Duration: 10/01/2013 to 09/30/2018

Administrative Advisor(s):

NIFA Reps:

Non-Technical Summary

Statement of Issues and Justification

Food production, particularly beef, in the United States is transitioning from a loose commodity-based system to a system that allows buyer choice based on knowledge of production and/or measures of quality. This knowledge of production or quality is derived from the label. In the Western United States, this type of beef production is greatly challenged as lands and forages are highly variable requiring cows with different genetic potentials for optimum production. Thus, the product is not uniform. Furthermore, the industry continues with a segmented infrastructure making genetic improvement under these variable environmental and economic conditions a very complex issue. Genetic improvement tools for beef production have adapted historically to the changing dynamics of this industry. They were initiated with crossbreeding and performance testing programs that expanded to genetic prediction technologies, which eventually included multi-breed evaluations. Researchers and breeders are now developing models which incorporate molecular markers into genetic prediction technologies to improve accuracy of selection

The multi-decade history of this committee (WERA1) reveals that its activities impacted genetic improvement of beef cattle in the Western Region of the United States, nationally and internationally. In the recent past, the committees purpose/goal was to develop enhanced methods of genetic improvement using the latest quantitative and molecular techniques to increase the probability of making economically-sound breeding decisions and to disseminate new information to the industry. With evolving technologies and methodologies, the committee needs to continue to strive to achieve this goal as it remains a subject that is substantial. Achieving the goal will only come through the evolution of research and continued testing of its outputs within varied production scenarios. Dissemination of these results through educational efforts is greatly needed for the industry to actually realize the impact of the new tools on genetic improvement. The concept of new tools in beef cattle breeding (such as marker assisted and genomic selection) has been introduced, but many of the tools still require substantial research, development, and educational effort before breeders can adopt and realize a measurable change in their rate of genetic improvement.

The membership in this committee includes an important expertise-balance of quantitative with molecular geneticists that can collaborate and share resources as they strive to achieve their goal. This is in contrast to past committees in which members were primarily quantitative geneticists. Thus, the committee is evolving within the discipline of breeding and genetics and has the ability to pursue the mission for agriculture animal genomics recently described by the USDA Animal Genomics Strategic Planning Task Force (Green et al., 2007).

The committee also includes a geneticist specializing in wildlife. This allows a comparative approach to understanding genetic variation and fitness of wild populations and domestic livestock (e.g., Cronin et al. 2006). Understanding variation among wild populations can provide important insights to comparisons of breeds and lines of cattle (Cronin et al. submitted). In addition, the expertise of the WERA1 committee on the topic of genetics and fitness (i.e. performance traits) is extremely relevant to the increasing endangered species issues that affect livestock producers. Wildlife biologists often speculate without supporting data that populations are locally adapted or genetically distinct to justify endangered species designations (e.g., Ramey et al., 2006). The WERA1 committee must contribute to these debates through review of these issues with the quantitative and empirical approach used in cattle performance trait evaluations, and bring rigor to the endangered species issues that are increasingly affecting livestock producers. This will contribute to a more sustainable industry with proper consideration of environmental issues that are dealt with in an empirical and professional manner.

The beef industry in the Western United States will benefit greatly from activities of this committee through ecologically-sound production systems that are economically viable. The sustainability of these systems will continue to be challenged through consumer preferences, climate change, and economic forces. The work of this committee aims to address these challenges through a multi-institutional approach addressing the critical interactions amongst breeding, genetics, genomics, and phenomics to improve sustainability of the U.S. beef industry.

Phenomics is the study of optimum animal phenotypes for genomics research and gene discovery, and for use with quantitative methodologies for the design and implementation of genomic selection and genetic improvement programs. For genetic and genomic research to be successful researchers must have or have access to: useful cattle resource populations, performance and health data collected from the cattle (i.e., phenotype data), DNA and RNA from the cattle, and the statistical ability to conduct analyses involving the phenotypic, genotypic and expression data. The coordinated efforts of the committee compile a more comprehensive range of the required resources and expertise for leading-edge phenomics research than can be provided by any one member. During the time frame of the previous petition, the group started a database to support phenomics. This database has continued to grow and will be up-loaded to a new website by the Fall of 2013. Objective 2 will be achieved by maintaining and growing this database as well as the research activities of several committee members. In addition, committee members are collaborators on large multi-institutional multi-disciplinary projects where phenomic databases are being developed for use by the genetic research community. Access and knowledge of these databases is facilitated through WERA1 committee members who are on these projects, thereby extending research opportunities to the WERA1 members and the greater genetics community.

Objectives

Procedures and Activities

WERA1 (W-1, WRCC-1, and WCC-1 in previous years) has a multi-decade history of collaborative research and efforts to relay scientific information to the beef industry. Examples of this work can be viewed on the committees website with much more information presented in the committees annual report. The committee is currently moving its website to the Colorado State University webpage (www.wera1.agsci.colostate.edu) and will be available by Fall of 2013. Citations presented in these e-delivery systems are voluminous. Furthermore, the committee wants to point-out that it also puts forth considerable service effort to breed associations, which includes activity within the organization known as the Beef Improvement Federation (BIF). These efforts include educational presentations as well as membership and consultation to Breed Improvement Committees. The WERA1 group will continue this effort to achieve objective 1. The relationships established by WERA1 allows for the committee members to interact and prepare for presentation of technical knowledge to producer organizations. A specific example of such an activity was a program titled Incorporating Every Tool Every Time for the International Brangus Breeders Association  Breed Improvement Committee presented by Drs. Thomas (NM) and Herring (TX) in their fall meeting in 2007. Dr. Thomas presented Economically Relevant Traits for Commercial Cow-Calf Production: Reproduction at the 2012 Annual Meeting of the Beef Improvement Federation and Dr. Enns co-organized a symposium on improvement of feed utilization in the beef industry at the same convention . Dr. Enns also presented The Genetics of Disease Resistance and Susceptiblity at the National Cattlemens Beef Association Annual Conventions Cattlemens College in 2012. Similar efforts have occurred for the American Simmental Association, American Waygu Association, Canadian Charolais and Hereford Associations, and the Olds College Bull test group.

Recent examples of the committees ability to achieve Objective 3 (i.e., Integrate quantitative and molecular research tools that contribute to the understanding of genetic associations among economically important traits and their indicators) are the publications of Peter et al. (2012a,b), Snelling et al. (2012a,b), Fortes et al. (2012), Minozzi et al. (2012), Zanella et al. (2011), Neibergs et al. (2011, 2010), and Kessler et al. (2012). Additionally, committee members (Cammack, Thomas, and Enns) jointly published a review in 2009, also contributing to the achievement of Objective 3. These are publications that demonstrate that a team of scientists is needed to produce meaningful results when the subject is as complex as phenomics. Even though the group produced these multi-disciplinary publications under the scope of the previous petition, this is a new objective and demonstrates that committee members understand the need to conduct interdisciplinary and multi-institutional research. The WERA1 committee has been directly responsible for integrating molecular and quantitative geneticists into teams for a funded Coordinated Agricultural Program project. Work shared at an annual WERA1 meeting set the stage for the development of this project; this is one of the projects that is contributing to the development of the phenomic database described in Objective 2. These funded projects and publications demonstrate the willingness of the committee members to work as a team. The data included within the scope of this objective is growing exponentially in the research community. Implementation of molecular data into genetic improvement programs continues to be dependent on the ability of quantitative and molecular geneticists to incorporate them into genetic prediction methodologies. This subject is at the forefront of the subject of animal genomics and genetic evaluation. Because of the resources/expertise from the combined committee members, the members are well-suited to conduct collaborative research to further elucidate the monumental challenge of how to use the associations of genotype to phenotype in genetic prediction.

The optimal integration of genomic tools such as SNP genotypes and haplotypes with phenotypic and pedigree data, which largely arises from collaborations within the committee, will lead to the next-generation of marker-assisted and genomic selection models as well as improve our knowledge about non-traditional inheritance and influences on economically important traits. Maintaining databases which allow for investigation of the synergy between molecular tools and phenotypic data will lead to valuable insight not only into advanced genetic prediction models with higher information density, but also into potentially important gene × gene (e.g., dominance and epistasis effects) and gene × environment interactions, as well as providing a resource for measuring the longer term impact of marker- and gene-selection on phenotypic performance; it also provides a powerful resource to reinvestigate data following new discoveries. These concepts and resources are key to understanding how to optimize single-gene with polygenic selection, and is a more comprehensive and sustainable approach than strictly limiting genetic improvement tools to either a quantitative or genomic basis alone. Further, the work of the committee in the phenomics and genetic prediction areas will be well positioned to continue advances arising from high-density, whole-genome characterization and selection strategies (e.g., Meuwissen et al., 2001), but also furthering those concepts with appropriate phenotypic and quantitative resources and expertise in order to ensure industry adoption and benefit.

Objective 4 is one of the most important for this committee. Even though this paragraph appears reiterative, it is important to state that: exchange of information will occur among committee members who are knowledgeable and informed of other members activities will facilitate cooperative efforts in research as has been demonstrated through collaborative publications and jointly funded proposals. Given the recent turnover in committee membership due to retirement and faculty moves, developing these relationships is essential to successful phenomics research. Most importantly, the interactions of the group will foster pooling of resources, more efficient use of resources, and most importantly enhanced productivity of the committee members. To address the recent decline in WERA1 membership due to retirements, the committee has invited >10 individuals from academic and government institutions to become members of WERA1. These potential new members were solicited based on their contributions to the Animal Breeding community and will ensure the continued success and livelihood of the WERA1 committee. Cumulatively, the beef industry in the Western United States and its academic resources are strong and accessible. The premier strength and success of the committee has arisen from discussion and collaboration among its members throughout its multi-decade history.

Expected Outcomes and Impacts

Projected Participation

View Appendix E: Participation

Educational Plan

The W-1, WRCC-1, and WCC-1 committees have historically been very active in extending scientific information regarding the understanding of beef cattle selection and genetics to livestock producers. This committee plans to continue this tradition while expanding its educational activities to be very competitive on a global basis. This committee has experience with this type of educational activity as many of its members work closely with international beef cattle breed associations. Collaboration stemming from this committee has also led to previous coordinated graduate education efforts in animal breeding and genetics (Herring et al., 2001; Lewis et al., 2009; Thomas et al., 2012). Examples of WERA1 involvement in industry organizations includes American Simmental Association, International Brangus Breeders Association, Canadian Charolais and Hereford associations, Red Angus Association of America, Washington Cattlemens Association and numerous international research and producer groups. The WERA1 committee will continue to welcome and include industry members in its annual meetings, such as the Red Angus Association of America. The members of this committee continue to be diligent in getting information to producers through popular press outlets and producer field days in their respective states. It should also be noted that several members of this committee have extension appointments and/or work closely with extension specialists and that the committee as a whole strives to achieve missions of the land grant university system, which is to share the technical information generated from research with students and beef producers.

Members of this committee have large impacts in the education of both undergraduate and graduate students through animal breeding and genetics courses and beef cattle production courses in the western half of the United States (Table 1). One member of this committee (Enns) has recently been participating in two (awarded sequentially) USDA Challenge grants to develop graduate-level animal breeding education modules. WERA1 committee members will be involved in development of these modules. Development of beef cattle breeding modules that could be packaged for undergraduates and/or producers, especially in other countries (e.g., a Spanish version), is anticipated to be an outcome during the next project period. Finally, WERA1 members routinely use the Understanding Animal Breeding textbook by R.M. Bourdon in their undergraduate courses. This textbook does not include up-to-date information on topics such as marker-assisted selection, genomics, and phenomics. WERA1 members plan to undertake efforts to update and revise this textbook during the upcoming project period.

Organization/Governance

Before the conclusion of each annual meeting, a chairman, host, and recording secretary are elected for the next meeting. There are no duplication of duties within a year. There is also an alphabetical list of both the host institution and the institution which will provide the chairman. This list is followed except when the committee votes to hold the meeting in a location not associated with one of the participating institutions. Examples of this deviation include holding the meeting in conjunction with the Beef Improvement Federation or the Western Section of the American Society of Animal Science. The only budget requested for this committee is that the experiment station directors of the states from which members originate support the travel of specified representatives and the administrative advisor to attend annual meetings.

Literature Cited

Cammack, K.M., M. Thomas and M. Enns. 2009. Genetic analysis of reproduction traits in livestock: a review. PAS. 25:517-528.

Cronin, M. A., M. D. MacNeil, and J. C. Patton. 2006. Mitochondrial DNA and microsatellite DNA variation in domestic reindeer (Rangifer tarandus tarandus) and relationships with wild caribou (Rangifer tarandus granti, Rangifer tarandus groenlandicus, and Rangifer tarandus caribou). J. Heredity 97:525-530.

Cronin, M.A., M.D. MacNeil, N. Vu, V. Leesburg, H. Blackburn, and J. Derr. Submitted. Genetic variation and differentiation of extant bison subspecies and comparison with cattle breeds and subspecies. J. Heredity.

Fortes, M.R.S., W.M. Snelling, A. Reverter, S. H. Nagaraji, S. A. Lehnert, R. J. Hawken, K. L. DeAtley, S. O. Peters, G. A. Silver, G. Rincon, J. F. Medrano, A. Isla-Trejo, M. G. Thomas. 2012. Gene network analyses of first service conception in Brangus heifers: use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors. J. Anim. Sci. 90:2894-2906.

Green, R.D. et al. 2007. Blueprint for USDA efforts in Agricultural Animal Genomics 2008-2017. http://www.csrees.usda.gov/nea/animals/pdfs/animal_genomics_blueprint.pdf.

Herring, A. D., M. G. Thomas, and R. M. Enns. 2001. Development of a multi-institutional, web-based, graduate animal breeding course. NACTA Journal. 44:11-17.

Kessler, K.L., K.C. Olson, C.L. Wright, K.J. Austin, K. McInnerney, P.S. Johnson, R.R. Cockrum, A.M. Jons, and K.M. Cammack. 2012. Effects of high-sulfur water on hepatic gene expression of steers fed forage-based diets. J. Anim. Phys. Anim. Nutr. In press. doi: 10.1111/j.1439-0396.2012.01327.x.

Kessler, K.L., K.C. Olson, C.L. Wright, K.J. Austin, P.S. Johnson, and K.M. Cammack. 2012. Effects on performance of forage-fed steers supplemented with molybdenum and receiving high-sulfur water. J. Anim. Sci. In press. doi:10.2527/jas.2011-4453.

Lewis, R. M., B. B. Lockee, M. S. Ames, G. C. Marquez, R. M. Enns, J. M. Rumph, T. W. Wilkinson, and E. J. Pollak. 2009. Solving a dilemma in graduate education: Animal Breeding and Genetics Online. J. Anim. Sci. vol. 87. E-Suppl. 2 (Abstract). Pg. 531.

Malherbe, C., T.N. Holt, J. Marquard, K.M. Cammack, and D. OToole. 2012. Right ventricular hypertrophy with heart failure in Holstein heifers at 1,600 m. J. Vet. Diagn. Invest. 24(5):867-877.

Meuwissen, T. H. E., B. J. Hayes, and M. E. Goddard. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819-1829.

Minozzi, G., J.L. Williams, A. Stella, F.S.M. Luini, M. Settles, J.F. Taylor, R.H. Whitlock, R. Zanella, H.L. Neibergs. 2012. Meta-analysis of two genome wide association studies of bovine paratuberculosis. PLoS One 7(3):e32578.

Neibergs, H.L., M.L. Settles, R.H. Whitlock, J.F. Taylor. 2010. GSEA-SNP identifies genes associated with Johnes disease in cattle. Mammalian Genome 7-8: 419-425.

Neibergs, H.L., R. Zanella, E. Casas, G.D. Snowder, J. Wenz, J.S. Neibergs, D. Moore. 2011. Loci on BTA2 and BTA26 are linked with bovine respiratory disease and associated with persistent infection of bovine viral diarrhea virus. Journal of Animal Science 89:907-915.

Peters, S.O., K. Kizilkaya, D.J. Garrick, R.L. Fernando, J.M. Reecy, R.L. Weaber, G.A. Silver, and M.G. Thomas. 2012. Bayesian quantitative loci inference from whole genome analyses of growth and yearling ultrasound measures of carcass traits in Brangus heifers. J. Anim. Sci. 90:3398-3409.

Peters, S.O., K. Kizilkaya, D.J. Garrick, R.L. Fernando, J.M. Reecy, R.L. Weaber, G.A. Silver, and M.G. Thomas. 2012. Heritability and Bayesian genome-wide association study of first service conception and pregnancy in Brangus heifers. J. Anim. Sci. 90:(doi:10.2527/jas.2012-5580).

Ramey, R.R. J.D. Wehausen, H.-P. Liu, C.W. Epps, and L.M. Carpenter. 2006. Response to Vignieri et al. (2006). Should hypothesis testing or selective post hoc interpretation of results guide the allocation of conservation effort. Animal Conservation 9:244-247. (Prebles meadow jumping mouse endangered species).

Snelling, W.M. R.A. Cushman, M.R.S. Fortes, A. Reverter, G.L. Bennett, J.W. Keele, L.A. Kuehn, T.G. McDaneld, R.M. Thallman, and M.G. Thomas. 2012. How SNP chips will advance our knowledge of factors controlling puberty and aid in selecting replacement females. J. Anim. Sci. 90:1152-1165.

Snelling, W.M., R.A. Cushman, J.W. Keele, C. Maltecca, M.G. Thomas, M.R.S. Fortes, and A. Reverter. 2012. Networks and pathways to guide genomic selection. J. Anim. Sci. 90(E-2012-5784-R1):accepted 10/9/2012.

Thomas, M. G., G. R. Hagevoort, T. T. Ross, R. M. Enns, H. Van Campen, A. L. Van Eenennaam, H. L. Neibergs, C. Chase, S. V. doindot, N. d. Cohen, and J. E. Womack. 2012. Integrated program for reducing bovine respiratory disease complex (BRDC) in beef and dairy cattle, coordinated agricultural project (CAP): overview of the teaching program. J. Anim. Sci. Vol. 90, Suppl. 3, Pg. 498.

Zanella, R., E.G. Casas, G.D. Snowder, H.L. Neibergs. 2011. Fine mapping of loci on BTA2 and BTA26 associated with bovine viral diarrhea persistent infection and linked with bovine respiratory disease in cattle. Frontiers in Livest. Genomics. 2:82. doi: 10.3389/fgene.2011.00082

Attachments

Land Grant Participating States/Institutions

AZ, CO, MT, ND, SD, TX, WA

Non Land Grant Participating States/Institutions

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