while still utilizing their genetics when the value of their merit overrides the discount associated with their carrier status. Improvement of dairy animal well-being by genetic dehorning (USDA NIFA grant 2015-67015-23316, Collaboration S. Fahrenkrug (PD). D. Carlson, J.D. Murray, E.A. Maga and A.L. Van Eenennaam, UC Davis Department of Animal Science) This project aims to use genome editing to produce genetically dehorned cattle. Two cloned dairy bulls were produced by TALEN editing to introduce the polled allele into a Holstein background. The two bulls, which were phenotypically polled and genotypically homozygous polled, were brought to UC Davis, phenotyped, and semen was collected. A considerable amount of public outreach was involved with these bulls including film interviews with NPR's Science Friday and the BBC. Genetic containment of livestock via CRISP-mediated gene knock-in (USDA BRAG Competitive Grant 2015-33522-24106 A.L. Van Eenennaam (PD)) The long-term goals of this project are to advance current biotechnology tools to develop a cisgenic approach of biological genetic containment through sterility, and to concomitantly develop an approach to improve the efficiency of beef production. Usefulness of Findings: The overall objective of Dr. Van Eenennaam's research and extension program is to provide research and education on the use of DNA-based information and biotechnologies in livestock production systems. Towards that end, she and her collaborators are working to develop large populations of phenotyped, genotyped animal to help with genetic marker discovery and validation, and also translation of research results to various industries. The main aim of the bovine respiratory disease project (BRD CAP; USDA NIFA grant 2011-68004-30367) is to reduce the incidence of BRD in beef and dairy cattle by capitalizing on recent advances in genomics to enable novel genetic approaches to select for cattle that are less susceptible to disease. The ultimate objective of the fertility research project (USDA NIFA grant 2013-68004-20364) is to use genomics approaches to identify potential lethal recessive alleles and develop tools forimplementation of strategic matings to reduceincidence of carrier matings, thereby reducingincidence of pregnancy failure. Computerized mating programs offer a simple, inexpensive solution for avoiding affected matings. The populations generated by the numerous projects discussed will help to validate genetic markers and also inform the management of animals to decrease disease incidence and select for animal welfare traits.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Behura SK, Tizioto PC, Kim J, Grupioni NV, Seabury CM, Schnabel RD, Gershwin LJ, Van Eenennaam AL, Toaff-Rosenstein R, Neibergs HL, Regitano LCA, Taylor JF. 2017. Tissue Tropism in Host Transcriptional Response to Members of the Bovine Respiratory Disease Complex. Sci Rep. 20;7(1):17938
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, Zhou H. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics. 2018 19(1):684
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Van Eenennaam, AL. 2018. The Importance of a Novel Product Risk-Based Trigger for Gene-Editing Regulation in Food Animal Species. The CRISPR Journal 1(2): 1-6. https://www.liebertpub.com/doi/pdf/10.1089/crispr.2017.0023
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Van Eenennaam, AL. 2018. The contribution of transgenic and genome-edited animals to agricultural and industrial applications. Rev. Sci. Tech. Off. Int. Epiz., 37 (1), 97-112
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Buchanan, J., MacNeil, M.D., Raymond, R.C., Nilles, A.R., Van Eenennaam, A.L. 2018. Comparison of economic returns among genetic evaluation strategies in a 2-tiered Charolais-sired beef cattle production system. Journal of Animal Science 96(10): 4076-4086.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Karle, B.M., Maier, G.U., Love, W.J., Dubrovsky, S.A., William, D.R., Anderson, R.J., Van Eenennaam, A.L., Lehenbauer, T.W., ALy, S.S. 2018. Regional management practices and prevalence of bovine respiratory disease in California's preweaned dairy calves. Journal of Dairy Science. Published ahead of print. https://www.ncbi.nlm.nih.gov/pubmed/30527977
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Van Eenennaam, AL and A.E. Young. 2018. Gene editing in livestock: promise, prospects and policy. CAB Reviews. 13(27).
  • Type: Book Chapters Status: Published Year Published: 2018 Citation: Van Eenennaam, A.L. 2018. Chapter 7: The Use of Biotechnology to Improve Animal Welfare. In Cattle Welfare. T. Engle, D. Klingborg and B. Rollin (eds.). Taylor and Francis.
  • Type: Book Chapters Status: Published Year Published: 2018 Citation: Van Eenennaam, A.L. and A.E. Young. 2018. Public Perception of Animal Biotechnology. Chapter in Animal Biotechnology 2: Emerging Breeding Technologies H. Neiman (ed) Springer Publishing Company. Chapter 13. Pages 275-303. https://doi.org/10.1007/978-3-319-92348-2_13
  • Type: Book Chapters Status: Awaiting Publication Year Published: 2019 Citation: Van Eenennaam, A.L. and A.E. Young. 2019. Genetic Improvement of Food Animals: Past and Future. In Encyclopedia of Food Security and Sustainability. R. Birner (ed.) 171180.


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:The target audience included scientists (academic and industry), educators, veterinarians (academic and private practice), beef and dairy cattle producers and breeders, policy makers, as well as undergraduate, graduate and veterinary students. I have also done a lot of genomics and biotechnology presentations to explain basic plant and animal breeding methods to a more general public audience during the reporting period. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Several graduate students and one postdoctoral researcher have worked on the projects described in this report. These include two personnel on the Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP; USDA NIFA grant 2011-68004-30367) Sasha Dubrovsky, a Master's student who worked on risk factors affecting BRD in preweaned dairy calves, and post-doctoral researcher Justin Buchanan who worked on determining the value of using genomics to select against BRD on a vertically-integrated beef cattle enterprise. Master's student Lindsay Upperman worked on the project "Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle" (USDA NIFA grant 2013-68004-20364, and Master's student Maci Lienemann Mueller is working on the grant "Improvement of dairy animal well-being by genetic dehorning" (USDA NIFA grant 2015-67015-23316). Ph.D. student Joseph Owen is supported on the grant "Genetic containment of livestock via CRISP-mediated gene knock-in" (USDA BRAG Competitive Grant 2015-33522-24106). How have the results been disseminated to communities of interest?Presentations: 64 in this reporting period (10/1/2016-9/30/2017) 1. The synergistic use of molecular markers, biotechnology, genomic selection and advanced reproductive technologies in livestock breeding programs. XVI Latin American Genetics Congress,Uruguay 10/10/2016 2. Using genome editing to introgress desirable intragenic and intergenic alleles to accelerate the rate of genetic gain in meat animal breeding programs. XVI Latin American Genetics Congress, Uruguay 10/10/2016 3. Genome Editing: What's all the fuss?, NBCEC Brown Bagger Series, Videoconference, 10/12/2016 4. Genome Editing, National Association of Animal Breeders (NAAB), Green Bay, WI 10/14/2016 5. Translating BRD genomic information to industry outcomes, USMARC Clay Center, NE 10/17/2016 6. A Comparison of the Utilization of Genomic Technologies in the Beef and Dairy Industry. Livestock GenTec, Edmonton, Canada 10/19/2016 7. Communicating Food Science, Student IFT Global Summit teleconference, 11/9/2016 8. Beef Genetics and Genomics Extension in US, University of New England, Armidale, Australia 11/10/2016 9. Effective communication about agriculture: what works and what does not, A-FAN, Lincoln, NE 11/21/2016 10. Animal Biotechnology: What is, what could be, and will it be?" UC Berkeley, CA 11/29/2016 11. Genomics 101 and potential uses of gene editing in the California's Beef Industry, CCA, Reno, NV12/1/2016 12. Update on Rustici-funded EBA sequencing project and genome editing for BRD-resistant cattle, Cattle Health Meeting, California Cattlemen's Annual Meeting, Reno, NV 12/2/2016 13. Host gene expression response to BVDV and other BRD pathogens, 7th U.S. BVDV Symposium, Chicago, IL 12/7/2016 14. Food Evolution, GMOs and Health - What Role Does Science Have to Play? Annual Gamma Sigma Delta Fall Banquet, Davis, CA 12/8/2016 15. Breaking Down the Ivory Tower: Cooperative Extension Specialists. Talk to Science Policy & Communication Group graduate students, UC Davis 12/13/2016 16. GMOs: 101, Sunrise Rotary Club, Davis, CA 1/6/2017 17. The Synergistic use of Molecular Markers, Biotechnology, Genomic Selection, and Advanced Reproductive Technologies in Livestock Breeding Programs, UC Davis Vet Med Farm Club, Davis, CA 1/7/2017 18. GMO Labeling and the Impact on the Feed Industry Update, 2017 Grain & Feed Industry Conference, Monterey, CA 1/11/2017 19. Do Kingdoms Matter? Regulation of Animal Breeding Technologies, PAG XXV, San Diego, CA 1/15/2017 20. Gene Editing - The Pros and Cons and Relevance to the Beef Sector, British Cattle Breeders Club, Shropshire, UK 1/24/2017 21. Turning Loss Into Gain: Managing Genetic Risk to Improve Fertility, Cattlemen's College, NCBA Annual Meeting, Nashville, TN 1/31/2017 22. Using genetics to select for healthier cattle, NCBA Annual Meeting, Nashville, TN 2/1/2017 23. GMOs: What are they and what are they good for? Auburn High School, Auburn, Alabama, 2/14/2017 24. Animal Biotechnology: What is it, what could it be, and will it be allowed? Auburn, Alabama, 2/14/2017 25. How Genome Editing Can Synergistically Accelerate Animal Genetic Improvement Programs, AAAS, Boston, MA 2/17/2017 26. Genetics of disease resistance, Snyder Bull Test Sale, Nevada, 3/11/2017 27. Advanced Genetic Technologies, Snyder Bull Test Sale, Nevada, 3/11/2017 28. Will gene editing face the same fate as genetic engineering? The #scicomm challenge. LaTrobe University, Bundoora, Australia 3/21/2017 29. Making complex simple, Herd '17 Dairy Conference, Bendigo, Australia 3/22/2017 30. The #SciComm Challenge Facing Agriculture, Hunter College of the City University of New York, NY 3/31/2017 31. Animal breeding: an important component of agricultural sustainability, or animal cruelty? Purdue University, Indianapolis, IN 4/11/2017 32. Connecting with Skeptical Audiences, Purdue University, Indianapolis, IN 4/12/2017 33. Impacts of the Revolutionary Technology (CRISPR & other biotech) on Crop & Livestock Agriculture and Bio-Engineering Value Chains. UC Berkeley's Agrifood Supply Chains, Berkeley, CA 4/18/2017 34. Regulatory environment for new technologies, The Analytical Excellence through Industry Collaboration (AEIC) Spring Meeting 2017, Santa Clara, CA 4/19/2017 35. Animal-Based Food Systems: The Place of Agriculture Products within Context of a Healthy Diet, Food Systems, Nutrition and Health in a Changing Environment, Experimental Biology 2017, Chicago, IL 4/21/2017 36. Understanding GMOs, 2017 ADPI/ABI Annual Conference, Chicago, IL 4/24/2017 37. The #scicomm challenge facing animal agriculture, School of Veterinary Medicine, UC Davis, CA 4/26/2017 38. Gene Editing in Animal Breeding, GeneSeek Science Advisory Counsel, Lincoln, NE 5/9/2017 39. Will breeders be able to use genome editing in livestock improvement programs?. Michigan State University Genetics 40. Impact and Applications of Genome Editing Technologies, Mini-symposium, East Lansing, MI 5/10/2017 41. Genetic and GMO trends in modern agricultural food systems, US Dairy Consortium, Clovis, NM 5/16/2017 42. What is the cost of giving up on technology? Zoetis Dairy Wellness Summit, Phoenix, AZ 5/18/2017 43. Transferring scientific information to the general public, UCCE Brown Bag Lunch Series, Davis, CA 5/19/2017 44. New Players, New Tools: Insights in Science Communications, Science into Story, ICABR, Berkeley, CA 5/30/2017 45. Genetic Improvement of Food Animals: Past and Future, Animal Agriculture: CRISPR, Transgenic Animals and Regulations, ICABR, Berkeley, CA 5/31/2017 46. Where are we going with genomics and genetic improvement? Joint presentation with Matt Spangler, BIF Annual Convention, Athens, GA 6/1/2017 47. Genetics of Reproduction, BIF Annual Convention, Athens, GA 6/1/2017 48. Communicating with skeptical audiences, University of Georgia, Athens, GA 6/2/2017 49. How genome editing could synergistically accelerate animal genomics, Advancements in Emerging Technology, BIF Annual Convention, Athens, GA 6/2/2017 50. Agriculture biotech, public policy, and media in a post-truth era, Boot Camp on Public Trust in Agricultural Technology, Guelph, Canada 6/6/2017 51. Regulatory trends and New Breeding Techniques: Canada, US, Europe, Boot Camp on Public Trust in Agricultural Technology, Guelph, Canada 6/7/2017 52. How genome editing could synergistically accelerate animal genomics, Monsanto Fellows Colloquium, St Louis, MO 6/8/2017 53. Animal Biotechnology: Opportunities and Obstacles, Genetic Engineering in Agriculture - Science, Policy, and Law, Agribusiness Committee of the California State Bar Business Section, Davis, CA, 6/13/2017 54. The use of DNA and Genetic Markers in Beef Cattle Selection, Idaho Cattle Association Summer Round-up, Jackpot, NV, 6/21/2017 55. Genomic Selection in Livestock Improvement Programs, 3rd International Workshop on Regulation of Animal Biotechnology, Charlottesville, VA 6/26/2017 56. Scientific Communication, 3rd International Workshop on Regulation of Animal Biotechnology, Charlottesville, VA 6/26/2017 57. Economic Value of Genomic Selection in a Vertically Integrated Beef Cattle Production System, AAABG, Townsville, Australia, 7/5/2017 58. Will Animal Genetics Innovations Be Embraced Or Eschewed? The #Scicomm Challenge Facing Agricultural Biotechnology, ISAG, Dublin, Ireland, 7/20/2017 59. Understanding GMOs, Idaho Milk Processors Association Meeting in Sun Valley, Idaho 8/11/2017 60. The Science of Science Communication, Transgenic Animal Research Conference, Tahoe City, CA 8/15/2017 61. Science communication to obtain social license for use of genome editing in animal breeding programs, EAAP, Tallin, Estonia, 8/29/2017 62. Innovation in Agricultural Science, NASDA 2017 Annual Meeting, New Orleans, LA 9/14/2017 63. The future of genetic alteration in food animal production, AABP, Omaha, NE 9/15/2017 64. Understanding GMO's - Can GMO's be detected in Dairy Products?, International Whey Conference, Chicago, IL 9/20/2017 What do you plan to do during the next reporting period to accomplish the goals?We plan to produce more content for eBEEF and put on a series of educational seminars in collaboration with National Cattlemens' Beef Association (NCBA). Information from three NIFA-supported grants (Integrated Program for Reducing Bovine Respiratory Disease Complex in Beef and Dairy Cattle; National Program for Genetic Improvement of Feed Efficiency in Beef Cattle; and Identification and Management of Alleles Impairing Heifer Fertility While Optimizing Genetic Gain in Beef Cattle) will continue to be hosted on the eBEEF.org site. Dr. Van Eenennaam will continue to speak to both live audiences and the press nationally and internationally on topics related to animal biotechnology and genomics.

Impacts
What was accomplished under these goals? Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle (USDA NIFA grant 2013-68004-20364, Dave Paterson, MO): The ultimate objective of this research project is to identify lethal recessive alleles and develop tools for the implementation of strategic mating. Alison Van Eenennaam has been working with Dr. Brian Kinghorn, at the University of New England in Armidale, Australia, and graduate student Lindsay Upperman (UC Davis) to develop a computer program to optimize mating between animals carrying multiple loss of function alleles. Mating programs can help to simplify the use of DNA information to ensure that carriers are mated strategically to minimize the incidence of affected offspring while still utilizing their genetics when the value of their merit overrides the discount associated with their carrier status. Data will be presented at WCGALP in February 2018. A manuscript is in preparation. Risk Assessment, welfare analysis, and extension education for dairy calf respiratory disease management in California (Collaboration with Sharif Aly, UC Davis School of Veterinary Medicine Alison Van Eenennaam, UC Davis) Graduate student Sasha Dubrovsky completed a dairy BRD longitudinal study for her Master's degree at UC Davis on the project "Risk Assessment, welfare analysis, and extension education for dairy calf respiratory disease management in California", PD Dr. Sharif Aly, funded by the University of California. Over 13,000 calves were enrolled including 1,096 cases and 3,061 control Holstein heifers from a single dairy where all of the calves have been 50K genotyped. Each case record includes date of treatment, a 0/1 for absence/presence of symptoms and medications administered. The possible symptoms are ocular discharge, nasal discharge, head tilt/ear droop, cough, rapid respiration, and temperature. The general calf data includes calf ID, date of birth,type of housing it was in, whether or not it was a twin, if ART was used, its status (sold, dead, alive), and if it was dead or sold on the datethe event happened. She completed her Master's in December 2016 on evaluating risk factors for BRD on dairies and presented the data at the Conference of Research Workers in Animal Diseases (CRWAD). Manuscripts are in preparation. Improvement of dairy animal well-being by genetic dehorning: (USDA NIFA grant 2015-67015-23316, Collaboration S. Fahrenkrug (PD). D. Carlson, J.D. Murray, E.A. Maga and A.L. Van Eenennaam, UC Davis Department of Animal Science) This project aims to use genome editing to produce genetically dehorned cattle. Two cloned dairy bulls were produced by TALEN editing to introduce the polled allele into a Holstein background. The two bulls, which were phenotypically polled and genotypically homozygous polled, were brought to UC Davis, phenotyped, and semen was collected. Six pregnancies were obtained in horned Hereford dams and calves were born in September 2017. A considerable amount of public outreach was involved with these bulls including two documentary film crews, one from Sweden and one from NetFlix. Comparative evaluation of the phenotype, genome, and animal products derived from offspring of a genome edited, hornless bull and controls:(USDA - Biotechnology Risk Assessment Competitive Grant 2017-33522-27097 A.L. Van Eenennaam (PD)) The goals of this project are to provide empirical data on the phenotypic and genotypic durability of the polled genome edited trait, the health and development of offspring from a genome edited polled bull, the composition of animal products derived from the offspring of a genome edited bull and control bulls, and evaluate levels of fetal-maternal microchimerism. This research will further our understanding of any novel risks associated with the use of genome editing in livestock. Six calves of gene edited bulls were born and are being analyzed and phenotyped, along with controls. Genetic containment of livestock via CRISPR-mediated gene knock-in": (USDA - Biotechnology Risk Assessment Competitive Grant 2015-33522-24106 A.L. Van Eenennaam (PD))The overall goals of this project are to advance current knowledge of gene editing tools to develop a cisgenic sterility method for genetic containment, and to concomitantly develop an approach to improve the efficiency of beef production. The idea behind the project is to try to use the SRY gene, which results in maleness, as a way to create visually-appearing males from genotypic XX females. This would be advantageous in beef cattle production where females are less efficient during the finishing phase as compared to males. The development of an approach to develop all-male feedlot cattle using XSRYY bulls would improve the efficiency of beef production over the production of 50% male: 50% female offspring. Graduate student Joseph Owen achieved SRY knock ins this year, and plans are in place to produce cattle in the new year. Development of http://www.ebeef.org website:(Collaboration with Darrh Bullock, University of Kentucky; Jared Decker, University of Missouri; Megan Rolf and Bob Weaber, Kansas State University; Matt Spangler, University of Nebraska; and Alison Van Eenennaam, University of California, Davis) eBEEF (www.ebeef.org) is part of the national eXtension program with the goal of being a one-stop site for beef cattle genetics and genomics information. Beef cattle specialists from five land grant institutions have joined forces to provide educational materials that are pertinent to today's beef cattle producers, without searching multiple sites or filtering through countless hits on a search. The site contains factsheets, short frequently asked question (FAQ) video clips, relevant conference recordings and webinars, a newsletter and links to other useful beef sites. Twenty-eight factsheets have been written, reviewed by the team, and posted to the eBEEF.org and eXtension sites. For more information or to make suggestions please contact any of the eBEEF.org team members or visit www.ebeef.org and click on "Suggest topics that you would like to see covered at eBEEF.org". Determine the value of genomics on a vertically-integrated beef cattle enterprise: (Collaboration with Michael D. MacNeil, Simplot Land and Livestock, and GeneSeek and Alison Van Eenennaam, University of California) As part of the Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP; USDA NIFA grant 2011-68004-30367), post-doctoral scholar Dr. Justin Buchanan is working to determine the value of genomics on a vertically-integrated beef cattle enterprise. The objective of this study was to estimate the economic returns associated with five strategies of genetic evaluation combining genotypes, phenotypes, and pedigree information from a combined purebred (PB) and commercial (CM) beef cattle system. Five genetic evaluations were assembled using combinations of phenotypes, genotypes, and pedigree information in a Charolais PB and CM vertically-integrated production system. Scenario PB_A contained PB phenotypes and traditional pedigrees. Scenario PB_H contained the same information as A with the addition of 25K (GeneSeek® Genomic Profiler LDTM) genotypes from CM animals. Scenario PB_G contained phenotypes from PB animals and the pedigree relationship matrix from PB_A as well as genotypes from PB and CM animals. Scenario PBCM_A contained the same information as PB_A with the addition of phenotypes from CM animals. Scenario PBCM_G contained the same information as PB_G with the addition of phenotypes from CM animals. Estimates of (co)variance and selection index parameters were used to estimate accuracy and response to selection. Results were presented at AAABG in 2017, and a manuscript is in preparation.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Van Eenennaam, A.L. 2017. The future of genetic alteration in food animal production, American Association of Bovine Practitioners, September 14-16, 2017, Omaha, NE.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Petracca, Y., Van Eenennaam, A.L., Lema, M.A. 2016. Gene Editing: Do not forget about Animal Agriculture. Journal of Advanced Research in Biotechnology. 1(1):1-2.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Buchanan, J.W., James, S.T., Marquess, F.L., Woronuk, G.N., Deobald, H., Welly, B.T., Van Eenennaam, A.L. 2016. Analysis of validated and population specific SNP parentage panels in pedigreed and commercial beef cattle populations. Canadian Journal of Animal Science. 97(2): 231-240.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Van Eenennaam, A. 2016. Gene editing: Breeding or GMO? National Institutes of Bioscience Journal, 1. http://www.nibjournal.ed.ac.uk/article/view/1747
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Van Eenennaam, A.L. 2017. Genetic Modification of Food Animals. Current Opinion in Biotechnology 44:27-34.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Van Eenennaam, A.L. and A.E. Young. 2017. Invited Review: Detection of dietary DNA and protein in meat, milk and eggs. Journal of Animal Science. 95:3247-3269.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Owen, J.R., Noyes, N., Young, A.E., Prince, D.J., Blanchard, P.C., Lehenbauer, T.W., Aly, S.S., Davis, J.H., O'Rourke, S.M., Abdo, Z., Belk, K., Miller, M.R., Morley, P., Van Eenennaam, A.L. 2017. Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease. G3: Genes, Genomes, Genetics.7(9):3059-3071.
  • Type: Theses/Dissertations Status: Published Year Published: 2016 Citation: Dubrovsky, S.A. 2016. Epidemiology of Bovine Respiratory Disease in Preweaned Calves on California Dairies. Submitted in partial satisfaction of the requirement for the degree of Masters of Animal Biology, University of California, Davis.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Van Eenennaam, A.L. 2016. The synergistic use of molecular markers, biotechnology, genomic selection and advanced reproductive technologies in livestock breeding, XVI Latin American Genetics Congress, Oct 9-12, 2016, Montevideo, Uruguay.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Van Eenennaam, A.L. 2016. Using genome editing to introgress desirable intragenic and intergenic alleles to accelerate the rate of genetic gain in meat animal breeding, XVI Latin American Genetics Congress, Oct 9-12, 2016, Montevideo, Uruguay.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Van Eenennaam, A.L. 2016. Genome editing, 26th National Association of Animal Breeders (NAAB) Technical Conference, Oct 13-14, 2016, Green Bay, WI.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Van Eenennaam, A.L. 2017. Gene Editing - The Pros and Cons and Relevance to the Beef Sector, British Cattle Breeder's Club, January 24, 2017, Telford, Shropshire, England.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Van Eenennaam, A.L. 2017. Using genetics to select for healthier cattle, National Cattlemen's Beef Association Annual Meeting and Convention Cattlemen's College, January 31 - February 1, 2017, Nashville, TN.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Upperman, L.R., Kinghorn, B.P., MacNeil, M.D., Van Eenennaam, A.L. 2017. "Management of lethal recessive alleles while optimizing genetic gain in beef cattle", American Society of Animal Science, Western Section, June 20-23, 2017, Fargo, ND.
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2018 Citation: Buchanan, J.W., MacNeil, M.D., Raymond, R.C., McClain, A.R., Van Eenennaam, A.L. 2017. Economic value of genomic selection in a vertically integrated beef cattle production system, Association for the Advancement of Animal Breeding and Genetics (AAABG), July 2-5, 2017, Townsville, Queensland, Australia Proc. Assoc. Advmt. Anim. Breed. Genet. (2017) 22:in press.


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:The target audience reached through my outreach efforts during this period included scientists (academic and industry), educators, veterinarians (academic and private practice), beef and dairy cattle producers and breeders, policy makers, as well as undergraduate, graduate and veterinary students. I have also done a lot of genomics and biotechnology presentations to explain basic plant and animal breeding methods to a more general public audience during the reporting period. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Several graduate students and one postdoctoral researcher are working on the projects described in this report. These include two personnel on the Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP; USDA NIFA grant 2011-68004-30367) Sasha Dubrovsky a Master's student working on risk factors affecting BRD in preweaned dairy calves, and post-doctoral researcher Justin Buchanan who is working on determining the value of using genomics to select against BRD on a vertically-integrated beef cattle enterprise. Master's student Lindsay Upperman is working on the project "Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle" (USDA NIFA grant 2013-68004-20364, and Master's student Maci Lienemann Mueller is working on the grant "Improvement of dairy animal well-being by genetic dehorning" (USDA NIFA grant 2015-67015-23316). And Ph.D. student Joseph Owen is supported on the grant "Genetic containment of livestock via CRISP-mediated gene knock-in" (USDA BRAG Competitive Grant 2015-33522-24106). How have the results been disseminated to communities of interest?65 outreach presentations to audiences nationally and globally during the reporting period 1. Selection for cattle that are less susceptible to BRD. DNA Technology: Where we've been, where we are, and where we're headed. Meat Animal Research Center, Clay Center, NE 10/19/15 2. Bovine Respiratory Disease Complex BIF Guidelines Development. NBCEC Brownbagger Internet conference 10/21/15 3. The use of GMOs in the dairy industry and implications for mandatory GE process-based labeling. Global Cheese Forum, Reno, NV 10/28/15 4. GMO/Biotechnology use for sustainability of the dairy industry. ADSA Discover Conference, Itasca, IL 11/4/15 5. Potential impacts of mandatory labeling for GE food in the United States. Western Growers' Annual Meeting, Del Mar, CA 11/9/15 6. Potential impacts of mandatory labeling for GE food in the United States. National Restaurant Association Webinar. 11/17/15 7. Engagement of University with Industry Partners University of Melbourne, Australia, 12/3/15 8. Overview of the Ethical Issues of Germ Line Modification in Animals at The National Academies' Board on Life Sciences/Institute for Laboratory Animal Research meeting on "Workshop on Gene Editing to Modify Animal Genomes for Research - Scientific and Ethical Considerations" in Washington DC 12/8/15 9. The use of biotechnology in animal agriculture: past, present, and future CTNBio, Brasilia, Brazil 12/9/15 10. Assessing the potential impacts of biotechnology: evaluating risks and benefits CTNBio, Brasilia, Brazil 12/10/15 11. The Use of Biotechnology in Animal Agriculture, Seminar for 17 faculty from Jiangsu Province, China, who are attending the One Health for Food Safety Conference for Animal and Veterinary Scientists, Nov 30-Dec 18, 2015, UC Davis, CA 12/15/15 12. Social media to deliver Extension, DAIReXNET seminar, 12/15/15 13. Gene Editing: Breeding or Genetic Engineering? Plant and Animal Genome XXIV. San Diego, CA 1/09/16 14. Will PAG Innovations Be Embraced Or Eschewed? The #Scicomm Challenge Facing Agricultural Biotechnology Plant and Animal Genome XXIV. San Diego, CA 1/10/16 15. The use of GMOs in animal agriculture Western Canadian Association of Bovine Practitioners (WCABP), Calgary, AB, Canada 1/14/16 16. Utilizing DNA Information in Cattle Selection Programs Western Canadian Association of Bovine Practitioners (WCABP), Calgary, AB, Canada 1/15/16 17. GMOs Use In Animal Agriculture, National Cattlemen's Beef Association Cattlemen's College, San Diego, CA 1/27/16 18. GMOs in the Dairy Industry, Colusa Farm Show, Colusa, CA 2/3/16 19. UCCE" Newsmakers Press Conference, Tulare Ag Show, Tulare, CA 2/9/16 20. Genome selection: Basics and experience in animal systems, UC Davis Seed Biotechnology Center Breeding with Genomics Class, Davis, CA 2/17/16 21. Genomics and Bull Selection given to 5 UCCE producer meetings in February 2016 26. Prevalence, use and perception of genetically engineered crops for food in the United States, Cultiv8, Carmel, CA 2/24/16 27. Genomics and Bull Selection, Southern San Joaquin UCCE Livestock Symposium, Bakersfield, CA 2/27/16 28. Genomics and Bull Selection, Southern San Joaquin UCCE Livestock Symposium, Exeter, CA 2/27/16 29. Alba: the Fluorescent Bunny and Other Tales of Animal Genetics, Genomics and GMOs, Lifelong Learning Center, UC Davis Extension, Davis, CA 3/1/16 30. Introduction to GMOs and the Issues, Aquarium of the Pacific, Long Beach, CA 3/2/16 31. Potential impacts of mandatory labeling for GMO foods in the United States, American Feed Industry Association (AFIA), New Orleans, LA 3/9/16 32. Communicating Science in a Networked World, American Feed Industry Association (AFIA), New Orleans, LA 3/9/16 33. Animal Biotechnology and the Livestock Revolution, Cornell University Plant Breeding Symposium, Ithaca, NY 3/11/16 34. Introduction to GMOs and the Issues, Produce Marketing Association Genetic Engineering Webinar 3/22/16 35. Communicating Science in a Networked World, Institute of Food Technologists Student Association Pacific Southwest Area meeting, Cal Poly, San Luis Obispo, CA 4/2/16 36. The Role of Animal Biotechnology in the 21st Century, BioVision, Alexandria, Egypt 4/13/16 37. Four Legs, Two Legs, No Legs: What Does Science Tell Us About the Best Sources of Sustainable Protein? California Academy of Nutrition and Dietetics Annual Conference, Riverside, CA 4/21/16 38. Food for Thought: An Opportunity for Interaction Food: Sustainability and Innovation Series, Genome British Columbia, Vancouver, BC 4/25/16 39. Scientific Communication about Agriculture in a Networked World, UC Davis Aggie Ambassadors, UC Davis, 5/3/16 40. The Current and Future Uses of Biotechnology in Animal Agriculture, Ensminger University Conference, Honduras, 5/14/16 41. Emerging Genetic Advancements, Center for Food Integrity Conference, Hamburger University, McDonald's Campus, Chicago, IL, 5/18/16 42. Scientific Communication About Animal Agriculture, Center for Food Integrity's Animal Agriculture Committee Meeting, Hamburger University, McDonald's Campus, Chicago, IL, 5/19/16 43. Use of GMOs in Animal Agriculture Production, Sonoma-Marin Cattlemen's Association Field Day & BBQ, 6/5/16 44. Animal Biotechnology, BIO 2016 FutureMakers Ted-style talk, BIO convention, San Francisco, CA 6/8/16 45. The Future of Meat, Breakthrough Institute Dialogue, Sausalito, CA, 6/23/16 46. Animal genomics and biotechnology in production systems, Ninth Latin American and Caribbean Agricultural and Forestry Biotechnology meeting, IX Encuentro REDBIO 2016-PERU, Lima, Peru 6/28/16 47. The potential of gene editing in animal agriculture, Presentation to a group of New Zealand pastoral producers, Palo Alto, CA 7/8/16 48. How might genomic information get translated into industry outcomes?, ASAS/ADSA Joint Annual Meeting, Salt Lake City, UT 7/20/16 49. Identification and characterization of a novel pathogen causing bovine abortion, International Society of Animal Genetics conference, Salt Lake City, UT 7/24/2016 50. Navigating the World of Genetic Testing, 2016 Texas A&M Beef Cattle Short Course, College Station, TX 8/1/16 51. New developments in selection for replacement heifers, disease resistance and other economically relevant traits, 2016 Texas A&M Beef Cattle Short Course, College Station, TX 8/2/16 52. What is a GMO? Sonoma County Alliance Central Membership Meeting, Santa Rosa, CA 8/3/16 53. Gene editing: Breeding or Genetic Engineering? Riverview LLP Cattle Company, Google Hangout webinar, 8/17/16 54. Gene editing: Breeding or GMO? 11th International Marine Biotechnology Conference (IMBC), 8/31/16 55. Gene editing: Breeding or GMO? Genome Editing and the Future of Farming, Edinburgh, Scotland, 9/6/16 56. "Use of genetic marker information in beef cattle selection", Applied Reproductive Strategies in Beef Cattle, Ames, IA, 9/8/16 57. "Animal Biotechnology: Opportunities and Challenges", Cornell Alliance for Science Fellows Training Program, Ithaca, NY, 9/12/16 58. "Gene editing what is it and how might it be used in animal breeding programs", American Wagyu Association Conference, Coeur d'Alene, ID, 9/15/16 59. "The GMO debate: Twenty years of animal health and livestock feeding studies", 2016 Allen D. Leman Swine Conference, St. Paul, MN, 9/20/16 60. "The #Scicomm challenge facing animal agriculture", 2016 Allen D. Leman Swine Conference, St. Paul, MN, 9/20/16 61. "Animal Health and Welfare Session", Animal Biotech Summit, Bethesda, MD 9/21/16 62. "Navigating the World of Genetic Testing", UC Davis Veterinary School Farm Club, Davis, CA, 9/26/16 63. "Reputation Challenges and Tactics", Biotech University, Saskatchewan, Canada, 9/29/16 64. "The #SciComm Challenge Facing Agriculture Technologies", Biotech University, Saskatchewan, Canada, 9/29/16 65. "Gene editing: Breeding or Genetic Engineering?, Biotech University, Saskatchewan, Canada 9/30/16 What do you plan to do during the next reporting period to accomplish the goals?We plan to produce more content for eBEEF and start to merge information from three NIFA-supported grants (Integrated Program for Reducing Bovine Respiratory Disease Complex in Beef and Dairy Cattle; National Program for Genetic Improvement of Feed Efficiency in Beef Cattle; and Identification and Management of Alleles Impairing Heifer Fertility While Optimizing Genetic Gain in Beef Cattle) onto the eBEEF.org site. Work on the BRD CAP will finish and data from the large dairy and beef populations will be migrated to public repositories. Data collected from some of the projects listed above will be used for validation of genetic markers, risk assessment of management factors associated with BRD, and estimation of the value of genomics to the beef industry. The fertility markers identified by genotyping the 10,000 heifers with the F250 chip will be incorporated into MateSel software for modeling of how they impact fertility, and offspring of the polled bulls will likely be born in the Fall of 2017. Dr. Van Eenennaam will continue to speak to both live audiences and the press nationally and internationally on topics related to animal biotechnology and genomics.

Impacts
What was accomplished under these goals? Development of http://www.ebeef.org website (Darrh Bullock, Univ of Kentucky; Jared Decker, Univ of Missouri; Megan Rolf and Bob Weaber, Kansas State Univ; Matt Spangler, Univ of Nebraska; and Alison Van Eenennaam, UC Davis) As part of the Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP; USDA NIFA grant 2011-68004-30367), the www.ebeef.org website (the beef genetics/genomics community of practice within eXtension) was officially launched with the goal of being a one-stop site for beef cattle genetics and genomics information. Beef cattle specialists from five land grant institutions have joined forces to provide educational materials pertinent to today's beef cattle producers, without searching multiple sites or filtering through countless hits on a search. The site contains factsheets, short FAQ video clips, relevant conference recordings and webinars, a newsletter and links to other useful beef sites. Twenty four factsheets have been written, reviewed, and posted: · Value of Collecting Phenotypes · The Random Shuffle of Genes: Putting the E in EPD · EPD Basics and Definitions · Beef Sire Selection Recommendations · Beef Cattle Economic Selection Indices · Decreasing Generation Interval to Increase Genetic Progress · Genetic Correlations and Antagonisms · Economically Relevant Traits · Use of DNA Information · DNA Sample Collection · Parentage Testing · How DNA Testing Will Affect the Accuracy of EPD Information · Recent Developments In Genetic Evaluations and Genomic Testing · Initial Genome-Wide Association Study of Feed Intake Related Traits in Beef Cattle · Genetic Markers of Bovine Respiratory Disease Complex (BRDC) Susceptibility · Genetic Practices to Improve Beef Cattle Reproduction · Commercial Replacement Heifer Selection · Mating Systems in Commercial Beef Cattle Operations · Simple Inheritance in Beef Cattle · Color Patterns in Crossbred Beef Cattle · Genetic Defects · Managing Genetic Defects · The Genetics of Horned, Polled and Scurred Cattle · What is Gene Editing? The site also archives the information generated from current and future beef genetics integrated grants funded by USDA-NIFA. All eBEEF.org team members are a part of one or more of the three current grants (Integrated Program for Reducing Bovine Respiratory Disease Complex in Beef and Dairy Cattle; National Program for Genetic Improvement of Feed Efficiency in Beef Cattle; and Identification and Management of Alleles Impairing Heifer Fertility While Optimizing Genetic Gain in Beef Cattle). For more information or to make suggestions please contact any of the eBEEF.org team members or visit www.ebeef.org. Determine the value of genomics on a vertically-integrated beef cattle enterprise (Michael D. MacNeil, Simplot Land and Livestock, and GeneSeek and Alison Van Eenennaam, University of California) As part of the Bovine Respiratory Disease Coordinated Agricultural Project (USDA NIFA 2011-68004-30367), post-doctoral scholar Dr. Justin Buchanan is working to determine the value of genomics on a vertically-integrated beef cattle enterprise. He has data on 12,812 genotyped (19/26K GGP-LD versions 1.1-4) calves, of which 1,167 were treated at least once for BRD. Of those 1,167, 1,108 had a temperature recorded at treatment, 1,031 had a sire identified (285 different sires; Range of # calves 1-114; average = 31), and 65 died. There were 312 sires that had no calves treated for BRD (Range of # calves 1-81; average = 9). He calculated the variance component estimates and relative economic impact of BRD during finishing and determined the relative economic value of BRD in an economic selection index. Risk Assessment, welfare analysis, and extension education for dairy calf respiratory disease management in California (Sharif Aly, UC Davis School of Veterinary Medicine, Alison Van Eenennaam, UC Davis) Graduate student Sasha Dubrovsky is working on dairy BRD longitudinal study for her Master's degree at UC Davis on the project "Risk Assessment, welfare analysis, and extension education for dairy calf respiratory disease management in California", PD Dr. Sharif Aly, funded by the University of California. She has over 13,000 enrolled calves including 1,096 cases and 3,061 control Holstein heifers from a single dairy where all of the calves have been 50K genotyped. Each case record includes the date of treatment, a 0/1 for absence/presence of symptoms and the medications administered. The possible symptoms are ocular discharge, nasal discharge, head tilt/ear droop, cough, rapid respiration, and temperature. The general calf data includes the calf ID, date of birth, the type of housing it was in, whether or not it was a twin, if ART was used, its status (sold, dead, alive), and if it was dead or sold on the date that the event happened. She completed her Master's in December 2016 on evaluating risk factors for BRD on dairies and presented the data at the Conference of Research Workers in Animal Diseases (CRWAD). Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle (USDA NIFA 2013-68004-20364, Dave Paterson, MO) As part of a collaborative grant entitled "Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle" (USDA NIFA grant 2013-68004-20364), collaborator Dr. Jerry Taylor at Univ of Missouri is sequencing more than 250 bulls to identify loss of function alleles. These will be tested on populations of 10,000 heifers with reproductive and breeding data that are part of the Show-Me-Select heifer replacement program. The ultimate objective is to identify lethal recessive alleles and develop tools for the implementation of strategic mating. Dr. Van Eenennaam has been working with Dr. Kinghorn, at the Univ of New England in Armidale, Australia, and graduate student Lindsay Upperman (UC Davis) to develop a computer program to optimize mating between animals carrying multiple loss of function alleles. Mating programs can help simplify the use of DNA information to ensure that carriers are mated strategically to minimize the incidence of affected offspring while still utilizing their genetics when the value of their merit overrides the discount associated with their carrier status. Improvement of dairy animal well-being by genetic dehorning (USDA NIFA 2015-67015-23316, S. Fahrenkrug (PD). D. Carlson, J.D. Murray, E.A. Maga and A.L. Van Eenennaam, UC Davis Department of Animal Science) This project aims to use genome editing to produce genetically dehorned cattle. Two cloned dairy bulls were produced by TALEN editing to introduce the polled allele into a Holstein background. The two bulls, which were phenotypically polled and genotypically homozygous polled, were brought to UC Davis, phenotyped, and semen was collected. A considerable amount of public outreach was involved with these bulls including film interviews with NPR's Science Friday and the BBC. Genetic containment of livestock via CRISP-mediated gene knock-in (USDA BRAG Competitive Grant 2015-33522-24106 A.L. Van Eenennaam (PD)) The long-term goals are to advance current biotechnology tools to develop a cisgenic approach of biological genetic containment through sterility, and to concomitantly develop an approach to improve the efficiency of beef production. The overall objective of Dr. Van Eenennaam's research and extension program is to provide research and education on the use of DNA-based information and biotechnologies in livestock production systems. Towards that end, she and her collaborators are working to develop large populations of phenotyped, genotyped animal to help with genetic marker discovery and validation, and also translation of research results to various industries.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Buchanan, J. W., M. D. MacNeil, R. C. Raymond, A. R. McClain, and A. L. Van Eenennaam. 2016. Rapid Communication: Variance component estimates for Charolais-sired fed cattle and relative economic impact of bovine respiratory disease. J. Anim. Sci. 94:5456-5460
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Carroll, D., Van Eenennaam, A., Taylor, J.R., Seger, J., Voytas, D. 2016. Regulate genome-edited products, not genome editing itself. Nature Biotechnology. 34(5):477-479.
  • 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. http://dx.doi.org/10.3168/jds.2015-9394
  • 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. http://vdi.sagepub.com/content/28/2/119
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Murray, J.D., Ross, P.J., Van Eenennaam, A.L. and E.A. Maga. 2016. Ten transgenic animal research conferences and counting. Transgenic Res. 25: 271-272.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Weber, K.L., Welly, B.T., Van Eenennaam, A.L., Young, A.E., Portoneto, L.R., Reverter, A., Rincon, G. 2016. Identification of gene networks for residual feed intake in Angus cattle using genomic prediction and RNA-seq. PLoS One 11(3): e0152274. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152274
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Buchanan, J.W., James, S.T., Marquess, F.L., Woronuk, G.N., Deobald, H., Van Eenennaam, A. 2016. Evaluation and Development of SNP-Based Parentage Identification Panels in Commercial Beef Cattle Populations. [abstract]. Plant and Animal Genome Conference XXIV, Jan 9-13, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Kern, C., Ross, P.J., Saelao, P., Wang, Y., Halstead, M.M., Chitwood, J.L., Korf, I., Delany, M., Medrano, J.F., Cheng, H., Van Eenennaam, A., Tuggle, C.K., Ernst, C.W., Zhou, H. 2016. Identification of Tissue-Specific Long Non-Coding RNAs in Three Livestock Species [abstract]. Plant and Animal Genome Conference XXIV, Jan 9-13, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Zhou, H., Ross, P.J., Kern, C., Saelao, P., Wang, Y., Halstead, M.M., Chitwood, J.L., Kim, T.H., Korf, I., Delany, M., Cheng, H., Medrano, J.F., Van Eenennaam, A., Tuggle, C.K., Ernst, C.W. 2016. Genome-wide Functional Annotation of Regulatory Elements in Livestock Species [abstract]. Plant and Animal Genome Conference XXIV, Jan 9-13, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Van Eenennaam, A.L. 2016. Gene Editing: Breeding or Genetic Engineering? Plant and Animal Genome Conference XXIV, Jan 9-13, San Diego, CA. https://pag.confex.com/pag/xxiv/meetingapp.cgi/Paper/19390
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Van Eenennaam, A.L. 2016. Twenty years of TARC: time to accelerate real change Transgenic Research 25: 113  114.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Van Eenennaam, A.L. 2016. Four Legs, Two Legs, No Legs: What Does Science Tell Us About the Best Sources of Sustainable Protein? California Academy of Nutrition and Dietetics, April 21-23, 2016, Riverside, CA http://www.dietitian.org/pdfs/am2016handouts-thursday/THU-115-FourLegsTwoLegsNoLegs-AVanEenennaam.pdf
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Van Eenennaam, A.L. 2016. The Current and Future Uses of Biotechnology in Animal Agriculture Ceiba, 54:72-81.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Van Tassell, C.P., Spangler, G., Bickhart, D.M., Wiggans, G.R., Cole, J.B., Taylor, J.F., Neibergs, H.L., Seabury, C.M., Van Eenennaam, A.L. and J.E. Womack. 2016. Calculation of genomic predicted transmitting abilities for bovine respiratory disease complex in Holsteins, ASAS/ADSA Joint Annual Meeting, July 19-23, 2016, Salt Lake City, UT, J. Animl Sci. 94(E-suppl. 5)/J. Dairy Sci. 99(E-suppl. 1): 133.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Van Eenennaam, A.L. 2016. How might genomic information get translated into industry outcomes? ASAS/ADSA Joint Annual Meeting, July 19-23, 2016, Salt Lake City, UT, J. Animl Sci. 94(E-suppl. 5)/J. Dairy Sci. 99(E-suppl. 1): 134.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Kiser, J.N., Seabury, C.M., Taylor, J.F., Womack, J.E., Hagevoort, R., Lehenbauer, T.W., Aly, S.S., Van Eenennaam, A.L. and H.L. Neibergs 2016. Clinical signs associated with bovine respiratory disease diagnosis and high heritability in beef and dairy cattle ASAS/ADSA Joint Annual Meeting, July 19-23, 2016, Salt Lake City, UT, J. Animl Sci. 94(E-suppl. 5)/J. Dairy Sci. 99(E-suppl. 1): 177.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Taylor, J.F., Schnabel, R.D., Simpson, B., Decker, J.E., Rolf, M., Kinghorn, B.P., Van Eenennaam, A.L., MacNeil, M.D., Brown, D.S., Smith, M.F., Patterson, D.J. 2016. Detection and selection against early embryonic lethals in United States beef breeds ASAS/ADSA Joint Annual Meeting, July 19-23, 2016, Salt Lake City, UT, J. Animl Sci. 94(E-suppl. 5)/J. Dairy Sci. 99(E-suppl. 1): 324.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Thomas, M.G., Enns, R.M., Hagevoort, R., Neibergs, J.S., Van Eenennaam, A.L., Neibergs, H.L., Womack, J.E. 2016. History of the development of the Beef Reproduction Task Force (BRTF) and impacts of the BRTF on beef cattle reproductive management ASAS/ADSA Joint Annual Meeting, July 19-23, 2016, Salt Lake City, UT, J. Animal Sci. 94(E-suppl. 5)/J. Dairy Sci. 99(E-suppl. 1): 838.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Johnson, S., Cooke, R.F., Dahlke, G.R., Funston, R.N., Hall, J.B., Kesler, D.J., Lamb, G.C., Lauderdale, J., Patterson, D.J., Perry, G.A., Strohbehn, D.R., Van Eenennaam, A.L. 2016. History of the development of the Beef Reproduction Task Force (BRTF) and impacts of the BRTF on beef cattle reproductive management ASAS/ADSA Joint Annual Meeting, July 19-23, 2016, Salt Lake City, UT, J. Animal Sci. 94(E-suppl. 5)/J. Dairy Sci. 99(E-suppl. 1): 549.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Patterson, D.J., Cooke, R.F., Dahlke, G.R., Funston, R.N., Hall, J.B., Lamb, G.C., Lauderdale, J., Perry, G.A., Van Eenennaam, A.L. 2016. Physiological and management advances enhancing adoption of applied reproductive management procedures in beef cattle ASAS/ADSA Joint Annual Meeting, July 19-23, 2016, Salt Lake City, UT, J. Animal Sci. 94(E-suppl. 5)/J. Dairy Sci. 99(E-suppl. 1): 550.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Welly, B.T., Miller, M.R., Stott, J.L., Blanchard, M.T., Islas-Trejo, A., ORourke, S.M., Young, A.E., Medrano, J.F., Van Eenennaam, A.L. 2016. Identification and characterization of a novel pathogen causing bovine abortion International Society of Animal Genetics conference, July 23-27, 2016, Salt Lake City, UT
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Zhou, H., Delany, M.E., Cheng, H., Ross, P.J., Korf, I., Kern, C., Saelao, P., Wang, Y, Kim, T., Chitwood, J., Halstead, M., Medrano, J.F., Van Eenennaam, A.L., Tuggle, C.K., Ernst, C.W. 2016. Identification of regulatory elements in three domesticated species International Society of Animal Genetics conference, July 23-27, 2016, Salt Lake City, UT
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Van Eenennaam, A.L. 2016. Gene editing: Breeding or GMO? 11th International Marine Biotechnology Conference (IMBC), Aug 31, 2016, Baltimore, MD.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Van Eenennaam, A.L. 2016. Use of genetic marker information in beef cattle selection, Applied Reproductive Strategies in Beef Cattle conference, Sept 6-8, 2016, Ames, IA.


Progress 10/01/14 to 09/30/15

Outputs
Target Audience:The target audience reached through my outreach efforts during this period included scientists (academic and industry), educators, veterinarians (academic and private practice), beef and dairy cattle producers and breeders, policy makers, as well as undergraduate, graduate and veterinary students. I have also done a lot of genomics and biotechnology presentations to explain basic plant and animal breeding methods to a more general public audience during the reporting period. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? The Applied Reproductive Strategies in Beef Cattle Conference (ARSBC) 2015 brought together 183 attendees, including producers, veterinarians, researchers, extension educators, undergraduate, graduate, veterinary students from 11 different academic institutions and industry representatives from many states. Overall, responses from the attendees were very positive. Results from the post-conference evaluation included an average score of 4.53/5 for speaker knowledge and 4.15/5 for speaker effectiveness. All of the papers presented at the ARSBC meeting were printed in a hard copy proceedings which are available on the website (www.appliedreprostrategies.com). The AABP BRD symposium papers presented were published in the 2015 Proceedings of the 48th Annual Conference of the American Association of Bovine Practitioners; and the papers and abstracts presented at the 10th Transgenic Animal Conference will be published in an upcoming issue of Transgenic Research. How have the results been disseminated to communities of interest?I gave 67 outreach presentations to audiences nationally and globally during the reporting period Adapting Animal Feedstuffs to Meet Global Demand, Innovate 2014 American Society of Animal Science Conference, MN Use of Parentage Testing: Implications for Bull Fertility and Productivity, Applied Reproductive Strategies in Beef Cattle, OK Implications of Improper Management of Known Genetic Abnormalities, Applied Reproductive Strategies in Beef Cattle, OK The Livestock Revolution Borlaug CAST Communication Award Acceptance Speech, IA MateSel: A Software Mating Tool to Aid in Selection for Improved Fertility NBCEC Brownbagger, Internet presentation The Livestock Revolution: The role of animals in feeding the future, Cornell University Graduate Student Seminar Series NY The Livestock Revolution: The role of animals in feeding the future, Ag TechCon Preview: Emerging Technologies from UC Davis, CA Prevalence and impacts of genetically engineered feedstuffs on livestock populations Presentation to 2 biotechnology 11th grade class at Davis High School, CA Food and Feed Safety of Genetically Modified Organisms: The Hype and the Facts Keynote Address, American College of Toxicology, FL The Livestock Revolution: The role of animals in feeding the future Challenge 2050 FL GMO technology: What do the facts say? University of Florida York Lecture Series, FL Overview: Animal genomics and biotechnology research projects and activities, UCCE Meat Production and Food Safety Program Team meeting, NV Eating Meat from Cattle Fed GMOs: How Natural is That? California Cattlemen's Convention, Zoetis Cattlemen's College, NV Intelligence squared (IQ2) Oxford style Debate Genetically Modified Food?, NY Beef Heifer Replacement: Considerations Related to Breed and Biological Type, OR Testimony on GMO safety before the Congressional House Energy and Commerce Subcommittee on Health, Washington DC Eating Meat from Cattle Fed GMOs: How Natural is That? Nebraska Cattlemen's Convention, Zoetis Cattlemen's College, NE GMO technology: What do the facts say? Seed Business 101, CA GMO Feed and Animal Health: Facts vs. Fiction UCCE Winter Ag Meeting, CA Animal breeding and biotechnology: Have we always been creating GMOs! Presentation to Matt Spangler's Beef Bull Production Class, NE Genetically Modified Animals: The Facts, the Fear Mongering and the Future. Heuermann Lecture, University of Nebraska, NE Can early embryonic losses that reduce reproduction efficiency be managed through genetics?' Kentucky Beef Efficiency Conference, KY The use of GMOs in the dairy industry Progressive Dairy Producer Magazine Educational Session, CA The potential impacts of mandatory labeling for genetically engineered food in the United States World Ag Expo General Agricultural Educational Session, CA The Practical Use of Genomics Beef Magazine Educational Session, CA Bovine Respiratory Disease Prevention: Opportunities for Genetic Selection Western Dairy Management Symposium, NV Bovine Respiratory Disease Complex Coordinated Agricultural Project: BRD CAP Cooperative Extension Service 2015 Professional Development Day, NM The potential impacts of mandatory labeling for genetically engineered food in the United States UC Davis Agribusiness Workshop, CA GM feeds and Animal Health: What do the data say? 2015 Midwest Poultry Federation Convention, MN The use of GMOs in the dairy industry UCCE Dairy Production Team Meeting, CA Alba: the fluorescent bunny, Leonardo Art Science Evening Rendezvous, CA The future of animal biotechnology and the importance of science communication George Washington Carver Lecture Series, , AL The use of GMOs in the dairy industry Oregon Dairy Industry Conference, Salem, OR Communicating Science in a Networked World, 2015 CAST Borlaug Communication Award Winner Announcement Meeting, National Press Club Washington DC Lysenkoism: learning from the past to facilitate the future of animal breeding Chapman Memorial Lectureship, University of Wisconsin, WI Biotechnology and animal breeding: a match made in heaven Chapman Undergraduate Lecture, University of Wisconsin, Madison, WI Bovine Respiratory Disease Prevention: Opportunities for Genetic Selection in Dairy Cattle U.S. Dairy Education & Training Consortium NM The use of GMOs in the dairy industry, and implications for mandatory GE Process-based labeling, U.S. Dairy Education & Training Consortium, NM Science Advocacy, UC Davis Biotech Literacy Project Boot Camp (BLP), Davis, CA Connecting with Skeptical Audiences, BLP, CA GMO animals: What is approved, what is not ? BLP, CA GMO Salmon: Sustainable? UC Davis Food Center Agricultural Literacy Project, CA Needs and Challenges in Agricultural Production: The Livestock Perspective APEC, Philippines GMO animals: What is approved, what is not Sino-USA Workshop on Regulatory and Scientific Aspects of Animal Biotechnology, Beijing, China Communicating Science in a Networked World Sino-USA Workshop on Regulatory and Scientific Aspects of Animal Biotechnology, Guangzhou, China Myths & Realities of GE Food 8th Korea-American Student Conference, California State University, CA Social media to deliver Extension, ASAS/ADSA Joint Annual Meeting, Orlando, FL Performance Trends in Commercial Livestock Populations before and subsequent to the inclusion of GMO feed in livestock diets, EU MARLON conference, Belgium (via internet conference) Myths & Realities of GE Food , Healthy Eating Club, Kilaga Springs Lodge, CA Prospects for GMOs and GMO Labeling, 2015 Agricultural & Applied Economics Association and WAEA Joint Annual Meeting, CA Communicating GMOs to the public: a wicked scientific communication problem, National Conference of State Legislature's Natural Resources and Infrastructure Committee, WA Utilizing Molecular Information in Beef Cattle Selection, Angus Genomics Forum, CA Twenty years of TARC: Time to Accelerate Real Change, Transgenic Animal Research Conference, CA Targeting multiple end?uses in beef cattle breeding programs Applied Reproductive Strategies in Beef Cattle, CA Safety and Labeling of GE Food, Hong Kong Dietitians Association and Hong Kong Nutrition Association, Hong Kong Regulation and Utilization of Biotech in U.S. Food System - Pre-market Safety Assessment and Biotech Labeling, American Consulate General, Hong Kong Global Prevalence of GE Trade: Implications of Alternative Labeling Policies for Foods Derived from GE Crops American Center, Taipei, Taiwan Animal cloning, gene transformation and GM feed Presentation to Taiwan Council Of Agriculture, Taipei Food for Thought: Innovations and Opportunities for Animal Breeding, Explorit Science Center lecture series, CA Animal Biotechnology: Opportunities and Challenges Cornell Alliance for Science Global Fellows Science Week, Cornell, NY How Animals are Genetically Engineered Cornell GMO Debate Course, NY Ask Me Anything- An evening for the curious, Unitarian Church, NY Prevalence and impacts of genetically engineered feedstuffs on livestock populations, Minnesota Nutrition Conference, MN Producer Uptake: How might genomic information to translated to industry outcomes BRD symposium, American Association of Bovine Practitioners conference, LA GMO Myths, Facts and the Future. Internet Webinar for dieticians and nutritionists, organized by Southeast United Dairy Industry Association, GA Communicating the hard stuff, Dairy Australia, Melbourne, Australia A public:private collaboration to evaluate the potential value of genomic information to a vertically-integrated commercial beef cattle enterprise. Association for the Advancement of Animal Breeding and Genetics Conference Australia What do you plan to do during the next reporting period to accomplish the goals?We plan to produce more content for eBEEF and start to merge information from three NIFA-supported grants (Integrated Program for Reducing Bovine Respiratory Disease Complex in Beef and Dairy Cattle; National Program for Genetic Improvement of Feed Efficiency in Beef Cattle; and Identification and Management of Alleles Impairing Heifer Fertility While Optimizing Genetic Gain in Beef Cattle) onto the eBEEF.org site. The BRD CAP is planning a half day research symposium July 20, 2016 at the ASAS meeting, and members of eBEEF are planning a December 2016 symposium in Kansas City, MO summarizing the results of the BRD CAP, in addition to the other large beef genomics grants. This symposium will be modeled on the successful NBCEC symposiums that have been held at this time and location before and will involve participation of all of the eBEEF team. Presentations will be recorded and loaded on the eBEEF.org website. I will continue to speak nationally and internationally on topics related to animal biotechnology and genomics.

Impacts
What was accomplished under these goals? Objective 2: Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes. As part of the Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP; USDA NIFA grant 2011-68004-30367) the eBEEF.org website (the beef genetics/genomics community of practice within eXtension) was officially launched at BIF 2015 in Biloxi, MS. eBEEF.org is part of the national eXtension program with the goal of being a one-stop site for beef cattle genetics and genomics information. Beef cattle specialists from six land grant institutions have joined forces to provide educational materials that are pertinent to today's beef cattle producers, without searching multiple sites or filtering through countless hits on a search. The site contains factsheets, short frequently asked question (FAQ) video clips, relevant conference recordings and webinars, a blog and links to other useful beef sites. Another goal of the eBEEF.org website is to archive the information generated from current and future beef genetics integrated grants funded by USDA-NIFA. All eBEEF.org team members are a part of one or more of the three current grants (Integrated Program for Reducing Bovine Respiratory Disease Complex in Beef and Dairy Cattle; National Program for Genetic Improvement of Feed Efficiency in Beef Cattle; and Identification and Management of Alleles Impairing Heifer Fertility While Optimizing Genetic Gain in Beef Cattle. The other team members are Dr. Darrh Bullock (University of Kentucky); Dr. Jared Decker, University of Missouri; Dr. Megan Rolf, Oklahoma State University; Dr. Matt Spangler, University of Nebraska; and Dr. Bob Weaber, Kansas State University. As part of a collaborative grant entitled "Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle" (USDA NIFA grant 2013-68004-20364), collaborator Dr. Jerry Taylor at University of Missouri is sequencing more than 250 Angus, Hereford, Simmental, Charolais, Gelbvieh, Red Angus, Maine Anjou, Beefmaster and Limousin bulls to identify loss of function alleles. These will then be tested on a populations of 10,000 heifers with reproductive and breeding data that are part of the Show-Me-Select heifer replacement program. The ultimate objective of this research project is to identify lethal recessive alleles and develop tools for the implementation of strategic mating. I have been working with Dr. Brian Kinghorn, at the University of New England in Armidale, Australia to develop a computer program to optimize mating between animals carrying multiple loss of function alleles. Results from a simulation exercise were presented at the Applied Reproductive Strategies in Beef Cattle Conference. Computerized mating programs can help to simplify the use of DNA information to ensure that carriers are mated strategically to minimize the incidence of affected offspring, while still utilizing their genetics when the value of their merit overrides the discount associated with their carrier status. A NIFA conference grant (USDA NIFA grant 2015-67015-23693) was obtained for the Applied Reproductive Strategies in Beef Cattle Conference (ARSBC) that was held at UC Davis from August 17th-18th, 2015. A total of 183 attendees registered for the meeting. Summaries, PowerPoint slides and audio of speaker presentations are published online on the Newsroom tab of the conference website (www.appliedreprostrategies.com). Other conferences that I helped organize this year included a half-day BRD Symposium is being planned in conjunction with the annual American Association of Bovine Practitioners (AABP) meeting which was held in September 2015 in New Orleans; and the 10th Transgenic Animal Conference will was held at Tahoe City, CA August 9-13, 2015. Usefulness of Findings: The overall objective of the bovine respiratory disease project (BRD CAP; USDA NIFA grant 2011-68004-30367) is to reduce the incidence of BRD in beef and dairy cattle by capitalizing on recent advances in genomics to enable novel genetic approaches to select for cattle that are less susceptible to disease. The ultimate objective of the fertility research project (USDA NIFA grant 2013-68004-20364) is to use genomics approaches to identify potential lethal recessive alleles and develop tools for the implementation of strategic matins to reduce the incidence of carrier matings thereby reducing the the incidence of pregnancy failure. Computerized mating programs offer a simple, inexpensive solution for avoiding affected matins. They can help to simplify the use of DNA information to ensure that carriers are mated strategically to minimize the incidence of affected offspring, while still utilizing their genetics when the value of their merit overrides the discount associated with their carrier status. Audiences targeted from outcomes stemming from this project include various segments of the beef cattle industry, including: breed associations; seedstock and commercial beef producers; the AI industry; the academic community; and extension livestock specialists. The Applied Reproductive Strategies in Beef Cattle Conference (ARSBC) 2015 brought together 183 attendees, including producers, veterinarians, researchers, extension educators, undergraduate, graduate, veterinary students from 11 different academic institutions and industry representatives from many states. Overall, responses from the attendees were very positive. Results from the post-conference evaluation included an average score of 4.53/5 for speaker knowledge and 4.15/5 for speaker effectiveness. All of the papers were printed in a hard copy proceedings which are available on the website (www.appliedreprostrategies.com). The AABP BRD symposium papers presented were published in the 2015 Proceedings of the 48th Annual Conference of the American Association of Bovine Practitioners; and the papers and abstracts presented at the 10th Transgenic Animal Conference will be published in an upcoming issue of Transgenic Research.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Neibergs HL, Seabury CM, Wojtowicz AJ, Wang Z, Scraggs E, Kiser J, Neupane M, Womack JE, Van Eenennaam A, Hagevoort GR, Lehenbauer TW, Aly S, Davis J, Taylor JF. Susceptibility loci revealed for bovine respiratory disease complex in pre-weaned Holstein calves. BMC Genomics. 2014 Dec 22; 15(1):1164.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Van Eenennaam, A., Neibergs, H, Seabury, C. Taylor, J., Wang, Z., Scraggs, E., Schnabel, R.D., Decker, J., Wojtowicz, A., Aly, S., Davis, J., Blanchard, P., Crossley, B., Rossitto, P., Lehenbauer, T., Hagevoort, R., Chavez, E., Neibergs, J.S., Womack, J.E. 2014. Results of the BRD CAP: progress toward identifying genetic markers associated with BRD susceptibility. Animal Health Research Reviews 15(2): 157-160.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Aly, S., Love, W., Williams, D., Lehenbauer, T., Van Eenennaam, A., Drake, C., Kass, P., Farver, T. 2014. Agreement between bovine respiratory disease scoring systems for pre-weaned dairy calves. Animal Health Research Reviews 15(2): 148-150.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ng, TF, Kondov, NO, Deng, X, Van Eenennaam, A, Neibergs, HL, Delwart, E. 2015. A metagenomics and case-control study to identify viruses associated with bovine respiratory disease. Journal of Virology. 89(10): 5340-9.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Gershwin, L. J., Van Eenennaam, A.L., Anderson, M. L., Heather A McEligot, H. A., Matt X Shao, M. X., Toaff-Rosenstein, R., Taylor, J. F., Neibergs, H. L. Single Pathogen Challenge with Agents of the Bovine Respiratory Disease Complex: developing a tissue resource for RNA sequence analysis of disease response. PLoS One 10(11): e0142479.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Tizioto, P., Kim, J., Seabury, C., Schnabel, R., Gershwin, L., Van Eenennaam, A., Roaff-Rosenstein, R., Neibergs, H., Taylor, J. 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(6): e0131459


Progress 01/03/14 to 09/30/14

Outputs
Target Audience: The target audience reached through my outreach efforts during this period included scientists (academic and industry), educators, veterinarians (academic and private practice), beef and dairy cattle producers and breeders, policy makers, as well as undergraduate, graduate and veterinary students. I have also done a lot of genomics and biotechnology presentations to explain basic plant and animal breeding methods to a more general public audience during the reporting period. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? The BRD Symposium provided training and development for producers and veterinarians, as well as students, through the dissemination of new information that is directly applicable to feedlots and dairies, not only in the U.S., but globally. Presentations provided cutting edge information in a variety of fields, from recognized experts, and the structure of the meeting allowed for the audience to see how all of these subjects fit together in the management of this complex disease. The availability of published papers and recorded presentations will continue to provide training to interested parties in the future. All papers were published in the December 2015 issue of Animal Health Research Reviews. How have the results been disseminated to communities of interest? After the BRD Symposium, recorded presentations and proceedings were immediately made available to AVC members on the AVC website. Proceedings books have been available to interested parties for a small fee to cover printing and mailing since the conclusion of the meeting. There are plans to have the recordings from the meeting made available on the eXtension Beef Genetics and Breeding CoP, as well as for educational purposes through the USDA BRD-CAP group. I gave the following presentations during the reporting period · "GMOs in animal agriculture: time to consider both costs and benefits in regulatory evaluations, The 11th World Congress on Animal Production, Beijing, China 10/17/2013 · "The California Commercial Beef Cattle Ranch Project", 20th Association for the Advancement of Animal Breeding and Genetics Conference, Napier, New Zealand, 10/21/2013 · "Update on animal genomics and biotechnology research projects and activities" UCCE Meat Production and Food Safety Program Team meeting, Sparks, NV 11/14/2013 · "Animal Biotechnology and Genomics Extension Program", Colorado State University Extension Graduate Class Internet Lecture, 11/20/2013 · "Regulation and Commercialization of Transgenics in the Livestock Sector" XXII International Plant & Animal Genome Meeting, San Diego, CA, 1/11/2014 · "Regulation and Commercialization of Transgenics in the Livestock Sector" XXII International Plant & Animal Genome Meeting, San Diego, CA, 1/11/2014 · "'Delivering genomics to the beef herd" 2014 Saskatchewan Beef and Forage Symposium. Saskatoon, SK, Canada 1/22/2014 · "Labeling Genetically Engineered Feed: The Science and the Facts" International Dairy Foods Association Dairy Forum, Palm Springs, CA. 1/27/2014 · Genomics in the beef cattle industry: the US situation" Armidale Animal Breeding Summer Course 2014. Armidale, NSW, Australia 2/7/2014 · "Genome selection: Basics and experience in animal systems" UC Davis Seed Biotechnology Center Breeding with Genomics Class, Davis, CA 2/12/201 · "Cost-benefit considerations of livestock genomics: who pays, who benefits", Genome Alberta/Alberta Livestock and Meat Association will be organizing and hosting the conference Livestock Genomics in Alberta: Economic, Environmental, Ethical, Legal and Social (GE3LS) Implications Calgary, Alberta, Canada 4/23/2014 · "The governance of precise breeding techniques: can science win one for a change?" Seed Central, Davis, CA 5/8/2014 · "Innovations in identifying genetically superior animals: impact of genomic technologies in genetic evaluations" (Inovações na identificação de animais geneticamente superiores: impactos das tecnologias genômicas nas avaliações genéticas) - IX SIMCORTE, Federal University of Viçosa - UFV, Brazil 6/19/2014 · "Performance trends in commercial livestock populations in the United States before and subsequent to the inclusion of GMO (Genetically Engineered) feed in livestock diets" 2014 ADSA-ASAS-CSAS Joint Annual Meeting, July 20-24, 2014, Kansas City, MO 7/21/2014 · "Beef heifer replacement: Considerations related to breed and biological type" 2014 ADSA-ASAS-CSAS Joint Annual Meeting, July 20-24, 2014, Kansas City, MO 7/22/2014 · "Genetically Modified Organisms and Livestock Feed (ruminants)" 7th Annual Cross Border Livestock Health Conference (CBLHC)/ 2014 Pacific Northwest Economic Region (PNWER) 24th Annual Summit July 20-24, 2014, Whistler, British Columbia, Canada 7/23/2014 · "BRD CAP Research Update", NC1192 Meeting, Denver, CO 7/29/2014 · "Results of the BRD CAP project: Progress towards identifying genetic markers associated with BRD susceptibility", Bovine Respiratory Disease Symposium (BRDS) 2014: New Approaches to Bovine Respiratory Disease Prevention, Management and Diagnosis, July 30-31, 2014, Denver, CO 7/30/2014 · "Update on the Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP): Progress and Perspectives" AVC meeting, Denver, CO 8/1/2014 · "Modern Biotechnology-Introduction: History of biotech - how the technology has evolved over time all the way to present day", Biotechnology regulation immersion course 2014, University of Missouri, Columbia, 8/12/2014 · "Modern Biotechnology - Genetic Engineering: Animal transformation", Biotechnology regulation immersion course 2014, University of Missouri, Columbia, 8/12/2014 · "Biotech Pipeline - Animal biotech pipeline", Biotechnology regulation immersion course 2014, University of Missouri, Columbia, 8/12/2014 · "BRD CAP Extension Progress: Advisory Board Report" Seattle, WA 8/14/2014 · "Distilling Your Message on Animal Biotechnology", Livestock Biotech Summit, Sioux Falls Convention Center, Sioux Falls SD, 9/16/14 · "Biomedical and Agricultural Animal Regulatory Pathway" Livestock Biotech Summit, Sioux Falls Convention Center, Sioux Falls SD, 9/18/14 What do you plan to do during the next reporting period to accomplish the goals? As part of my outreach responsibilities I am organizing three symposiums in 2015. A half-day BRD Symposium is being planned in conjunction with the annual American Association of Bovine Practitioners (AABP) meeting which will be held in September 2015 in New Orleans. Speakers tentatively to include Dr. Holly Neibergs (Washington State University), Dr. Laurel Gershwin (UC Davis), Dr. Shannon Neibergs (Washington State University), Dr. Alison Van Eenennaam (UC Davis), Dr. John Richeson (West Texas State University), Dr. Amelia Woolums (University of Georgia), Dr. Jim Lowe (University of Illinois). The 10th Transgenic Animal Conference will be held at Tahoe City, CA August 9-13, 2015; and the annual conference of Applied Reproductive Strategies for Beef Cattle (ARSBC) is going to be held in Davis, CA on August 16-18, 2015. I am on the organizing committee for all of these scientific conferences to share the results of research projects with the target audiences of these research projects.

Impacts
What was accomplished under these goals? Objective 2: Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes. As part of the Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP; USDA NIFA grant 2011-68004-30367) I am collaborating on efforts to develop large bovine respiratory disease case:control populations of dairy and beef cattle. These populations are being used to identify markers associated with animals that are less susceptible to disease. Additionally challenge experiments with viral pathogens BRSV, IBR and BVD and bacterial pathogens, Mycoplasma bovis, Mannheimnia hemolytica, and Pasteurella multocida were conducted at UC Davis. Extensive clinical data have been collected from six steers individually challenged with each pathogen and host response is currently being evaluated at the gene level with RNA-Seq in conjunction with BRD CAP collaborators at several US universities to understand the pathways involved in respiratory disease infection (MO,TX,WA). As part of a collaborative grant entitled "Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle" (USDA NIFA grant 2013-68004-20364), collaborator Dr. Jerry Taylor at University of Missouri is sequencing more than 250 Angus, Hereford, Simmental, Charolais, Gelbvieh, Red Angus, Maine Anjou, Beefmaster and Limousin bulls to identify loss of function alleles. These will then be tested on a populations of 10,000 heifers with reproductive and breeding data that are part of the Show-Me-Select heifer replacement program. The ultimate objective of this research project is to identify lethal recessive alleles and develop tools for the implementation of strategic mating. I have been working with Dr. Brian Kinghorn, at the university of New England in Armidale, Australia to develop a computer program to optimize mating between animals carrying multiple loss of function alleles. Results from a simulation exercise were presented at the World Congress of Genetic Applied to Livestock Production (WCGALP). Computerized mating programs can help to simplify the use of DNA information to ensure that carriers are mated strategically to minimize the incidence of affected offspring, while still utilizing their genetics when the value of their merit overrides the discount associated with their carrier status. A NIFA conference grant (USDA NIFA grant 2013 --01236) was obtained for the Bovine Respiratory Disease Symposium (BRDS) 2014: New Approaches to Bovine Respiratory Disease Prevention, Management and Diagnosis, that was held at the Renaissance Denver Hotel in Denver, CO, USA from July 30th to July 31st, 2014. The major goal of the BRD Symposium was to provide a forum for scientists and veterinarians to come together to learn about new genomic and management technologies to limit the impact of BRD, and to work together to proactively identify approaches that could realistically be used to minimize the incidence of BRD and improve animal well-being in a way that is acceptable to 21st century customers. This conference succeeded in bringing together 304 attendees, representing 35 states and 10 countries. Of the 304, 222 attendees were AVC members and 7 were students. Speakers included academics, veterinarians and industry representatives and covered topics ranging from clinical and laboratory diagnoses to host response to genetics to management. Question and discussion sessions with speakers were held after every section and provided opportunities to explore topics in greater depth and allowed attendees to share their perspectives on the issues at hand. Overall, responses from the attendees were very positive. Results from the post-conference evaluation included an average score of 4.53/5 for speaker knowledge and 4.15/5 for speaker effectiveness. Evaluation comments included observations that the conference was well organized, covered all aspects of the syndrome and brought light to new information. Usefulness of Findings: The overall objective of the bovine respiratory disease project (BRD CAP; USDA NIFA grant 2011-68004-30367) is to reduce the incidence of BRD in beef and dairy cattle by capitalizing on recent advances in genomics to enable novel genetic approaches to select for cattle that are less susceptible to disease. The ultimate objective of the fertility research project (USDA NIFA grant 2013-68004-20364) is to use genomics approaches to identify potential lethal recessive alleles and develop tools for the implementation of strategic matins to reduce the incidence of carrier matings thereby reducing the the incidence of pregnancy failure. Computerized mating programs offer a simple, inexpensive solution for avoiding affected matins. They can help to simplify the use of DNA information to ensure that carriers are mated strategically to minimize the incidence of affected offspring, while still utilizing their genetics when the value of their merit overrides the discount associated with their carrier status. Audiences targeted from outcomes stemming from this project include various segments of the beef cattle industry, including: breed associations; seedstock and commercial beef producers; the AI industry; the academic community; and extension livestock specialists.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Weber, K. L. G. Rincon, and A. L. Van Eenennaam. 2014. Genome-Wide Association Study and Differential Expression Analysis of Feed Efficiency using HD SNP Genotyping and Multiple Tissue RNAseq Abstract #W146 and P545. Final program and abstract guide. XXII International Plant & Animal Genome Meeting, San Diego, CA, Jan.11-15, 2014
  • Type: Other Status: Published Year Published: 2014 Citation: Van Eenennaam, A. L. 2014. Safety and supply of milk, meat and eggs from livestock that have consumed GMO feed. 16th Annual Dairy Ingredients Symposium, Shell Beach, CA 3/26/2014
  • Type: Other Status: Published Year Published: 2014 Citation: Welly, B.T., M. R. Miller, J. L. Stott, J. F. Medrano, M. T. Blanchard, S. O'Rourke, A. E. Young, A. D. Islas-Trejo and A. L. Van Eenennaam. 2014. Genome assembly of the putative etiologic agent of epizootic bovine abortion. Proceedings, Western Section, American Society of Animal Science. Vol. 65, 8-13.
  • Type: Other Status: Published Year Published: 2014 Citation: Van Eenennaam, A. Performance trends in commercial livestock populations in the United States before and subsequent to the inclusion of GMO (Genetically Engineered) feed in livestock diets 2014 ADSA-ASAS-CSAS Joint Annual Meeting, July 20-24, 2014, Kansas City, MO 7/21/2014
  • Type: Other Status: Published Year Published: 2014 Citation: Van Eenennaam, A. Beef heifer replacement: Considerations related to breed and biological type 2014 ADSA-ASAS-CSAS Joint Annual Meeting, July 20-24, 2014, Kansas City, MO 7/22/2014
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Van Eenennaam, A. 2014. Update on the Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP):� Progress and Perspectives" AVC meeting, August 1, 2014, Denver, CO.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Van Eenennaam, A. 2014. Results of the BRD CAP project: Progress towards identifying genetic markers associated with BRD susceptibility. Bovine Respiratory Disease Symposium, July 30, 2014, Denver, CO.
  • Type: Other Status: Published Year Published: 2014 Citation: Beef Producer Combat BRD, Other Beef Cattle Health Issues with Genetic Selection, July 24, 2014. http://beefproducer.com/story-combat-brd-beef-cattle-health-issues-genetic-selection-10-115469-nl_23_nlr_93?utm_source=newsletter&utm_medium=email&utm_campaign=24+July+2014
  • Type: Other Status: Published Year Published: 2014 Citation: Bovine Veterinarian From the BIF conference: Genetics and BRDC, June 25, 2014. http://www.bovinevetonline.com/news/industry/bif-conference-genetics-and-brdc
  • Type: Other Status: Published Year Published: 2014 Citation: Drover's Cattle Network Selection for disease resistance, August 7, 2014. http://www.bovinevetonline.com/news/industry/selection-disease-resistance
  • Type: Other Status: Published Year Published: 2014 Citation: Drover's Cattle Network BRD trends, August 6, 2014. http://www.bovinevetonline.com/news/industry/brd-trends
  • Type: Other Status: Published Year Published: 2014 Citation: Drover's Cattle Network Genetic Selection for healthier cattle, July 23, 2014. http://www.cattlenetwork.com/animal-health-center/genetic-selection-healthier-cattle?utm_source=6567F1189245F1A&utm_medium=eNL&utm_campaign=Drovers+CattleNetwork+Alerts_20141126&utm_term=&utm_content
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Love WJ, Lehenbauer TW, Kass PH, Van Eenennaam AL, Aly SS. 2014. Development of a novel clinical scoring system for on-farm diagnosis of bovine respiratory disease in pre-weaned dairy calves. PeerJ 2:e238 http://dx.doi.org/10.7717/peerj.238.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Van Eenennaam, A.L., K. L. Weber, and D. J. Drake. 2014. Evaluation of bull prolificacy on commercial beef cattle ranches using DNA paternity analysis. Journal of Animal Science. 92:2693-701.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Schnabel, RD, JF Taylor, AL Van Eenennaam, DS Brown, MF Smith, MM Rolf, MD MacNeil, BP Kinghorn, and DJ Patterson. Reducing the incidence of early embryonic mortality in beef cattle. Proceedings, 10th World Congress of Genetics Applied to Livestock Production. August, 2014. Vancouver, BC, Canada.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Van Eenennaam, AL, and BP Kinghorn. 2014. Use of Mate Selection software to manage lethal recessive conditions in livestock populations. Proceedings, 10th World Congress of Genetics Applied to Livestock Production. August, 2014. Vancouver, BC, Canada.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Van Eenennaam, A.L., J.F. Taylor, D.S. Brown, M.F. Smith, R.D. Schnabel, S.E. Poock, J.E. Decker, F.D. Dailey, M.M. Rolf, B.P. Kinghorn, M.D. MacNeil, and D.J. Patterson. 2014. Identification and Management of Loss of Function Alleles. Proceedings, Applied Reproductive Strategies in Beef Cattle. Stillwater, OK
  • Type: Other Status: Published Year Published: 2014 Citation: Van Eenennaam, A. L. 2014. Regulation and Commercialization of Transgenics in the Livestock Sector. Abstract # W144. Final program and abstract guide. XXII International Plant & Animal Genome Meeting, San Diego, CA, Jan.11-15, 2014.