Progress 01/01/09 to 12/31/13
Outputs
Target Audience: The target audience of this project included beef cattle producers and extension professionals interested in the use of DNA markers on commercial beef cattle operations. The results of this Integrated project have been presented to audiences at a total of ~ 100 outreach events in 13 states and 5 countries over the past 5 years. Collaborating ranchers were involved in several one-on-one educational events and participated in surveys documenting their learnings over the course of the grant. In August 2012 a producer education day were held on the property of one of the collaborating ranches. This educational event attracted about 100 producers and involved presenting the results of the project, and also a field demonstration exercise on bull selection in August. The grant was also used to help fund a national educational event entitled “Integrating DNA Information into Beef Cattle Production Systems”. This event was held in Kansas City in March, 2013 in collaboration with extension educators from the National Beef Cattle Evaluation Consortium. All talks at this educational event were recorded and are free to use at the National Beef Cattle Evaluation Consortium (NBCEC) website (http://www.nbcec.org/workshops/). Changes/Problems: In June 8, 2011 permission was obtained to redirect $30K of grant funds to develop the capacity to store and analyze high density SNP data at UC Davis. These funds were used towards the purchase of a server and the software (CLC Genomics Workbench from CLC bio) required to analyze high density genotyping data. Additionally, a one-year no cost extension was requested for this project through to 12/31/2013 to allow time for the collection of the final carcass data from the Year 3 cattle on the trial. Additionally the planned national NBCEC educational symposium for cattle producers entitled "Integrating DNA Information into Beef Cattle Production Systems" summarizing the results of this integrated research project was held in March 4-5, 2013 in Kansas City, MO Data from this project was also presented at the American Society of Animal Science (ASAS) meetings, and the Association for the Advancement of Animal Breeding and Genetics (AAABG) in 2013. What opportunities for training and professional development has the project provided? This research funded by this grant was Kristina Weber’s Ph.D. research project. Kristina graduated in September, 2013 with expertise in • Sample collection and DNA extraction • Paternity determination • Databasing of genotypic, phenotypic and pedigree data • Use of linear models • Variance component estimation • Development of numerator and genomic relationship matrices • Genomic prediction using phenotypic and EPD data • Comparative analysis of high density genotyping platforms • Programming using R During the course of her Ph.D. she participated in Genomic selection training opportunities at Iowa State University and the Summer Institute in Statistical Genetics at the University of Washington. She also undertook an internship at Zoetis in Kalamazoo, MI. She has since been employed there as a PostDoctoral scholar. PD Van Eenennaam took a sabbatical for 3 months in 2009 at the University of Melbourne with Professor Mike Goddard to undertake the value proposition work that resulted in the Journal of Animal Science publication. Additionally the results of this project have been of great interest to the beef cattle community and have resulted in many professional development opportunities for Dr. Van Eenennaam to attend a number of conferences and events as an invited speaker as can be seen by the dissemination events information listed below. How have the results been disseminated to communities of interest? 2012 · “Implications and Application of Whole Genome (re) Sequencing.” National Beef Cattle Evaluation Consortium Brownbagger, Internet teleconference series. 10/24/2012 · “Translational Genomics: Delivering Value to the Beef Cattle Industry”, Alberta Livestock and Meat Agency, Calgary, Canada, 11/6/2012 · “What is the value of DNA-based information?”, Alberta Livestock and Meat Agency, Calgary, Canada, 11/6/2012 · “Using DNA to determine performance and economics of commercial herd bulls in multisire natural service breeding groups” Applied Reproductive Strategies in Beef Cattle, December 3-4, 2012; Sioux Falls, SD, 12/3/2012 2013 · “Developing tools to simplify the use of DNA information in beef cattle breeding”, Extension In-service training, University of Missouri, Columbia, MO 2/12/2013 · “Using DNA information in beef cattle production”, World Agri-Expo, Tulare, CA 2/13/2013 · “Bull performance and contribution to ranch income”, Winter Ag Meeting o Montague, CA 2/21/2013 o Willows, CA, 2/22/2013 o Cottonwood, CA, 2/22/2013 o Eureka, CA, 2/23/2013 o Calistoga, CA, 2/24/2013 · “Economics of commercial ranch bulls: matching marketing strategy to bull selection” NBCEC workshop “ Integrating DNA Information into Beef Cattle Production Systems”, Kansas City, MO 3/5/2013 · “Cattle Genomics Research at UC Davis”, UCCE North Valley Dairy Day, Orland, CA 3/14/2013 · “Using DNA paternity testing to evaluate commercial bull performance”, American Society of Animal Science Annual Meeting, Indianapolis, IN 7/9/2013 · “The California Commercial Beef Cattle Ranch Project”, 20th Association for the Advancement of Animal Breeding and Genetics Conference, Napier, New Zealand, 10/21/2013 · “Natural service bull performance and production in commercial beef herds”. Applied Reproductive Strategies in Beef Cattle October 15, 2013; Staunton, VA · “Update on animal genomics and biotechnology research projects and activities” UCCE Meat Production and Food Safety Program Team meeting, Sparks, NV 11/14/2013 · “'Delivering genomics to the beef herd” 2014 Saskatchewan Beef and Forage Symposium. Saskatoon, SK, Canada 1/22/2014 What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The overall research objective of this project was to develop a genotyped, phenotyped population to permit the assessment of different DNA-enabled approaches for predicting the genetic merit of Angus sires on commercial beef ranches. Approximately 5,400 progeny conceived in natural-service, multiple sire breeding pastures on 3 commercial cow-calf ranches in Northern California from 2009-2011 were assigned to a single herd bull using SNP data. The number of calves born per sire per calf drop varied greatly, ranging from 0 in ~ 7% of bull seasons to 64. The total adjusted 205d weight per bull per calf drop was almost totally explained by prolificacy (R2=0.98), and showed little correlation (R2=0.09) with average calf weaning weight per sire. Over 4,000 offspring were followed through the feedlot, and processing plant to obtain carcass data. Progeny data from the bulls’ first calf crop were used to calculate commercial ranch genetic (rEBV) evaluations for the bulls. These rEBVs were then compared to breed association (bEBV) EBV and genomic predictions (gMBV). Genomic predictions were derived using two multi-breed populations, one of approximately 2,000 mixed purebred animals with EBV and the other of approximately 3,400 crossbred animals with phenotypes. Though moderately accurate in cross-validation, these predictions had low genomic prediction accuracy and demonstrated ability to predict future progeny performance in Angus-sired commercial cattle. In contrast, Angus-derived genomic predictions from several thousand animals were more accurate and demonstrated superior ability to predict future progeny performance relative to typical yearling bull breed association EBV. The traits analyzed included weaning weight, hot carcass weight, ribeye area, marbling score, and backfat thickness. In all cases, the EPV were found to not be equally predictive based on χ2 test (P<0.05). In general genomic EPV derived from an analysis of over 3,000 Angus bulls (gEBV) were more predictive than bEBV and rEBVs. The gEBV and rEBV became more comparable when rEBV included larger numbers of progeny derived from more than a year’s worth of calf data. However, this scale of progeny testing required to generate ranch EPDs is prohibitively expensive for commercial beef bulls as the beef industry is currently structured. Therefore, gEBV appear to be a more cost-effective selection tool than rEBVs for commercial beef cattle producers selecting young Angus herd bulls. The population resource developed in this research may be useful in the future in combination with other populations to further refine beef cattle genomic predictions and toward that end, the phenotypic and genotypic database will be made available to other researchers in this field. Progeny hair samples will be available for further genotyping and potentially genomic prediction of progeny phenotypes. The extension objectives of this integrated proposal were to develop and deliver educational materials to a national audience on the integration of DNA information into beef cattle selection programs. Materials developed included background information on DNA technologies, as well as producer-targeted materials detailing the outcomes and applications of the research findings. These materials were made available on eXtension and in many proceedings and journal articles. As can be seen from the extensive dissemination summary these objectives were completed successfully. Additionally, several independent but related evaluations of data have led to management changes on the cooperating ranches. Breeding objectives were developed for these ranches that identified optimal economic weighting of valuable traits. This weighting was significantly different and more comprehensive than current selection tools available at bull purchase. In addition, bull prolificacy evaluations highlighted the value of improved bull fertility. Specifically the greater contribution of bull fertility compared to progeny growth toward total ranch beef output, and the tremendous variability in individual bull contribution to genetic improvement due to variable calf production, and thus replacement heifer creation. Additional cost comparisons of natural service breeding using values generated from the cooperating ranches and comparisons with artificial insemination costs led to one of the cooperating ranches introducing AI to their herd. This introduction was further motivated by increasing recognition of the difference in EPD accuracies associated with natural service versus AI studs.
Publications
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2013
Citation:
Weber, K. L. 2013. Genomic prediction in practice: Refining a new selection tool for commercial beef cattle producers. Animal Biology Ph.D. Dissertation. University of California, Davis, CA.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2014
Citation:
Van Eenennaam, A.L., K. A. Weigel, A. E. Young, M. A. Cleveland, and J. C. M. Dekkers 2014. Applied Animal Genomics: Results from the Field. Annual Review of Animal Biosciences. 2:105-139
- Type:
Journal Articles
Status:
Under Review
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.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2012
Citation:
Van Eenennaam, A. L. 2012. Using DNA to determine performance and economics of commercial herd bulls in multisire natural service breeding groups . Proceedings, Applied Reproductive Strategies in Beef Cattle. December 3-4, 2012; Sioux Falls, SD. Pages 145-164.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Van Eenennaam, A. L., K. L. Weber, and D. J. Drake. 2013. The California Commercial Ranch Project. Proceedings 20th Conference of the Association for the Advancement of Animal Breeding and Genetics (AAABG), October 20- 23, 2013; Napier, New Zealand 20: 10-13.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2013
Citation:
Drake, D.J., K. L. Weber, and A. L. Van Eenennaam. 2013. Natural service bull performance and production in commercial beef herds. Proceedings, Applied Reproductive Strategies in Beef Cattle October 15 16, 2013; Staunton, VA
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Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: Twenty outreach presentations were given to beef cattle audiences regionally, nationally and internationally to disseminate information about the project as follows: -"Genomic Selection 101: Basics and experiences in cattle breeding systems", Plant Breeding Academy, Davis, CA 2/15/2012 -"What are herd bulls accomplishing in multiple-sire breeding pastures" Winter Ag Meeting 2012 -Alturas, CA, 2/21/2012 -Montague, CA 2/23/2012 -Maxwell, CA 2/24/2012 -Cottonwood, CA 2/24/2012 -Eureka, CA 2/25/2012 -"Challenges to Adoption of Molecular Information," NBCEC Symposium - Delivering Genomic Technology to the Beef Industry, Kansas City, MO, 3/6/2012 -"What are herd bulls accomplishing in multiple-sire breeding pastures" Oakdale Livestock Forum, Winter Ag Meeting 2012 -"Assessing the accuracy of genomic predictions: Results from the California commercial ranch project" Beef Improvement Federation Meeting, Houston, TX 4/19/2012 -"Interbeef workshop: US report" International Committee for Animal Recording (ICAR) Conference, Cork, Ireland, 5/27/2012 -"How might DNA-based information generate value in the beef cattle sector" 38th International Committee for Animal Recording (ICAR) Conference, Cork, Ireland, 5/29/2012 -"Genetics Research Project Update" California Cattlemen's Association (CCA) Cattle Health, Marketing & BQA Joint Committee Meeting, Harris Ranch, Coalinga, CA 6/14/2012 -"Reduced SNP Panels-creation, realistic expectations, and use in different livestock industries," Weight Trait Project Meeting, Lincoln, NE 6/27/2012 -"The California Commercial Ranch Project" Siskiyou County 63rd Annual Cattle Tour, Cowley Ranch, Montague, CA, 8/23/2012 -"Beef Cattle Genomics - where we have been, where we are now, and where we are headed" National Ultrasound Technicians Teleconference 8/28/2012 -"What's Happening in Beef Genomics" 24th National Association of Animal Breeders (NAAB) Technical Conference, Milwaukee, WI, 9/20/2012 -"Implications and Application of Whole Genome (re) Sequencing." National Beef Cattle Evaluation Consortium Brownbagger, Internet teleconference series. 10/24/2012 -"Translational Genomics: Delivering Value to the Beef Cattle Industry", Alberta Livestock and Meat Agency, Calgary, Canada, 11/6/2012 -"What is the value of DNA-based information", Alberta Livestock and Meat Agency, Calgary, Canada, 11/6/2012 -"Using DNA to determine performance and economics of commercial herd bulls in multisire natural service breeding groups" Applied Reproductive Strategies in Beef Cattle, December 3-4, 2012; Sioux Falls, SD, 12/3/2012 Management changes associated with the interim findings of the project were presented at winter agriculture meetings in Northern California in February 2012, and a field day on one of the collaborating ranches in August of 2012. PARTICIPANTS: Collaborators: Dr. Darrh Bullock, Extension Professor, University of Kentucky, KY Dr. Leslie Bees Butler, Extension Marketing Specialist, UC Davis, CA Dr. Daniel Drake, UC Cooperative Extension Livestock Advisor, CA Dr. Dorian Garrick, Professor, Iowa State University, IA Dr. John Pollak, Professor, , US Meat Animal Research Center, Clay Center, NE Dr. Mark Thallman, US Meat Animal Research Center, Clay Center, NE Graduate Students Kristina Weber, Ph.D. Candidate, UC Davis, CA Trained in -Sample collection and DNA extraction -Paternity determination -Databasing of genotypic, phenotypic and pedigree data -Use of linear models -Variance component estimation -Development of numerator and genomic relationship matrices -Genomic prediction using phenotypic and EPD data -Comparative analysis of high density genotyping platforms -Programming using R Kristina will graduate with her PhD in 2013. Producer Collaborators: Jack Cowley, Cowley Rancher, Siskiyou County, CA Dale, Greg, and Richard Kuck, Kuck Ranch, Siskiyou County, CA Matt Parker, Mole-Richardson Ranch, Siskiyou County, CA Processor Collaborators: Harris Ranch Beef Company, Coalinga, CA Los Banos Abattoir, Los Banos, CA Software Collaborators: Jim Lowe, Cow Sense Herd Management Software, NE Other Contributors/Collaborators Dr. Jerry Taylor, University of Missouri, MO Dr. Mike Goddard, University of Melbourne and Victorian DPI, Australia TARGET AUDIENCES: The following deliverables and efforts to reach target local, national, and international audiences were completed for this integrated grant in 2012: A total of 20 outreach presentations were delivered to beef cattle audiences regionally, nationally and internationally. A field day to present the findings of this project was held at a collaborating ranch in August, 2012. Proceedings papers and accompanying presentations were given to producer audiences at 24th National Association of Animal Breeders (NAAB) Technical Conference, the Applied Reproductive Strategies in Beef Cattle Meeting and to the Alberta Livestock and Meat Agency, Calgary, Canada. All of these efforts were designed to cause a change in knowledge about DNA testing among beef cattle producers. PROJECT MODIFICATIONS: A one-year no cost extension was requested for this project through to 12/31/2013 to allow time for the collection of the final carcass data from the Year 3 cattle on the trial. Additionally a national NBCEC educational symposium for cattle producers entitled "Integrating DNA Information into Beef Cattle Production Systems" summarizing the results of this integrated research project is planned for March 4-5, 2013 in Kansas City, MO (see the following website for information http://www.nbcec.org/producers/workshops.html). Data from this project will also be presented at the American Society of Animal Science (ASAS) meetings, and the Association for the Advancement of Animal Breeding and Genetics (AAABG) in 2013.
Impacts
The overall objective of this project was to develop a genotyped population of cattle that had been phenotyped for growth and carcass traits to enable the evaluation and/or assessment of different DNA-enabled approaches for predicting the genetic merit of herd sires on commercial beef ranches. The research objective is to compare the current means of genetic prediction of herd sires, which is the use of breed-based expected progeny differences with DNA-assisted genetic predictions, and "commercial ranch" genetic evaluations based on the performance of their offspring under field conditions. As of the close of 2012, we have completed collection of birth weight, weaning weight, and projected feedlot in-weight records from three calf crops produced on three commercial and one University-affiliated cow-calf beef herds, encompassing approximately 2,500 cows bred per year to over 125 purebred Angus bulls. These phenotyped calves have all been genotyped at low density for the purpose of parentage testing and sample identification. Birthdate records were collected on 5,382 individually identified calves enrolled in the trial. Of these 5,272 (98%) were assigned an individual sire. In the first quarter of 2013, meat samples (est. N=967) will be collected from the final group of calves when they are processed at Harris Ranch. This population was used to "validate" the accuracies of DNA-based genetic merit prediction equations derived from data provided by US MARC and other genomic prediction products including Angus-derived Pfizer 50K MVPs, Merial genomic-enhanced EPDs, and Angus-derived predictions developed by collaborators at Iowa State University (Garrick) and the University of Missouri-Columbia (Taylor). In 2013, we plan to complete an analysis of several additional traits phenotyped during this project and prepare for the final analysis of the association between on-ranch EPDs, breed-association EPDs, and DNA-based genetic predictions. A national symposium for cattle producers summarizing the results of this integrated research project is planned for March 4-5, 2013. Several independent but related evaluations of data have led to management changes on the cooperating ranches. Breeding objectives were developed for these ranches that identified optimal economic weighting of valuable traits. This weighting was significantly different and more comprehensive than current selection tools available at bull purchase. In addition, bull prolificacy evaluations highlighted the value of improved bull fertility. Specifically the greater contribution of bull fertility compared to progeny growth toward total ranch beef output, and the tremendous variability in individual bull contribution to genetic improvement due to variable calf production, and thus replacement heifer creation. Additional cost comparisons of natural service breeding using values generated from the cooperating ranches and comparisons with artificial insemination costs led to one of the cooperating ranches introducing AI to their herd. This introduction was further motivated by increasing recognition of the difference in EPD accuracies associated with natural service versus AI studs.
Publications
- K. L. Weber, G. Rincon, A. L. Van Eenennaam, B. L. Golden, and J. F. Medrano. 2012. Differences in allele frequency distribution of bovine high-density genotyping platforms in Holsteins and Jerseys. 2012. Abstract 33. American Society of Animal Science Annual Meeting, Phoenix, AZ. J. Anim. Sci. Vol. 90, Suppl. 3: 153.
- M. C. McClure, T. S. Sonstegard, G. R. Wiggans, A. L. Van Eenennaam, K. L. Weber, C. Penedo, and C. P. Van Tassell. 2012. Imputation of microsatellite alleles from dense SNP genotypes for paternal verification. American Society of Animal Science Annual Meeting, Phoenix, AZ. Late Breaking Abstract Session, 7/15/2012.
- Weber, K. L., R. M. Thallman, J. W. Keele, W. M. Snelling, G. L. Bennett, T. P. L. Smith, T. G. McDaneld, M. F. Allan, A. L. Van Eenennaam, and L. A. Kuehn. 2012. Accuracy of genomic breeding values in multi-breed beef cattle populations derived from deregressed breeding values and phenotypes. Journal of Animal Science. 90:4177-4190.
- Weber, K. L., D.J. Drake, J. F. Taylor, D.J. Garrick, L.A. Kuehn, R.M. Thallman, R.D. Schnabel, W.M. Snelling, E.J. Pollak, A.L. Van Eenennaam. 2012. The accuracies of DNA-based genetic merit prediction equations derived from Angus- and multi-breed beef cattle training populations. Journal of Animal Science. 90:4191-4202.
- Van Eenennaam, A. L. 2012. "How might DNA-based information generate value in the beef cattle sector" International Committee for Animal Recording (ICAR) Session. Cork, Ireland. May 28-June 1, 2012
- Van Eenennaam, A. L. 2012. "What's Happening in Beef Genomics" 24th National Association of Animal Breeders (NAAB) Technical Conference, Milwaukee, WI, 9/20/2012. In press.
- Van Eenennaam, A. L. 2012. "Using DNA to determine performance and economics of commercial herd bulls in multisire natural service breeding groups". Proceedings, Applied Reproductive Strategies in Beef Cattle. December 3-4, 2012; Sioux Falls, SD.
- G. Rincon, K.L. Weber, A.L. Van Eenennaam, B.L. Golden, and J.F. Medrano. 2012. Performance of Illumina and Affymetrix Bovine High Density Genotyping Platforms in Holsteins and Jerseys. Plant and Animal Genome Plant & Animal Genomes XX Conference, January, 2012, Town & Country Convention Center, San Diego, CA
- Van Eenennaam, A. L. 2012. "How might DNA-based information generate value in the beef cattle sector" International Committee for Animal Recording (ICAR) Session. Cork, Ireland. May 28-June 1, 2012.
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: 32 outreach presentations: 1. "Integrating DNA Information into Beef Cattle Production Systems." Yreka, CA 1/11. 2. "Translational genomics: Progress in the adaptation of information derived from genome technologies for animal improvement." Invited speaker. PAG Conf. XIX. San Diego, CA 1/15. 3. "Translational genomics: Progress in the adaptation of information derived from genome technologies for animal improvement." U. of Nebraska, Lincoln, NE 1/28. 4. "Integrating DNA Information into Beef Cattle Production Systems." NBCEC Industry Council mtg., Denver, CO 2/1. 5. "Cloned Cows and Biotech Beef." GGG recruitment, UC Davis, CA 2/18. 6. "Biotech Beef and Cloned Cows: Progress in Translational Genomics." Animal Science Sem., CalPoly San Luis Obispo, CA 3/10. 7. "Uses of DNA information on Commercial Cattle Ranches." UC SFREC Producer Education Day, Browns Valley, CA 4/9. 8. "Update on USDA integrated grant." NBCEC Industry Council mtg., Bozeman, MT 6/1. 9. "What weighting should be given to BRD resistance in selection decisions" BIF mtg., Bozeman, MT 6/3. 10. "Application of Genomic Information: The California Commercial Ranch Project." Producer Education Event, USMARC, Clay Center, NE 6/21. 11. "Commercial Heifer Selection Using Genomics." Producer Education Event, USMARC, Clay Center, NE 6/21. 12. "Integrated Program for Reducing Bovine Respiratory Disease Complex in Beef and Dairy Cattle Coordinated Agricultural Project (BRD CAP)." Acad. of Veterinary Consultants mtg., Colorado Springs, CO 8/4. 13. "What are herd bulls accomplishing in multiple sire breeding pastures" Dorris, CA 8/25. 14-15. Two oral presentations at Appl. Repro. Strat. in Beef Cattle Sym., Joplin, MO 8/31-9/1. 16. "Translational Genomics: Moving animal biotechnologies from the lab to the field." U. of Missouri, Columbia, MO 9/2. 17-18. Two oral presentations at Appl. Repro. Strat. in Beef Cattle Sym., Boise, ID 10/1. 19. "Economic value of genomic information: Sire and commercial heifer selection." NBCEC Brownbagger Series Internet Distance Learning 10/17. 20. "DNA Technologies and Production Markers." Am. Wagyu Assoc. Ann. Conv., Reno, NV 10/27. 21. "Using genetic markers in bull selection." Nevada Cattlemen's Ann. Conv., Gardnerville, NV 11/15. 22. "Beef cattle breeding in Australia." Calif. Cattlemen's Ann. Conv., Reno, NV 11/16. 23-27. "Improving EPD Accuracy by Combining EPD Information with DNA Test Results." Beef Industry Tour in Baker City, Burns, Prineville, Roseburg, and Albany, OR. 12/5-9. In Australia 28. "BLUP and Genomic Selection." Austr. Wagyu Assoc. Genet. Improv. Conf., Armidale 4/30. 29. "Where in the beef cattle supply chain might DNA tests generate value" SMO Appl. Genomics for Sustainable Livestock Breeding Conf., Melbourne 5/5. 30. "The welfare, economic, and genetic impacts of recessive genetic factors (RGFs)." International recessive genetic factors wksp., Sydney 5/9. 31. "Beef translational genomics: Lessons from the literature." John Vercoe Memorial Lecture. AAABG 19th Conf., U. of Western Australia, Perth 7/20. 32. "Will DNA testing make me money" Beef and Dairy Breeding and Genetics Day, Vasse Research Centre 7/22. PARTICIPANTS: Collaborators: Dr. Darrh Bullock, Extension Professor, University of Kentucky, KY Dr. Leslie Bees Butler, Extension Marketing Specialist, UC Davis, CA Dr. Daniel Drake, UC Cooperative Extension Livestock Advisor, CA Dr. Dorian Garrick, Professor, Iowa State University, IA Dr. John Pollak, Professor, US Meat Animal Research Center, Clay Center, NE Dr. Mark Thallman, US Meat Animal Research Center, Clay Center, NE Graduate Students Kristina Weber, Ph.D. Candidate, UC Davis, CA Trained in -Sample collection and DNA extraction -Paternity determination -Databasing of genotypic, phenotypic and pedigree data -Use of linear models -Variance component estimation -Development of numerator and genomic relationship matrices -Genomic prediction using phenotypic and EPD data -Comparative analysis of high density genotyping platforms -Programming and simulation using R Producer Collaborators: Jack Cowley, Cowley Rancher, Siskiyou County, CA Dale, Greg, and Richard Kuck, Kuck Ranch, Siskiyou County, CA Matt Parker, Mole-Richardson Ranch, Siskiyou County, CA Processor Collaborators: Harris Ranch Beef Company, Coalinga, CA Los Banos Abattoir, Los Banos, CA Software Collaborators: Jim Lowe, Cow Sense Herd Management Software, NE Other Contributors/Collaborators Dr. Jerry Taylor, University of Missouri, MO Dr. Mike Goddard, University of Melbourne and Victorian DPI, Australia TARGET AUDIENCES: The following deliverables and efforts to reach target local, national, and international audiences were completed for this integrated grant in 2011: A total of 32 outreach presentations were delivered to beef cattle audiences regionally, nationally and internationally. Four fact sheets were developed and made available on the eXtension website, in addition to the UC Davis Animal Biotechnology websites. Two popular press articles were written for Beef Magazine and California Cattlemen's Magazine. All of these efforts were designed to cause a change in knowledge about DNA testing among beef cattle producers. Several independent but related evaluations of data from the project have led to management changes on the cooperating ranches. Breeding objectives (developed in collaboration with Wayne Upton, CRC Australia) were developed for these vertically integrated ranches that identified optimal economic weighting of genetic traits, an economic index or index traits. This weighting was significantly different and more multi-trait than current ranch genetic trait selection when purchasing herd bulls. In addition, bull prolificacy evaluations further highlighted the economic and genetic contributions of improved fertility in bulls. Specifically the greater contribution of bull fertility compared to progeny growth toward total ranch beef output, and the tremendous variability in individual bull's contribution to genetic improvement due to variable calf production, and thus replacement heifer creation. Additional cost comparisons of natural service breeding using values generated from the cooperating ranches and comparisons with artificial insemination costs lead to one of the cooperating ranches introducing AI as a breeding component. This introduction was further motivated by increasing recognition of EPD accuracies associated with natural service and AI studs. Management changes associated with these interim findings of the project will be presented at a field day on one of the collaborating ranches in August 2012. It is exceedingly difficult to measure producer changes especially in attitudes and understanding of genetic principals and application. The extension educator serving in the project as the primary direct outreach contact (Dr. Daniel Drake) observed that the cooperating ranchers have a profoundly different understanding and appreciation, and application, of genetic tools now compared to before the project. This is despite their long history in beef cattle production, including times when they raised purebred, registered beef cattle. An illustrative example is one producer who has used EPDs for selecting calving ease bulls had a spate of dystocias associated with a single calving ease bull. Previously they would likely have questioned the validity of EPDs but now suspect it is the normal variation seen in low accuracy EPDs from yearling bulls. This is directly related to the educational aspects regarding genetic selection tools the cooperating ranchers have seen from the on-going project results. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The overall objective of this project is to develop a genotyped, phenotyped population to enable the assessment of different DNA-enabled approaches for predicting the genetic merit of herd sires on commercial beef ranches. The research objectives are to compare the current means of genetic prediction of herd sires, which is breed-based expected progeny differences, with DNA-assisted genetic predictions and ranch genetic evaluations (on-ranch EPDs) based on offspring performance under field conditions on 4 commercial cow-calf ranches in Northern California. As of the close of 2011, we have collected 77% of projected birth weight records, 79% of projected weaning weight records, 55% of projected feedlot in-weight records, and 51% of projected carcass records from offspring sired by bulls involved in this project. We have two offspring groups that only require carcass trait and meat sample collection (to be completed during 2012) and one group for which all data collection will take place during 2012-2013. We have genotyped all samples we have collected at this point and have contracted all remaining genotyping. The genotyping of offspring hair and meat samples allows us to determine calf paternity, trace animals from birth to slaughter, and calculate commercial ranch genetic evaluations of bull sires which are used in our comparisons between genetic selection tools. Further, we have developed genomic predictions derived from data provided by USMARC and compared them to progeny performance for the commercial sires on our ranches as well as other genomic predictions provided by Pfizer Animal Genetics, IGENITY, and genomic predictions developed by collaborators at Iowa State University (Garrick) and the University of Missouri-Columbia (Taylor). Publications describing the results of these analyses have been submitted. Several independent but related evaluations of data have led to management changes on the cooperating ranches. Breeding objectives (developed in collaboration with Wayne Upton, CRC Australia) were developed for these ranches that identified optimal economic weighting of valuable traits. This weighting was significantly different and more comprehensive than current selection tools available at bull purchase. In addition, bull prolificacy evaluations highlighted the value of improved bull fertility. Specifically the greater contribution of bull fertility compared to progeny growth toward total ranch beef output, and the tremendous variability in individual bull contribution to genetic improvement due to variable calf production, and thus replacement heifer creation. Additional cost comparisons of natural service breeding using values generated from the cooperating ranches and comparisons with artificial insemination costs led to one of the cooperating ranches introducing AI to their herd. This introduction was further motivated by increasing recognition of the difference in EPD accuracies associated with natural service versus AI studs. Management changes associated with these interim findings of the project will be presented at a field day on one of the collaborating ranches in 2012.
Publications
- Rincon, G., K.L. Weber, A.L. Van Eenennaam, B.L. Golden, and J.F. Medrano. 2011. Performance of bovine high density genotyping platforms in Holsteins and Jerseys. Journal of Dairy Science. 94: 6116-6121.
- Van Eenennaam, A. L. 2011. Beef translational genomics: Lessons from the literature. Association for the Advancement of Animal Breeding and Genetics. 19: 271-278.
- Cooprider, K. L., F. M. Mitloehner, T. R. Famula, E. Kebreab, Y. Zhao, and A. L. Van Eenennaam. 2011. Feedlot efficiency implications on greenhouse gas emissions and sustainability. Journal of Animal Science. 89:2643-56.
- Van Eenennaam, A. L., J.H. van der Werf, and M.E. Goddard. 2011. The value of using DNA markers for beef bull selection in the seedstock sector. Journal of Animal Science. 89:307-320.
- Van Eenennaam, A.L. 2011. Uses of DNA Information on Commercial Cattle Ranches. UC Sierra Foothill Research & Extension Center Annual Beef & Range Field Day Proceedings, pages 1-8.
- Van Eenennaam, A. L. and M. D. MacNeil. 2011. What weighting should be given bovine respiratory disease (BRD) resistance in selection decisions Proceedings of the Beef Improvement Federation. Bozeman, MT, June 3, 2011, pages 61-68.
- Van Eenennaam, A. L. 2011. Improving EPD Accuracy by Combining EPD Information with DNA Test Results. Proceedings of the Applied Reproductive Strategies in Beef Cattle Symposium. August 31-September 1, 2011 Joplin, MO and September 30-October 1, 2011, Boise, ID, pages 163-180.
- Drake, D.J., K.L. Weber and A.L. Van Eenennaam. 2011. What are herd bulls accomplishing in multiple sire breeding pastures Proceedings of the Applied Reproductive Strategies in Beef Cattle Symposium. August 31-September 1, 2011 Joplin, MO and September 30-October 1, 2011 Boise, ID, pages 305-320.
- Van Eenennaam, A.L. 2011. Commercial heifer selection using genomics.
- Van Eenennaam, A.L. 2011. Application of Genomic Information: The California Commercial Ranch Project.
- Van Eenennaam, A.L. 2011. Improving the accuracy of EPDs with DNA information. Beef Magazine. March.
- Van Eenennaam, A. L. 2011. Californians Attend Seedstock Tour Down Under. California Cattleman Magazine. October/November. Pages 34-35.
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: Fifteen outreach presentations were given to beef cattle audiences regionally, nationally and internationally to disseminate information as follows: 1. "Economics of using DNA markers for sorting feedlot cattle", New York Beef Producers' Association, Annual Meeting and Feeder/Winter Management Conference, Syracuse, NY 1/22/10; 2. "Economic of DNA markers for the Cow/Calf Industry", New York Beef Producers' Association, Annual Meeting and Feeder/Winter Management Conference, Syracuse, NY 1/23/10; 3. "Update on DNA marker validation", NBCEC Advisory Council Meeting, San Ant., TX, 1/26/10; 4."What is the value of DNA testing" Beef CRC Genomics' Master Class, Armidale, NSW, Australia 3/30/10; 5. "Case Study: Extension efforts around the use of DNA tests for the U.S. beef cattle industry{" Beef CRC Genomics' Master Class, Armidale, NSW, Australia 3/31/10; 6. "Current Status of Genetically Engineered Animals" Ethics and Biotechnology: Genetically Engineered Animals Breakout session. BIO International Convention. Chicago, IL 5/4/10; 7. "Genomics Survey of producers in the audience using clickers" Producer Education Event, Meat Animal Research Center, Clay Center, NE, 6/7/10; 8. "Technology Review" Producer Education Event, Meat Animal Research Center, Clay Center, NE, 6/7/10; 9. "Economics of using DNA Markers in the seedstock sector" Producer Education Event, Meat Animal Research Center, Clay Center, NE, 6/7/10; 10. "Update on USDA integrated grant" NBCEC Industry Council meeting, Columbia, MO, 6/28/2010 ; 11. "Value of DNA marker information for beef bull selection" Beef Improvement Federation, Columbia, MO, 6/30/2010; 12. "The economics of using DNA markers for bull selection in the beef seedstock sector" ASAS meetings, Denver, CO, 7/14/2010; 13. "The value of DNA information for beef bull selection", World Congress of Genetics Applied to Livestock Production. Leipzig, Germany, 8/2/2010; 14. "Biotech Beef and Cloned Cows: Does Animal Biotechnology have a Future" Viagen presentation. Austin, TX. 11/11/2010; 15. "The Value of Accuracy". NBCEC Brown Bagger. Internet conference 11/17/2010. Additionally, two fact sheets entitled "Commercially-available DNA tests for Beef Cattle" and "Value of DNA information for beef bull selection" were developed and posted on the eXtension website, in addition to the NBCEC and the UC Davis Animal Biotechnology websites. PARTICIPANTS: PARTICIPANTS: Collaborators: Dr. Darrh Bullock, Extension Professor, University of Kentucky, KY Dr. Leslie Bees Butler, Extension Marketing Specialist, UC Davis, CA Dr. Daniel Drake, UC Cooperative Extension Livestock Advisor, CA Dr. Dorian Garrick, Professor, Iowa State University, IA Dr. John Pollak, Professor, Cornell University, NY Dr. Mark Thallman, US Meat Animal Research Center, Clay Center, NE Graduate Students Kristina Weber, Ph.D. Candidate, UC Davis, CA and Krista Cooprider, MS Candidate, UC Davis, CA Producer Collaborators: Jack Cowley, Cowley Rancher, Siskiyou County, CA Dale, Greg, and Richard Kuck, Kuck Ranch, Siskiyou County, CA Matt Parker, Mole-Richardson Ranch, Siskiyou County, CA Processor Collaborators: Harris Ranch Beef Company, Coalinga, CA Los Banos Abattoir, Los Banos, CA Software Collaborators: Jim Lowe, Cow Sense Herd Management Software, NE Other Contributors/Collaborators Dr. Jerry Taylor, University of Missouri, MO Dr. Mike Goddard, University of Melbourne and Victorian DPI, AustraliaKristina Weber, Ph.D. candidate undertook an internship at the Meat Animal Research Center for three months in the Summer (June-August, 2010). She also attended the Summer Institute in Statistical Genetics (SISG) at the University of Washington in June, 2010 TARGET AUDIENCES: The following deliverables and efforts to reach target local and national audiences of beef producers were projected for this integrated grant in 2010: A total of 15 outreach presentations were delivered to beef cattle audiences regionally, nationally and internationally. Two fact sheets were developed as part of a successful producer education event held at the Meat Animal Research Center, Clay Center, NE in June, 2010. Fact sheets were made available on the eXtension website, in addition to the NBCEC and the UC Davis Animal Biotechnology websites. Two popular press articles were written for Beef Magazine and California Cattlemen's Magazine. All of these efforts were designed to cause a change in knowledge about DNA testing among beef cattle producers. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The overall objective of this project is to develop a genotyped, phenotyped population to enable the evaluation and/or assessment of different DNA-enabled approaches for predicting the genetic merit of herd sires on commercial beef ranches. The research objectives are to compare the current means of genetic prediction of herd sires, which is the use of breed-based expected progeny differences with DNA-assisted genetic predictions, and "commercial ranch" genetic evaluations based on offspring performance under field conditions. Additionally, work will be undertaken to develop an approach to determine the costs and benefits associated with DNA testing in the beef cattle industry. This year we collected ranch data and slaughter phenotypes from calves derived from four commercial cow-calf herds (representing a total of ~ 2500 cows) that are using predominately Angus sires. Blood and hair samples were collected on the natural service bulls (45 from Ranch 1, 16 from Ranch 2, 40 from Ranch 3, and 26 from Ranch 4) siring 2009-, 2010-, and 2011-born calves and have been 50K genotyped. As of the close of 2010, Ranches 1-4 have produced 747 of 1887 projected birth weight records (40%), 2513 of 6103 projected weaning weight records (41%), 1533 of 5019 projected feedlot in-weight records (31%), and 1048 of 4426 projected carcass records (24%). Each calf has been given an electronic ID (EID) eartag with a unique RFID code to provide reliable animal identification in addition to visual ID. Hair samples have been collected for 99-SNP genotyping on all calves with recorded weaning weights, and meat samples have been collected for 3K genotyping on all steers and heifers with recorded carcass traits. A database has been established at UC Davis to house DNA and herd data and includes ranch identification, calving cohort, visual IDs, EIDs, dam IDs, sex, and birth dates for all calves and weaning weights and weaning weight dates for weaned calves. Bull data includes visual IDs, EIDs, registration numbers, breeds, birth dates, and seasons used for breeding at a minimum. We are the process of extracting DNA from these samples for genotyping. This will allow us to determine the paternity of the multi-sire pasture-derived calves, and further to calculate commercial ranch genetic evaluations. Further, we are participating in the development of genomic prediction equations derived from data provided by US MARC, and the resulting genomic predictions will be compared to progeny performance for the commercial sires on our ranches. We have purchased other genomic prediction products to evaluate relative to our validation population, including the Angus-derived Pfizer 50K MVPs and Merial genomic-enhanced EPDs. The extension objectives of this project are to develop and deliver educational materials to a national audience on the integration of DNA information into beef cattle selection programs. During 2010, I gave 15 presentations to various audiences regionally, nationally and internationally, I developed a series of series of fact sheets that are posted on the eXtension website, in addition to the NBCEC and the UC Davis Animal Biotechnology websites.
Publications
- Fahrenkrug, S. C., A. Blake, D. F. Carlson, T. Doran, A. L. Van Eenennaam, D. Faber, C. Galli, P. B. Hackett, N. Li, E. A. Maga, J. D. Murray, R. Stotish, E. Sullivan, J. F. Taylor, M. Walton, M. Wheeler, B. Whitelaw, B. P. Glenn. 2010. Precision Genetics for Complex Objectives in Animal Agriculture. Journal of Animal Science. 88:2530-9
- Van Eenennaam, A. L. and W.M. Muir. 2010. Animal biotechnologies and agricultural sustainability chapter in "The Role of Biotechnology in a Sustainable Food Supply." Cambridge University Press. In press.
- Duan, Q., J. Reecy, R. Tait, Q. Liu, A. Van Eenennaam, R. Mateescu, A. Garmyn, and D. Beitz. 2010. Genetic polymorphisms in bovine ferroportin are associated with longissimus dorsi muscle iron content. The FASEB Journal. 24 (1) 229.2
- Van Eenennaam, A. L., J.H. van der Werf, and M.E. Goddard. 2010. The economics of using DNA markers for beef bull selection in the seedstock sector. Journal of Animal Science. J. Anim. Sci. Vol. 88, E-Suppl. 2 745. 6. K.L. Cooprider, A.L. Van Eenennaam. 2010. Sustainability implications of feedlot management practices. J. Anim. Sci. Vol. 88, E-Suppl. 2. 8-9.
- Reecy, J.Tait, R., Van Overbeke, D.; Garmyn, A.; Mateescu, R., Van Eenennaam, A., Duan, Q., Liu, Q., Schoonmaker, J., Drewnoski, M., Beitz, D., Kizilkaya, K., Fernando, R., Garrick, D. 2010. Use of Genomics to Improve Healthfulness and Quality of Meat. 9th World Congress of Genetics Applied to Livestock Production. August 1-6, 2010, Leipzig, Germany, August.
- Van Eenennaam, A. L., J.H. van der Werf, and M.E. Goddard. 2010. Value of DNA information for beef bull selection. 9th World Congress of Genetics Applied to Livestock Production. August 1-6, 2010, Leipzig, Germany.
- Van Eenennaam, A.L. 2010. Value of DNA marker information for beef bull selection. Pages 98-102 in Proceedings of the Beef Improvement Federation 42nd Annual Research Symposium and Annual Meeting. June 28-July1, 2010. Columbia, MO. http://www.bifconference.com/bif2010/documents/11_vaneenennam_alison. pdf
- Van Eenennaam, A.L. 2010. DNA-based biotechnologies. Pages 68-78 in Beef Sire Selection Manual. Second Edition. National Beef Cattle Evaluation Consortium. http://www.ansci.cornell.edu/nbcec/producers/sire_selection/chapter13 .pdf
- Spangler, M., and A.L Van Eenennaam. 2010. Utilizing molecular information in beef cattle selection. Pages 79-84 in Beef Sire Selection Manual. Second Edition. National Beef Cattle Evaluation Consortium. http://www.ansci.cornell.edu/nbcec/producers/sire_selection/chapter14 .pdf
- K.L. Cooprider, F.M. Mitloehner A.L. Van Eenennaam. 2010. Sustainability implications of feedlot management practices Proceedings, Western Section, American Society of Animal Science Vol. 61. 78-81
- Reecy, J.Tait, R.; Van Overbeke, D.; Garmyn, A.; Mateescu, R.; Van Eenennaam, A.; Duan, Q.; Liu, Q.; Schoonmaker, J.; Drewnoski, M.; Beitz, D.; Kizilkaya, K.; Fernando, R.; Garrick, D. 2010. Use of Genomics to Improve Healthfulness and Quality of Meat. 9th World Congress of Genetics Applied to Livestock Production. August 1-6, 2010, Leipzig, Germany August.
- Van Eenennaam, A. L., J.H. van der Werf, and M.E. Goddard. 2010. Value of DNA information for beef bull selection. 9th World Congress of Genetics Applied to Livestock Production. August 1-6, 2010, Leipzig, Germany, August 1-6, 2010, Leipzig, Germany
- Van Eenennaam, A. L., 2010. Commercially-available DNA tests for Beef Cattle. http://animalscience.ucdavis.edu/animalbiotech/Biotechnology/MAS/Comm ercially-available_DNA_tests_for_Beef_Cattle[1].pdf
- Van Eenennaam, A. L., 2010. Value of DNA information for beef bull selection. http://animalscience.ucdavis.edu/animalbiotech/Biotechnology/MAS/Valu e_of_DNA_information_for_beef_bull_selection_final[1].pdf
- Van Eenennaam, A. L. 2010. Are DNA tests for you Beef Magazine. March. 18-23. http://beefmagazine.com/genetics/beef-dna-tests-20100301
- Van Eenennaam, A. L. 2010. What is the value of DNA testing California Cattlemen's Magazine. June. 30-31.
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Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: Nineteen outreach presentations were given to beef cattle audiences regionally,nationally and internationally to disseminate information as follows:Integrating DNA Information into Beef Cattle Production Systems, National Beef Cattle Evaluation Consortium Advisory Council Meeting, Phoenix,AZ,1/27/09.Genetic test for quantitative tests in beef cattle validation update, National Beef Cattle Evaluation Consortium Advisory Council Meeting, Phoenix,AZ,1/27/09.What has DNA done for me lately UC Cooperative Extension cattle producer educational meeting,Siskiyou County,CA,3/5/09.Curly Calf:What is it,UC Cooperative Extension cattle producer educational meeting Shasta Livestock Auction Yard,Cottonwood, CA,3/19/09.Genetic Improvement in Beef Cattle Where is it HeadedFarm Club Beef Night,UC Davis,4/1/09.DNA marker panel validation update by the National Beef Cattle Evaluation Consortium, Beef Improvement Federation Meeting, Sacramento, CA 4/31/09.There will be a quiz,Beef Improvement Federation Meeting, Sacramento,CA 5/1/09. Animal Biotechnology:How, What, and Why,Invited Presentation to 5 science classes in Green Valley Middle School, Fairfield-Suisun Unified School District,CA 5/29/09. Animal biotechnologies and agricultural sustainability,Institute of Food Technologists, Annual Meeting and Food Expo, San Diego,CA 6/8/09. Integrating DNA Information into Beef Cattle Production Systems, Western Section of Animal Science Association of America,Denver,CO, 6/18/09.Basics of SNPs and DNA-based genotyping, Producer Education Event, Meat Animal Research Center, Clay Center, NE, 6/22/09. DNA-based progeny testing and development of commercial ranch EPDs, Producer Education Event,Meat Animal Research Center, Clay Center, NE, 6/22/09. DNA Marker Validation , Producer Education Event, Meat Animal Research Center, Clay Center, NE, 6/22/09.Beef Cattle Industry Structure: Implications for whole genome selection ASAS meeting, Montreal, Canada, 7/13/09. Beef Cattle Industry Structure: Implications for whole genome selection Pfizer Animal Genetics, Global Audio conference Webinar. 8/5/09. Beef cattle industry structure: Implications for whole genome selection 2009 Australian Wagyu Association meeting, Coff's Harbor, NSW, 9/26/09. Validation and estimation of genetic variation associated with DNA tests for quantitative beef cattle traits 30th Association for the Advancement of Animal Breeding and Genetics (AAABG) meeting, Barossa Valley, South Australia, 9/29/09. Current status of adoption of DNA-testing by US beef breed associations CRC for Beef Genetic Technologies DNA Commercialization Coordination Forum No 2, Brisbane, Queensland, 12/10/09. Economics of using DNA-markers for bull selection in the seedstock sector CRC for Beef Genetic Technologies DNA Commercialization Coordination Technical BIN meeting, Brisbane, Queensland, 12/11/09. Additionally, a series of fact sheets about the use of DNA information in beef cattle production systems were developed and posted on the eXtension website,in addition to the NBCEC and the UC Davis Animal Biotechnology websites. A session on whole genome selection was featured at the 2009 Beef Improvement Federation meeting. PARTICIPANTS: Collaborators: Dr. Darrh Bullock, Extension Professor, University of Kentucky, KY Dr. Leslie Bees Butler, Extension Marketing Specialist, UC Davis, CA Dr. Daniel Drake, UC Cooperative Extension Livestock Advisor, CA Dr. Dorian Garrick, Professor, Iowa State University, IA Dr. John Pollak, Professor, Cornell University, NY Dr. Mark Thallman, US Meat Animal Research Center, Clay Center, NE Graduate Students Kristina Weber, Ph.D. Candidate, UC Davis, CA and Krista Cooprider, MS Candidate, UC Davis, CA Producer Collaborators: Jack Cowley, Cowley Rancher, Siskiyou County, CA Dale, Greg, and Richard Kuck, Kuck Ranch, Siskiyou County, CA Matt Parker, Mole-Richardson Ranch, Siskiyou County, CA Processor Collaborators: Harris Ranch Beef Company, Coalinga, CA Los Banos Abattoir, Los Banos, CA Software Collaborators: Jim Lowe, Cow Sense Herd Management Software, NE Other Contributors/Collaborators Dr. Jerry Taylor, University of Missouri, MO Dr. Mike Goddard, University of Melbourne and Victorian DPI, Australia I undertook a professional development sabbatical leave for 4 months to work with Dr. Mike Goddard, Chief Scientist of the CRC for Beef Genetic Technologies, at La Trobe University, Victoria, Australia. My sabbatical leave was very productive and I learned a great deal about selection index theory and methods to determine the economic consequences of selection decisions. Dr. Mike Goddard and I worked together on a project on the value of DNA testing to commercial beef cattle producers. I have written up this study and it is now in final draft form. In addition to this productive research interaction, I also took the opportunity to meet with researchers at the Animal Genetics and Breeding Unit, the Agricultural Business Research Institute, and the Cooperative Research Center for Beef Genetic Technologies all co-located at the University of New England, in Armidale, New South Wales. Additionally I gave presentations to beef producer groups. The graduate student on this grant, Kristina Weber, undertook training at Iowa State University by partaking in a short course entitled Use of High-density SNP Genotyping for Genetic Improvement of Livestock, which was taught June 1-10, 2009. TARGET AUDIENCES: The following deliverables and efforts to reach target local and national audiences of beef producers were projected for this integrated grant in 2009: Two meetings in Siskiyou county with cooperators and completion of genetic management evaluation survey for cooperating ranches Session on whole-genome selection to be held at BIF 2009 Completion of 3 fact sheets (SNPS and DNA-based genotyping, Whole-genome enabled selection, Marker-assisted selection) and posting to eXtension and other internet sites (e.g. NBCEC, UCD Animal Biotechnology website) Two outreach presentations at regional or national meetings Publication of one popular press article in breed association and/or trade magazines All of these deliverables were achieved or exceeded. A total of 19 outreach presentations were delivered to beef cattle audiences regionally, nationally and internationally. A series of fact sheets were developed a successful producer education event held at the Meat Animal Research Center, Clay Center, NE in June, 2009. Fact sheets were made available on the eXtension website, in addition to the NBCEC and the UC Davis Animal Biotechnology websites. Four popular press articles were written for Beef Magazine, California Cattlemen's Magazine, and the ABS Breeders Journal. All of these efforts were designed to cause a change in knowledge about DNA testing among beef cattle producers. A session on whole genome selection was featured at the 2009 Beef Improvement Federation meeting in Sacramento in April 2009. The goal of the BIF conference was to bring together research scientists, seedstock producers, and cow-calf producers to discuss recent developments of importance to the improvement of beef cattle genetics. The conference attracted 440 full registrants (including over 50 students) from 12 countries, 6 Canadian provinces, and 37 states. The breakdown of the participants was 57% cattle producers and seedstock producers, 11% educators, 10% students, 9% researchers, and 13% allied industry. Efforts made to change knowledge included plenary lectures, breakout sessions and workshops, and the use of audience input devices as an example of an innovative teaching methodology to encourage audience participation. We also ran an undergraduate student internship program to increase student attendance and participation in this conference. An effort was also made to increase the participation of underrepresented and minority groups at this conference. The four graduate student fellowships supported by this grant were awarded to three female students, and one Hispanic graduate student. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The overall objective of this project is to develop a genotyped, phenotyped population to enable the evaluation and/or assessment of different DNA-enabled approaches for predicting the genetic merit of herd sires on commercial beef ranches. The research objectives are to compare the current means of genetic prediction of herd sires, which is the use of breed-based expected progeny differences with DNA-assisted genetic predictions, and "commercial ranch" genetic evaluations based on the performance of their offspring under field conditions. Additionally, work will be undertaken to develop an approach to determine the costs and benefits associated with DNA testing in the beef cattle industry. This year we collected ranch data and slaughter phenotypes from calves derived from four commercial cow-calf herds (representing a total of 2500 cows) that are using predominately Angus sires. Blood samples (34 from Ranch 1, 12 from Ranch 2, 10 from Ranch 3, and 32 from Ranch 4) were collected on the natural service bulls siring 2009-born calves and have been submitted for 50K genotyping. During 2009, Ranch 1 produced 482 Spring calves and 369 Fall calves, Ranch 2 produced 153 Spring calves season, and Ranch 3 produced 200 Fall calves. Hair samples have been collected for genotyping on all Spring calves (N=635) as have weaning weights, and each calf has been given an electronic ID (EID) eartag with a unique RFID code to provide reliable animal identification in addition to visual ID. It is known that 569 Fall calves have been born on Ranches 1 and 3, while 1000 are projected for Ranches 2 and 4. A database has been established at UC Davis to house DNA and herd data. We are the process of extracting DNA from these samples for genotyping. This will allow us to determine the paternity of the muti-sire pasture derived calves, and further to calculate commercial ranch genetic evaluations. All data collected on this study will be stored on the Cornell University database for use in validation studies. I also undertook a sabbatical leave for 4 months to work with Dr. Mike Goddard, Chief Scientist of the CRC for Beef Genetic Technologies, at La Trobe University, Victoria, Australia. The objective of this leave was to develop an approach to undertake cost-benefit studies on the value of DNA testing to commercial beef cattle producers. This study is almost completed and a resultant paper is now in final draft form. The extension objectives of this project are to develop and deliver educational materials to a national audience on the integration of DNA information into beef cattle selection programs. During 2009, I gave 19 presentations to various audiences regionally, nationally and internationally, I developed a series of series of fact sheets that are posted on the eXtension website, in addition to the NBCEC and the UC Davis Animal Biotechnology websites. I also coordinated the successful execution of a session on whole genome selection at the 2009 Beef Improvement Federation meeting in Sacramento in April 2009, and helped support and delivered educational material to a producer education event held at the Meat Animal Research Center, Clay Center, NE in June,2009.
Publications
- Beef Improvement Federation. 2009.Proceedings of the Beef Improvement Federation 41st Annual Research Symposium and Annual Meeting, Van Eenennaam, A. L., and K. Cooprider, (ed), 182 pp. http://www.beefimprovement.org/PDFs/BIF%202009%20PROCEEDINGS_5-4-09.p df
- Drake, D.J., K. L. Weber, and A.L. Van Eenennaam. 2009. Developing carcass trait EPDs for commercial bulls using on-ranch genetic evaluations. Page 21 in Program of the 41st Beef Improvement Federation (BIF) Annual Research Symposium and Annual Meeting. April 30 - May 3, 2009, Sacramento, CA. Pages 21-22. http://www.beefimprovement.org/PDFs/BIF%202009%20PROGRAM.pdf
- Van Eenennaam, A.L., R.M. Thallman, R.L. Quaas, K. Hanford, and E. J. Pollak 2009. DNA marker panel validation update by the National Beef Cattle Evaluation Consortium. Page 20 in Program of the 41st Beef Improvement Federation (BIF) Annual Research Symposium and Annual Meeting. April 30 - May 3, 2009, Sacramento, CA. Page 20. http://www.beefimprovement.org/PDFs/BIF%202009%20PROGRAM.pdf
- Van Eenennaam, A. L., K.L. Weber, K. Cooprider, L.J. Butler, and D.J. Drake. 2009. The selection value of paternity information on calves derived from multisire breeding pastures on commercial cow-calf ranches. Proceedings, Western Section, American Society of Animal Science. 60: 15-18.
- D.J. Drake, A. L. Van Eenennaam, and J.D. Lowe. 2009. Development and implementation of a vertically-integrated beef cattle data collection system. 2009 ASAS Western Section Meeting. 60: 108-111.
- Van Eenennaam, A.L. 2009. Beef cattle industry structure: implications for whole genome selection. J. Anim. Sci. Vol. 87, E-Suppl. 2 175-176.
- D.J. Drake, A. L. Van Eenennaam, and J.D. Lowe. 2009. Development and implementation of a vertically-integrated beef cattle data collection system. 2009 ASAS Western Section Meeting. June 16-18, 2009, Denver, CO. J. Anim. Sci. Vol. 87, E-Suppl. 3 164-165.
- Van Eenennaam, A. L., K.L. Weber, K. Cooprider, L.J. Butler, and D.J. Drake. 2009. The selection value of paternity information on calves derived from multisire breeding pastures on commercial cow-calf ranches. 2009 ASAS Western Section Meeting. June 16-18, 2009, Denver, CO. J. Anim. Sci. Vol. 87, E-Suppl. 3 137-138.
- Van Eenennaam, A.L., R.M. Thallman, R.L. Quaas, K. Hanford, and E.J. Pollak. 2009. Validation and estimation of genetic variation associated with DNA tests for quantitative beef cattle traits. Association for the Advancement of Animal Breeding and Genetics. 18:129-132.
- Van Eenennaam, A.L. 2009 Biomedical Applications of Genetically Engineered and Cloned Animals
- Van Eenennaam, A.L. 2009 Genomics and Animal Agriculture
- Van Eenennaam, A.L. 2009 Waiter: Is there a Gene in my Steak
- Van Eenennaam, A.L. 2009 Animal Cloning
- Van Eenennaam, A.L. 2009 Genetically Engineered Animals: An Overview
- Van Eenennaam, A.L. 2009 Basics of DNA markers and genotyping
- Van Eenennaam, A.L. 2009 Validation of Marker Tests
- Van Eenennaam, A.L. 2009 DNA-based progeny testing and development of commercial ranch EPDs
- Van Eenennaam, A.L. 2009 Marker-Assisted Selection
- Van Eenennaam, A.L. 2009 Potential effects of biotechnology on animal health and well-being
- Van Eenennaam, A.L. 2009 Curly calf syndrome (Arthrogryposis multiplex) test available
- Van Eenennaam, A. L. 2009. Science in action. Genome sequencing aids in genetic testing. California Cattlemen's Magazine. March. Pages 36-37.
- Van Eenennaam, A. L. 2009. A rare opportunity. CBCIA, CCA host 2009 Beef Improvement Federation event. California Cattlemen's Magazine. June. Pages 33-40. http://www.calcattlemen.org/images/BIFCoverage_5-21.pdf
- Van Eenennaam, A. L. 2009. Do DNA tests work Beef. October. 52-56. http://beefmagazine.com/genetics/selection-tools/1001-dna-test-future
- Van Eenennaam, A. L. 2009. DNA markers Revolution or Evolution ABS Breeders Journal. Fall/Winter 2009. 5-6. http://www.absglobal.com/media/files/feature-articles/DNA_Markers.pdf
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