NCERA225: Implementation and Strategies for National Beef Cattle Genetic Evaluation

(Multistate Research Coordinating Committee and Information Exchange Group)

Status: Active

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SAES-422 Reports

Annual/Termination Reports:

[11/01/2022] [12/18/2023]

Date of Annual Report: 11/01/2022

Report Information

Annual Meeting Dates: 11/01/2022 - 11/01/2022
Period the Report Covers: 01/01/2022 - 12/31/2022

Participants

Brittney Keel (USMARC)
Mark Thallman (USMARC)
Warren Snelling (USMARC)
Larry Kuehn (USMARC)
John Kuehn (USMARC)
Cedric Gondro (Michigan State Universoty)
Jenny Bormann (Kansas State University)
Daniela Lourenco (University of Georgia)
Ryan Boldt (IGS).
Ignacy Misztal (University of Georgia)
Matt Spangler (University of Nebraska)
Duc Lu (Angus Genetics, Inc)
Andre Garcia (Angus Genetics, Inc,)
Kelli Retallick (Angus Genetics, Inc.)

Brief Summary of Minutes

NCERA-225: Implementation and Strategies for National Beef Cattle Genetic Evaluation

Business Meeting November 1, 2022 via Zoom

Chair: Dr. Brittney Keel

Secretary: Dr. Cedric

The meeting was called to order by chair Brittney Keel at 4:18 PM on Tuesday, November 1, 2022.

Administrative Advisor Dr. Joe Cassady made the announcement that he had been approached by USDA to continue in his supervisory role and that he was happy to do so. He highlighted that objectives for the group should continue to be the same: working together within the group and building additional collaborations.

Dr. Brittney Keel announced that the project has been renewed for another 5 years and that members need to be sure to go to the NIMSS website and update participation. She announced that she would be needing station reports to put together the annual report.

Dr. Cedric Gondro offered to host the NCERA-225 meeting at Michigan State University in 2023, and Dr. Daniela Lourenco volunteered to be secretary. By unanimous decision, Dr. Cedric Gondro was elected chairperson and Dr. Daniela Lourenco was elected secretary.

Attendees present at the business meeting were: Brittney Keel (USMARC), Mark Thallman (USMARC), Warren Snelling (USMARC), Larry Kuehn (USMARC), Cedric Gondro (Michigan State Universoty), Jenny Bormann (Kansas State University), Daniela Lourenco (University of Georgia), and Ryan Boldt (IGS).

Meeting adjourned at 4:37 PM.

Accomplishments

Accomplishments Objective 1: Provide a venue for the discussion and exchange of information for the many disconnected and diverse research activities--biological, genomic, statistical, computational, and economical--that support National Cattle Evaluation (NCE). <ul> <li>The previous NCERA-225 meeting was held virtually in December 2021. The 2022 meeting, held virtually on November 1, 2022, covers the timeframe from the January through December 2022. Efforts were made to hold the meeting in-person, but continued travel restrictions due to COVID-19 did not make that possible for many members. Therefore, the meeting was held virtually to ensure adequate attendance.</li> <li>During the reporting period, members of the group were active in NBCEC, the NBCEC Brown Bagger Series, and the BIF board and annual meeting.</li> <li>This committee’s meeting is one of the only places where leaders in the area of genetic evaluation in the beef industry meet on an annual basis. The most pioneering methods and technologies are discussed and debated. Ideas from the meeting help inform research priorities and activities for the coming year.</li> <li>Training of the next generation of producers and scientists is critical for advancements in the field of genetic evaluation. Committee members were involved in teaching activities such as undergraduate curriculum and graduate student training in addition to outreach to producer groups.</li> </ul> Objective 2: Develop through this exchange new tools for delivery and use of beef cattle genetic research, including genomic information, to beef breed associations and beef cattle producers. <ul> <li>The 2022 NCERA-225 annual meeting provided in-depth discussion on new avenues for development of new traits and tools for selection.</li> <li>Continued collaborations between committee members as well as beef breed associations and genetic evaluation groups have led to enhanced single breed evaluations as well as development of prototype multi-breed genetic evaluations with genomic enhancement. Specific examples include:</li> <li>USMARC and UNL members collaborate on applying results from low-pass genomic sequencing to problems in cattle evaluation programs.</li> <li>USMARC and UNL members estimated genetic parameters, heterosis, and breed effects for body condition score and mature cow weight to parameterize a multi-breed evaluation for these traits. IGS is currently prototyping this evaluation.</li> <li>CSU and USMARC members collaborated on pooled genotyping for late feedlot death due to heart failure to determine genetic susceptibility and inheritance.</li> <li>USMARC and CSU collaborated in initial stages to develop methods for recording variable methane emissions and grazing behaviors in beef cattle.</li> <li>UNL and USMARC members collaborated to test a multi-variate framework for genetic evaluation using pooled data.</li> <li>Committee members continue to collaborate on the development of genetic understanding and/or EPDs for novel traits, including early indicators for longevity; muscle and meat quality; biomarkers for traits such as BRD susceptibility, RFI, and temperament; software and data pipelines for improved genomic investigations; characterization of major histology complexes in cattle; effects of climate on genetic evaluations; among other traits.</li> </ul> Objective 3: Update the beef cattle industry on current developments in beef breeding and genetics research including changes in genomics tools and analyses. <ul> <li>Committee members R. Weaber and M. Spangler led the 2022 Brown Brown Bagger Series of webinars to provide education content to county, district, regional and state extension educators and breed association technical staff on new and emerging issues/developments in beef cattle genetic evaluation. This series is nationally known for its educational content. The 2022 series featured committee member S. Speidel. The series recordings and agenda is available here: <a href="http://www.nbcec.org/professionals/brownbag.html">http://www.nbcec.org/professionals/brownbag.html</a></li> <li>Committee members M. Spangler, R. Weaber, M. Rolf, and J. Decker collaborate with other researchers to maintain and expand the availability of beef genetics extension materials available online at eBEEF.org .</li> <li>A wide range of committee members interface beef producers and various organization involved in selection and genetic improvement via presentations, symposia or trade publications. A list of those are included is included with the annual report (see publications – abstracts and proceedings as well as presentations sections).</li> </ul> Objective 4: Collaborate with appropriate groups (e.g. BIF and USDA/NIFA funded integrated projects) on research and outreach. <ul> <li>A number of committee members are routinely engaged in genetic evaluation system development and deployment for various breed associations. This engagement leads to the direct incorporation of novel research and development into national cattle evaluation systems.</li> <li>Several committee members serve on the BIF board of directors: M. Rolf, M. Enns, M. Spangler, R. Weaber, and W. Snelling.</li> <li>Committee members B. Golden, L. Kuehn, M. Spangler, M. Thallman, R. Weaber, and W. Snelling completed testing of iGENDEC software to enable customizable economic index construction and are now working with BIF to implement the package.</li> </ul> Impacts <ol> <li>Committee members published 33 peer reviewed articles as part of their own research or as co-authors by supporting research stations outside this group.</li> <li>Research efforts were communicated through 37 published abstracts or proceedings at various conferences, domestically and internationally, thereby supporting graduate education and/or disseminating their own expertise to stations outside the group on topics of cattle evaluation.</li> <li>Continued and new collaborations among committee members as well as stations outside of this group will result in enhanced knowledge for breed associations to implement genetic evaluations.</li> <li>Graduate and undergraduate training relative to quantitative genetics and beef cattle evaluations will ensure future research and improvements for cattle producers can occur in genetic evaluations.</li> </ol>

Publications

Publications Peer reviewed <ol> <li>Abdollahi-Arpanahi, R., D. Lourenco, and I. Misztal. (2022) A comprehensive study on core size and type on prediction accuracy of algorithm of proven and young in single-step GBLUP evaluation. Genet Sel Evol 54:34. doi: 10.1186/s12711-022-00726-6.</li> <li>Aherin, D.G., R.L. Weaber, D.L. Pendell, J.L. Heier Stamm and R.L. Larson. (2022) Stochastic, individual-based systems model of beef cow-calf production: model development and validation. Transl Anim Sci. doi: 10.1093/tas/txac155.</li> <li>Baller, J.L., S.D. Kachman, L.A. Kuehn, and M.L. Spangler. (2022) Using pooled data for genomic prediction in a bivariate framework with missing data. J Anim Breed Genet 139(5):489-501. doi: 10.1111/jbg.12727.</li> <li>Bermann, M., D. Lourenco, and I. Misztal. (2022) Efficient approximation of reliabilities for single-step genomic BLUP models with the Algorithm for Proven and Young. J Anim Sci 100(1):skab353. doi: 10.1093/jas/skab353.</li> <li>Bermann, M., D. Lourenco, N. Forneris, A. Legarra, and I. Misztal. (2022) On the equivalence between marker effect models and breeding value models and direct genomic values with the Algorithm for Proven and Young. Genet Sel Evol 54:52. doi: 10.1186/s12711-022-00741-7.</li> <li>Bermann, M., A. Cesarani, I. Misztal, and D. Lourenco. (2022) Past, present, and future developments in single-step genomic models. Italian J Anim Sci 21(1):673-685. doi: 10.1080/1828051X.2022.2053366.</li> <li>Butler, M., A.R. Hartman, J. Bormann, R.L. Weaber, D. Grieger, and M.M. Rolf. (2021) Genetic parameter estimation of beef bull semen attributes. J Anim Sci 99(2):skab013. doi: 10.1093/jas/skab013.</li> <li>Butler, M., A.R. Hartman, J. Bormann, R.L. Weaber, D. Grieger, and M.M. Rolf. (2022) Genome wide association study of beef bull semen attributes. BMC Genomics 23:74. doi: 10.1186/s12864-021-08256-z.</li> <li>Campos, G.S., F.F. Cardoso, C.C.G. Gomes, R. Domingues, L.C.A. Regitano, M.C.S. Oliveira, H.N. Oliveira, R. Carvalheiro, L.G. Albuquerque, S. Miller, I. Misztal, and D. Lourenco. (2022) Development of genomic predictions for Angus cattle in Brazil incorporating genotypes from related American sires. J Anim Sci 100(2):skac009. doi: 10.1093/jas/skac009.</li> <li>Flesch, E., T. Graves, J. Thomson, K. Proffitt, and R. Garrott. (2022) Average kinship within bighorn sheep populations is associated with connectivity, augmentation, and bottlenecks. Ecosphere 13(3):e3972. doi: 10.1002/ecs2.3972.</li> <li>Garcia, A., I. Aguilar, A. Legarra, S. Miller, S. Tsuruta, I. Misztal, and D. Lourenco. (2021) Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP. Genet Sel Evol 54:66. doi: 10.1186/s12711-022-00752-4.</li> <li>Giess, L.K., B.R. Jensen, J.M. Bormann, M.M. Rolf, and R.L. Weaber. (2021) Genetic parameter estimates for feet and leg traits in Red Angus cattle. J Anim Sci 99(11): skab256. doi: 10.1093/jas/skab256.</li> <li>Han, J., J. Siegford, G. de los Campos, R.J. Tempelman, C. Gondro, and J.P. Steibel. (2022) Analysis of social interactions in group-housed animals using dyadic linear models. Appl Anim Behav Sci 256:105747. doi: 10.1016/j.applanim.</li> <li>Hay, E.A., S. Toghiani, A.J. Roberts, T. Paim, L.A. Kuehn, and H.D. Blackburn. (2022)</li> </ol> Genetic architecture of a composite beef cattle population. J Anim Sci 2022. Article 230. doi: 10.1093/jas/skac230. <ol start="15"> <li>Heaton, M.P., G.P. Harhay, A.S. Bassett, H.J. Clark, J.M. Carlson, E.E. Jobman,</li> </ol> H.R. Sadd, M.C. Pelster, A.M. Workman, L.A. Kuehn, T.S. Kalbfleisch, H. Piscatelli, M. Carrie, G.M. Krafsur, D.M. Grotelueschen, and B.L. Vander Ley. (2022) Association of ARRDC3 and NFIA variants with bovine congestive heart failure in feedlot cattle. F1000Research. 11. Article 385. doi: 10.12688/f1000research.109488.1. <ol start="16"> <li>Hille, M.M., M.L. Spangler, M.L. Clawson, K.D. Heath, H.L.X. Vu, R.E.S. Rogers, and J.D. Loy. (2022) A five year randomized controlled trial to asses the efficacy and antibody responses to a commercial and autogenous vaccine for the prevention of bovine keratoconjunctivitis. Vaccines 10:916. doi: 10.3390/vaccines10060916.</li> <li>Holder, A.L., M.A. Gross, A.N. Moehlenpah, C.L. Goad, M.M. Rolf, R.S. Walker, J.K. Rogers, and D.L. Lalman. (2022) Effects of diet on feed intake, weight change, and gas emissions in mature Angus cows. J Anim Sci 100(10):1-9. doi: 10.1093/jas/skac257.</li> <li>Hollifield, M.K., M. Bermann, D. Lourenco, and I. Misztal. (2022) Impact of blending the genomic relationship matrix with different levels of pedigree relationships or the identity matrix on genetic evaluations. J Dairy Sci Comm. doi: 10.3168/jdsc.2022-0229.</li> <li>Jang, S., D. Lourenco, S. Miller. (2022) Inclusion of Sire by Herd interaction effect in the genomic evaluation for weaning weight of American Angus. J Anim Sci 100(3):skac057. doi: 10.1093/jas/skac057.</li> <li>Junqueira, V.S., D. Lourenco, Y. Masuda, F.F. Cardoso, P.S. Lopes, F.F. Silva, and I. Misztal. (2022) Is single-step genomic REML with algorithm for proven and young more efficient when less generations of data are present? J Anim Sci 100(5):skac082. doi: 10.1093/jas/skac082.</li> <li>LaKamp, A.D., R.L. Weaber, J.M. Bormann, and M.M. Rolf. (2022) Relationships between enteric methane production and economically important traits in beef cattle. Livest Sci 265 (2022):105102. doi: 10.1016/j.livsci.2022.105102.</li> <li>McWhorter, T.M., M. Bermann, A.L.S. Garcia, A. Legarra, I. Aguilar, I. Misztal, and D. Lourenco. (2022) Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. J Anim Breed Genet 140(1):60-78. doi: 10.1111/jbg.12734.</li> <li>Misztal, I., Y. Steyn, and D. Lourenco. (2022) Genomic evaluation with multibreed and crossbred data. JDS Comm 3(2):156-159. doi: 10.3168/jdsc.2021-0177.</li> <li>Nawaz, M.Y., P.A. Bernardes, R.P. Savegnago, D. Lim, S.H. Lee, and C. Gondro. (2022) Evaluation of whole-genome sequence imputation strategies in Korean Hanwoo cattle. Animals 12:2265. doi: 10.3390/ani12172265.</li> <li>Ribeiro, A.M.F., L.P. Sanglard, W.M. Snelling, R.M. Thallman, L.A. Kuehn, and M.L. Spangler. (2022) Genetic parameters, heterosis, and breed effects for body condition score and mature cow weight in beef cattle. J Anim Sci 100:skac017. doi: 10.1093/jas/skac017.</li> <li>Ribeiro, A.M.F., L.P. Sanglard, H.R. Wijesena, D.C. Ciobanu, S. Horvath, and M.L. Spangler. (2022) DNA methylation profile in beef cattle is influenced by additive genetics and age. Sci Reports 12:12016. doi: 10.1038/s41598-022-16350-9.</li> <li>Sanglard, L.P., L.A. Kuehn, W.M. Snelling, and M.L. Spangler. (2022) Influence of environmental factors and genetic variation on mitochondrial DNA copy number. J Anim Sci 100(5):skac059. doi: 10.1093/jas/skac059.</li> <li>Schumacher, M., H. DelCurto-Wyffels, J. Thomson, and J. Boles. (2022) Fat deposition and fat effects on meat quality—a review. Animals 12(12):1550. doi: 10.3390/ani12121550.</li> <li>See, G.M., J.S. Fix, C.R. Schwab, and M.L. Spangler. (2022) Imputation of non-genotyped F1 dams to improve genetic gain in swine crossbreeding programs. J Anim Sci 100:skac148. doi: 10.1093/jas/skac148.</li> <li>Seo D., D.H. Lee, S. Jin, J.I. Won, D. Lim, M. Park, T.H. Kim, H.K. Lee,S. Kim, I. Choi, J.H. Lee, C. Gondro, and S.H. Lee. (2022) Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure. Sci Reports 12:6438. doi: 10.1038/s41598-022-09425-0.</li> <li>Silva, T.L., C. Gondro, P.A.S. Fonseca, D.A. da Silva, G. Vargas, H.H.R. Neves, I. Carvalho Filho, C.S. Teixeira, L.G. Albuquerque, and R. Carhalheiro. (2022) Testicular hypoplasia in Nellora cattle: genetic analysis and functional analysis of genome-wide association study results. J Anim Breed Genet. doi: 10.1111/jbg.12747.</li> <li>Singh, A., A. Kumar, C. Gondro, A.K. Pandey, T. Dutt, and B.P. Mishra. (2022) Genome wide scan to identify potential genomic regions associated with milk protein and minerals in Vrindavani cattle. Front Vet Sci 9:760364. doi: 10.3389/fvets.2022.760364.</li> <li>Snelling, W.M., R.M. Thallman, M.L. Spangler, and L.A. Kuehn. (2022) Breeding sustainable beef cows. Animals 12:1745. doi: 10.3390/ani12141745.</li> </ol>   Abstracts and proceedings <ol> <li>Abdollahi Arpanahi, R., D. Lourenco, and I. Misztal. 2022. Investigating the impact of APY core size and definition in single-step GBLUP evaluations. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Bermann, M., A. Cesarani, D. Lourenco, and I. Misztal. 2022. Young Scholar Award Talk: Computing Strategies for National Beef Cattle Evaluations. American Society of Animal Science Annual Meeting, Oklahoma City, OK.</li> <li>Bermann, M., D. Lourenco, A. Cesarani, and I. Misztal. 2022. ACCF90GS2: software for fast approximation of reliabilities of estimated breeding values in single-step GBLUP. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Bermann, M., I. Misztal, D. Lourenco, I. Aguilar, and A. Legarra, A. 2022. Definition of reliabilities for models with metafounders. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Bullock, K.D., M.L. Spangler, R.L. Weaber, T.N. Rowan, M.M. Rolf, J.E. Decker, D.D. Loy, B.L. Golden, J.J. White and A.L. Van Eenennaam. 2022. Conducting a National Beef Cattle Genetics Outreach Program. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Campos, G.S., D.A. Silva, H.H.R. Neves, D. Lourenco, G.A.F. Júnior, L.F.S. Fonseca, L.G. Albuquerque, and R. Carvalheiro. 2022. Including selected sequence variants in genomic predictions for age at first calving in Nellore cattle. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Carroll, A.L., M.L. Spangler, D.L. Morris, and P.J. Kononoff. 2022. Estimating between-animal variance of energy utilization in lactating Jersey cows. J Dairy Sci.</li> <li>Cuyabano, B.C.D., D. Boichard, P. Croiseau, T. Tribout, V. Ducrocq, and C. Gondro. 2022. Measures to quantify the accuracy and the erosion of genomic predicted breeding values. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Garcia, A., S. Miller, S. Tsuruta, D. Lourenco, I. Misztal, D. Lu, and K. Retallick. 2022. Updating the core animals in the algorithm for proven and young in the American Angus Association national evaluations. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Guinan, F.L., G.R. Wiggans, J.W. Dürr, H.D. Norman, J.B. Cole, C.P. Van Tassell, I. Misztal, and D. Lourenco. 2022. Changes in genetic trends for dairy cattle in the U.S. since the implementation of genomic selection. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Hay, E.H.A., S. Toghiani, A.J. Roberts, T. Paim, L.A. Kuehn, and H. Blackburn. 2022. Genetic architecture of a composite beef cattle population. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Hidalgo, J., I. Misztal, S. Tsuruta, M. Bermann, A. Garcia, K. Retallick, and D. 2022. Decreasing computing cost of categorical data analysis. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Hollifield, M.K., M. Bermann, D. Lourenco, and I. Misztal. 2022. Exploring the statistical nature of independent chromosome segments. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Hollifield, M.K., M. Bermann, D. Lourenco, and I. Misztal. 2022. Exploring the Statistical Nature of Independent Chromosome Segments. American Society of Animal Science Annual Meeting, Oklahoma City, OK.</li> <li>Hollifield, M.K., M. Bermann, D. Lourenco, and I. Misztal. 2022. Impact of blending the genomic relationship matrix with different levels of pedigree relationships or the identity matrix on genetic evaluations. American Dairy Science Association Annual Meeting, Kansas City, MO.</li> <li>Lakamp, A.D., A.C. Neujahr, M.M. Hille, J.D. Loy, S.C. Fernando, and M.L. Spangler. 2022. Variance component estimation of longitudinal alpha diversity metrics of the ocular microbiome in preweaned beef cattle. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Lourenco, D., S. Tsuruta, I. Aguilar, Y. Masuda, M. Bermann, A. Legarra, and I. Misztal. 2022. Recent updates in the BLUPF90 software suite. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Lourenco, D., S. Tsuruta, I. Aguilar, A. Legarra, and I. Misztal. 2022. Single-step GWAS: association mapping accounting for phenotypes on genotyped and non-genotyped individuals. Plant and Animal Genome Conference XXIX, San Diego, CA (Virtual).</li> <li>Macciotta, N.P.P. C. Dimauro, D. Lourenco, A. Cesarani, L. Degano, and D. Vicario. 2022. Strategies for choosing core animals in APY and their impact on the accuracy of single-step genomic predictions. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Makanjuola, B.O., G. Rovere, B.C.D. Cuyabanoooooooooo, S.H. le, and Gondro. 2022. Inccludiingg environmental variables into genomic models for carcass traits in Hanwoo beef cattle. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Nawaz, M.Y., and C. Gondro. 2022. Improving accuracy of genomic prediction in distant populations by collecting sequence data over generations. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Ostrovski, H., R.P. Savegnago, W. Huang, and C. Gondro. 2022. Investigating new technologies for on-site real-time sequencing for any animal scientist. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Rovere, G., B.C.D. Cuyabano, B. Makanjuola, S. Kelly, and C. Gondro. 2022. Phenotypic and genetic trends in American Angus associated with climate variability. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Russell, C.A., L.A.Kuehn, W.M. Snelling, and M.L. Spangler. 2022. Genetic prediction for growth traits in beef cattle using selected variants from imputed low-pass sequence data. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Sanglard, L.P., L.A.Kuehn, W.M. Snelling, and M.L. Spangler. 2022. Genotype concordance between SNP chip and imputed low-pass whole-genome sequence in beef cattle. J Anim Sci.</li> <li>Sanglard, L.P., G.M. See, and M.L. Spangler. 2022. Including gene-edited individuals in genetic evaluations can bias estimated breeding values in their progeny. J. Anim Sci.</li> <li>Sanglard, L.P. L.A. Kuehn, W.M. Snelling, and M.L. Spangler. 2022. Mitochondrial DNA copy number as a potential indicator of growth and carcass traits in beef cattle. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Schaff, N., J. Dafoe, D.L. Boss, J.M. Thomson, and J.A.Boles. 2022. PSIII-5 Late-Breaking: Genetic evaluation of energy efficiency in Bos taurus cows classified by residual feed intake. J Anim Sci, 100, Supp. 4, 35-36. doi: 10.1093/jas/skac313.051.</li> <li>See, G.M., J.S. Fix, C.R.Schwab, and M.L. Spangler. 2022. Filling information gaps in swine crossbreeding schemes by imputing non-genotyped F1 animals to improve genetic gain. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Silva, T.L., C. Gondro, P.A.S. Fonseca, D.A. da Silva, V. Giovana, H.H.R. Neves, I. Carvalho Filho, C.S. Teixeira, L.G. Albuquerque, and R. Carvalheiro. 2022. Genetic mechanisms underlying feet and leg conformation in Nellore cattle: prioritization of GWAS results. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Spangler, M.L., B.L. Golden, S. Newman, L.A. Kuehn, W.M. Snelling, R.M. Thallman, and R.L. Weaber. 2022. iGENDEC: A web-based decision support tool for economic index construction. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Spangler, M.L. 2022. An animal breeder’s view of under-utilized tools to improve fertility in beef herds. Proc. Applied Reproductive Strategies in Beef Cattle.</li> <li>Thomson, J.M., M.L. Schumacher, and J.A. Boles. 2022. 043 Utilizing RNAseq ro investigate molecular mechanisms impacting meat quality and carcass characteristics in beef steers. Animal-science proceedings 13, no. 3, 296-297. doi: 10.1016/j.anscip.2022.07.053.</li> <li>Tsuruta, S., D.A.L. Lourenco, and I. Misztal. 2022. Efficient genetic progress for quantitative traits through genomic selection. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> <li>Tsuruta S., D. Lourenco, and I. Misztal. 2022. Genetic gain for quantitative traits by genomic selection – a simulation study. Aquaculture 2022, San Diego, CA.</li> <li>Tsuruta S., D. Lourenco, and I. Misztal. 2022. Genetic progress for quantitative traits by genomic selection – a simulation study. Plant and Animal Genome Conference XXIX, San Diego, CA (Virtual).</li> <li>Valasek, H.F., B.L. Golden, and M.L. Spangler. 2022. Impact of planning horizon length on the relative emphasis of traits in economic breeding goals. Proc. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, NL.</li> </ol>   Presentations <ol> <li>Lourenco, D. Single-step GWAS: association mapping accounting for phenotypes on genotyped and non-genotyped individuals. Plant and Animal Genome Conference XXIX. Vitrual, 2022.</li> <li>Lourenco, D. Leveraging genomics to reshape animal improvement. Advances in Genome Biology and Technology in Agriculture, San Diego, CA, 2022.</li> <li>Lourenco, D. BLUPF90: updates and best practices. University of Florida, 2022.</li> <li>Lourenco, D. Are threshold models feasible for routine genetic evaluations? Purdue University, 2022.</li> <li>Lourenco, D. Single-step GWAS: accounting for the data structure of farm animal populations. Iowa State University, 2022.</li> <li>Lourenco, D. Recent updates in the BLUPF90 software suite. 12th World Congress on Genetics Applied to Livestock Production, Rotterdam, The Netherlands, 2022.</li> <li>Lourenco, D. Advances in beef cattle genomic evaluations in the US. Daejon University, South Korea, 2022.</li> <li>Lourenco, D. Experiences with genomic selection across species. 19th Asian-Australian Association of Animal Production, South Korea, 2022.</li> <li>Lourenco, D. Experiences with genomic selection across species. INRAE, 2022.</li> <li>Lourenco, D. Positive and negative aspects of genomic selection. SimMelhor, Vicosa, Brazil, 2022.</li> <li>Weaber, R.L. Emerging Technologies and Focus on the Future. Allied Genetic Resources Producer Conference. Manhattan, KS, 2022.</li> <li>Weaber, R.L. Building a Profitable Cow Herd: Cow Size-A Measurement of Herd Efficiency. LRF Stockman’s School. Aldam, South Africa, 2022.</li> <li>Weaber, R.L. Building better cattle: heritability and selection for improved feet and leg structure. Purina Genetic Summit. Grey Summit, MO, 2022.</li> <li>Weaber, R.L. Using Beef on Dairy data to increase accuracy of selection decisions for carcass traits. Beef Improvement Federation Annual Research Symposium. Las Cruces, NM, 2022.</li> <li>Weaber, R.L. Using commercial Beef on Dairy data to drive genetic improvement. Beef X Dairy Symposium. Texas Tech University, Lubbock, TX, 2022.</li> <li>Weaber, R.L. Using commercial Beef on Dairy data to drive genetic improvement. Beef X Dairy Symposium. Texas Tech University, Lubbock, TX, 2022.</li> </ol>   Book chapters   <ol> <li>Thomson, J.M. 2022. Sustainability of Wild Populations: A Conservation Genetics Perspective. In: Meyers, R.A. (eds) Encyclopedia of Sustainability Science and Technology. Springer, New York, NY.</li> </ol>     Extension   <ol> <li>Weaber, R.L. and M.L. Spangler. Application of advanced genetic technology in beef cattle. King Ranch Institute of Ranch Management. Kingsville, TX. February 24-25, 2022.</li> </ol>

Impact Statements

Date of Annual Report: 12/18/2023

Report Information

Annual Meeting Dates: 12/18/2023 - 12/20/2023
Period the Report Covers: 01/01/2023 - 12/31/2023

Participants

Brittney Keel (USMARC)
Mark Thallman (USMARC)
Warren Snelling (USMARC)
Larry Kuehn (USMARC)
Cedric Gondro (Michigan State Universoty)
Ryan Boldt (IGS).
Ignacy Misztal (University of Georgia)
Matt Spangler (University of Nebraska)
Scott Speidel (Colorado State University)
Andre Garcia (Angus Genetics, Inc,)
Kelli Retallick (Angus Genetics, Inc.)
Troy Rowan (University of Tennessee)

Brief Summary of Minutes

NCERA-225: Implementation and Strategies for National Beef Cattle Genetic Evaluation

Business Meeting December 18, Embassy Suites Airport, Kansas City, Missouri

Chair: Dr. Brittney Keel

Secretary: Dr. Cedric Gondro

The meeting was called to order by chair Brittney Keel Decebmer 18 at 6:00 pm

Administrative Advisor Dr. Joe Cassady announced that he was willing to allow a different administrator for the committee if anyone is interested. The group discussed options and will be approaching possible candidates.

Dr. Cedric Gondro offered to host the NCERA-225 meeting at Michigan State University in 2024 if cleared by Dr. Daniela :piremco who had volunteered to host in 2024 previously. Dr. Gondro and Dr. Lourenco were set as the new chairperson and secretary, respecitvely.

Attendees present at the business meeting were: Brittney Keel (USMARC), Scott Speidel (CSU), Mark Thallman (USMARC), Warren Snelling (USMARC), Larry Kuehn (USMARC), Cedric Gondro (Michigan State Universoty), and Ryan Boldt (IGS).

Meeting adjourned at 6:30 pm.

Accomplishments

Accomplishments Objective 1: Provide a venue for the discussion and exchange of information for the many disconnected and diverse research activities--biological, genomic, statistical, computational, and economical--that support National Cattle Evaluation (NCE). <ul> <li>The 2020, 2021, and 2022 NCERA-225 meetings were held virtually due to COVID-19.The 2023 meeting, held in Kansas City, MO on December 18, 2023, in conjunction with the BIF Genetic Improvement Workshop, covers the timeframe from the January through December 2023.</li> <li>During the reporting period, members of the group were active in NBCEC, the NBCEC Brown Bagger Series, and the BIF board and annual meeting.</li> <li>This committee’s meeting is one of the only places where leaders in the area of genetic evaluation in the beef industry meet on an annual basis. The most pioneering methods and technologies are discussed and debated. Ideas from the meeting help inform research priorities and activities for the coming year.</li> <li>Training of the next generation of producers and scientists is critical for advancements in the field of genetic evaluation. Committee members were involved in teaching activities such as undergraduate curriculum and graduate student training in addition to outreach to producer groups.</li> </ul> Objective 2: Develop through this exchange new tools for delivery and use of beef cattle genetic research, including genomic information, to beef breed associations and beef cattle producers. <ul> <li>The 2023 NCERA-225 annual meeting provided in-depth discussion on opportunities and obstacles to enhancing beef cattle evaluation with sequence data.</li> <li>Continued collaborations between committee members as well as beef breed associations and genetic evaluation groups have led to enhanced single breed evaluations as well as development of prototype multi-breed genetic evaluations with genomic enhancement. Specific examples include:</li> <li>USMARC and UNL members collaborate on applying low-pass genomic sequencing to problems in cattle evaluation programs.</li> <li>CSU and USMARC members collaborated on pooled genotyping for Bovine Respiratory Disease and Feedlot Heart Disease to determine genetic susceptibility and inheritance.</li> <li>USMARC and CSU collaborated in initial stages to develop methods for recording variable methane emissions and grazing behaviors in beef cattle.</li> <li>UNL and USMARC began a project, with support of the Red Angus Association of American and the American Simmental Association, to utilize data pooling techniques to model commercial data recovery programs.</li> <li>CSU collaborated with American Simmental Association and IGS in developing a pulmonary arterial pressure EPD and evaluation of genetic variability of pulmonary arterial pressure (PAP) dependent on elevation PAP is measured and the elevation of a bull’s intended use.</li> <li>Committee members continue to collaborate on the development of genetic understanding and/or EPDs for novel traits, including early indicators for longevity; muscle and meat quality; biomarkers for traits such as BRD susceptibility, RFI, and temperament; software and data pipelines for improved genomic investigations; characterization of major histology complexes in cattle; effects of climate on genetic evaluations; among other traits.</li> </ul> Objective 3: Update the beef cattle industry on current developments in beef breeding and genetics research including changes in genomics tools and analyses. <ul> <li>Committee members Spangler, W. Snelling, R. Weaber, C Gondro, R. Thallman, and L. Kueh,planned a genetic prediction workshop, focused on the use of low-pass sequencing for genetic prediction, and the use of commercial data in routine genetic evaluations.</li> <li>Committee member L. Hulsman-Hanna served as the Executive Secretary for the North Dakota Beef Cattle Improvement Association (NDBCIA). This role included organizing, planning, and hosting the annual meeting (January 17, 2023) and board meetings (January 17 and October 5, 2023).</li> <li>Committee members R. Weaber and M. Spangler led the 2023 Brown Brown Bagger Series of webinars to provide education content to county, district, regional and state extension educators and breed association technical staff on new and emerging issues/developments in beef cattle genetic evaluation. This series is nationally known for its educational content. The 2023 series featured committee member M. Spangler. The series recordings and agenda is available here: <a href="http://www.nbcec.org/professionals/brownbag.html">http://www.nbcec.org/professionals/brownbag.html</a></li> <li>Committee members M. Spangler, R. Weaber, M. Rolf, and J. Decker collaborate with other researchers to maintain and expand the availability of beef genetics extension materials available online at eBEEF.org .</li> <li>A wide range of committee members interface beef producers and various organization involved in selection and genetic improvement via presentations, symposia, or trade publications. A list of those are included is included with the annual report (see publications – abstracts and proceedings as well as presentations sections).</li> </ul> Objective 4: Collaborate with appropriate groups (e.g. BIF and USDA/NIFA funded integrated projects) on research and outreach. <ul> <li>A number of committee members are routinely engaged in genetic evaluation system development and deployment for various breed associations. This engagement leads to the direct incorporation of novel research and development into national cattle evaluation systems.</li> <li>Several committee members serve on the BIF board of directors: M. Rolf, M. Enns, M. Spangler, R. Weaber, and W. Snelling.</li> <li>The iGENDEC software, developed by committee members L. Kuehn, M. Spangler, M. Thallman, R. Weaber, and W. Snelling, is supported by BIF. This software currently supports the creation of economic selection indexes of 3 U.S. beef breed associations and has been used by extension personnel for programming in 6 states and in classroom instruction by 2 universities. A beta version of a beef x dairy module was completed in 2023.</li> <li>Committee member C. Gondro developed and delivered a two-week course on Genomic Analysis and Artificial Intelligence Applied to Animal Genetics as part of MSU’s Global Scholars program.</li> </ul> Impacts <ol> <li>Committee members published 32 peer reviewed articles as part of their own research or as co-authors by supporting research stations outside this group.</li> <li>Research efforts were communicated through 45 published abstracts or proceedings at various conferences, domestically and internationally, thereby supporting graduate education and/or disseminating their own expertise to stations outside the group on topics of cattle evaluation.</li> <li>Continued and new collaborations among committee members as well as stations outside of this group will result in enhanced knowledge for breed associations to implement genetic evaluations.</li> <li>Graduate and undergraduate training relative to quantitative genetics and beef cattle evaluations will ensure future research and improvements for cattle producers can occur in genetic evaluations.</li> </ol>

Publications

Publications Peer reviewed <ol> <li>Bermann, M., I. Aguilar, D. Lourenco, I. Misztal, and A. Legarra. (2023) Reliabilities of breeding values in models with metafounders. Genet. Sel. Evol. doi: 10.1186/s12711-023-00778-2.</li> <li>Berry, D.P., and L. Spangler. (2023) Animal Board Invited Review: Practical applications of genomic information in livestock. Animal. 17(11):100996. doi: 10.1016/j.animal.2023.100996.</li> <li>Bhowmik, N., T. Seaborn, K.A. Ringwall, C.R. Dahlen, K.C. Swanson, and L.L. Hulsman Hanna. (2023) Genetic distinctness and diversity of American Aberdeen cattle compared to common beef breeds in the United States. Genes. 14(10):1842. doi: 10.3390/genes14101842.</li> <li>Boldt, R.J., J.W. Keele, L.A. Kuehn, T.G. McDaneld, S.E. Speidel, and R.M. Enns. (2023) Comparison of genomic relationship matrices using differing number of SNP in pooled DNA analyses. J. Anim. Sci. (Submitted)</li> <li>Cesarani, A., M. Bermann, C. Dimauro, L. Dagano, D. Vicario, D. Lourenco, and N.P.P. Macciotta. (2023) Strategies for choosing core animals in APY and their impact on the accuracy of single-step genomic predictions. Animal. 100766. doi: 10.1016/j.animal.2023.100766</li> <li>Cesarani, A., D. Lourenco, M. Bermann, E.L. Nicolazzi, P.M. VanRaden, and I. Misztal. (2023) Single-step genomic predictions for crossbred Holstein and Jersey cows in the US. J. Dairy Sci. Comm. doi: 10.3168/jdsc.2023-0399.</li> <li>Dressler, E.A., C.M. Ahlberg, K. Allwardt, A. Broocks, K. Bruno, L. McPhillips, A. Taylor, C.R. Krehbiel, M.S. Calvo-Lorenzo, C.J. Richards, S.E. Place, U. DeSilva, L.A. Kuehn, R.L. Weaber, J.M. Bormann, and M.M. Rolf. (2023) Heritability and variance component estimation for feed and water intake behaviors.  Anim. Sci. 101:1-19.  doi: 10.1093/jas/skad386.</li> <li>Dressler, E.A., J.M. Bormann, R.L. Weaber, and M.M. Rolf. (2023)  Technical note: Characterization of the number of spot samples required for quantification of gas fluxes and metabolic heat production from grazing beef cows using a GreenFeed.  Anim. Sci. 101:1-9. doi: 10.1093/jas/skad176.</li> <li>Dressler, E.A., R.L. Weaber, J.M. Bormann, and M.M. Rolf. (2023) Use of methane production data for genetic prediction in beef cattle: A review.  Anim. Sci. txae014. doi: 10.1093/tas/txae014.</li> <li>Engle, B., R.M. Thallman, W.M. Snelling, T.L. Wheeler, S. Shackelford, D.A. King, and L.A. Kuehn. (2023) Breed-specific heterosis for growth and carcass traits in 18 U.S. cattle breeds. J. Anim, Sci. (Submitted)</li> <li>Freetly, H.C., D.R. Jacobs, R.M. Thallman, W.M. Snelling, and L.A. Kuehn. (2023) Heritability of beef cow metabolizable energy for maintenance. J. Anim. Sci. 101:skad145. doi: 10.1093/jas/skad145.</li> <li>Gonzalez-Murray, R.A., M.G. Thomas, T.N. Holt, S. Coleman, R.M. Enns, and S.E. Speidel. (2023) Heterosis effects on preweaning traits in a multibreed beef cattle herd in Panama.  Agriculture. (submitted).</li> <li>Haghani, A. C.Z. Li, T.R. Robeck, J. Zhang, A.T. Lu, J. Ablaeva, et al. (2023) DNA methylation networks underlying mammalian traits. Science. 381(6658):eabq5693. doi: 10.1126/science.abq5693.</li> <li>Hollifield, M.K., M. Bermann, D. Lourenco, and I. Misztal. (2023) Exploring the statistical nature of independent chromosome segments. Livest. Sci. 105207. doi: 10.1016/j.livsci.2023.105207.</li> <li>Jang, S., S. Tsuruta, N.G. Leite, I. Misztal, and D. Lourenco. (2023) Dimensionality of genomic information and its impact on GWA and variant selection: a simulation study. Genet. Sel. Evol. 55:49. doi: 10.1186/s12711-023-00823-0.</li> <li>Keele, J.W., B.A. Foraker, R.J. Boldt, C. Kemp, L.A. Kuehn, and D.R. Woerner. (2023) Genetic parameters for carcass traits of progeny of beef bulls mated to dairy cows. J. Anim. Sci. (Submitted)</li> <li>LaKamp, A.D., C.M. Ahlberg, K. Allwardt, A. Broocks, K. Bruno, L. McPhillips, A. Taylor, C.R. Krehbiel, M.S. Calvo-Lorenzo, C.J. Richards, S.E. Place, U. DeSilva, L.A. Kuehn, R.L. Weaber, J.M. Bormann, and M.M. Rolf. 2023. Variance component estimation and genome-wide association of predicted methane production in crossbred beef steers.  Anim. Sci. 101:1-12. doi: 10.1093/jas/skad179.</li> <li>Lee, H.J, J.H. Lee, C. Gondro, Y.J. Koh, and S.H. Lee (2023). deepGBLUP: joint deep learning networks and GBLUP framework for accurate genomic prediction of complex traits in Korean native cattle. Genet. Sel. Evol. 55:56. doi: 10.1186/s12711-023-00825-y.</li> <li>Lu, A.T., Z. Fei, A. Haghani, T.R. Robeck, J.A. Zoller, C.Z. Li, et al. (2023) Universal DNA methylation age across mammalian tissues. Nat. Aging. 3:1144-1166. doi: 10.1038/s43587-023-00462-6.</li> <li>McWhorter, T.M., M. Bermann, A.L.S. Garcia, A. Legarra, I. Aguilar, I. Misztal, and D. Lourenco. (2023) Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. J. Anim. Breed. Genet. doi: 10.1111/jbg.12734.</li> <li>McWhorter, T., M. Sargolzaei, C.G. Sattler, M.D. Utt, S. Tsuruta, I. Misztal, and D. Lourenco. (2023) Single-step genomic predictions for heat tolerance of production yields in U.S. Holsteins and Jerseys. J. Dairy Sci. doi: 10.3168/jds.2022-23144.</li> <li>Pauling, R.C., S.E. Speidel, M.G. Thomas, T.N. Holt, R.M. Enns. (2023) Genetic parameters for pulmonary arterial pressure, yearling performance, and carcass ultrasound traits in Angus cattle. J. Anim. Sci. 101:skad288. doi:10.1093/jas/skad288.</li> <li>Ramos, P.V.B., G.R.O. Menezes, D.A. Silva, D. Lourenco, G.G. Santiago, R.A.A. Torres Jr, F.F. Silva, P.S. Lopes, and R. Veroneze. (2023) Genomic analysis of feed efficiency traits in Nellore cattle using random regression models. J. Anim. Breed. Genet. doi: 10.1111/jbg.12840.</li> <li>Romero, A.R.S., A.V. do Nascimento, M.C.S. Oliveira, C.H. Okino, C.U. Braz, D.C.B. Scalez, D.F Cardoso, F.F. Cardoso, C.C.G. Gomes, A.R. Caetano, H. Tonhati, C. Gondro, and H.N. de Oliveira (2023) Genetic parameters and multi-trait genomic prediction for hemoparasites infection levels in cattle. Livestock Science. 273:105259. doi: 10.1016/j.livsci.2023.105259.</li> <li>Russell, C.A., L.A. Kuehn, W.M. Snelling, S.D. Kachman, and M.L. Spangler. (2023) Variance component estimates for growth traits in beef cattle using selected variants from imputed low-pass sequence data. J. Anim. Sci. 101:skad274. doi: 10.1093/jas/skad274.</li> <li>Sanglard, L.P., G.M. See, and M.L. Spangler. (2023) Strategies for accommodating gene-edited sires and their descendants in genetic evaluations. J. Anim. Sci. 101:skad077. doi: 10.1093/jas/skad077.</li> <li>Sanglard, L.P., W.M. Snelling, L.A. Kuehn, R.M. Thallman, H.C. Freetly, T.L. Wheeler, S.D. Shackelford, D.A. King, and M.L. Spangler. (2023) Genetic and phenotypic associations of mitochondrial DNA copy number, SNP, and haplogroups with growth and carcass traits in beef cattle. J. Anim. Sci. 101:skac415. doi: 10.1093/jas/skac415.</li> <li>Silva, T.L., C. Gondro, P.A.S. Fonseca, D.A. da Silva, G. Vargas, H.H.R. Neves, I.C. Filho, C.S. Teixeira, L.G. de Albuquerque, and R. Carvalheiro (2023). Feet and legs malformation in Nellore Cattle: genetic analysis and prioritization of GWAS results. Front. Genet. 14:1118308. doi: 10.3389/fgene.2023.1118308.</li> <li>Silva, T.L., C. Gondro, P.A.S. Fonseca, D.A. da Silva, G. Vargas, H.H.R. Neves, I. Carvalho Filho, C.S. Teixeira, L.G. Albuquerque, and R. Carvalheiro (2023) Testicular hypoplasia in Nellore cattle: genetic analysis and functional analysis of genome-wide association study results. J. Anim. Breed. Genet. 140(2):185-197. doi: 10.1111/jbg.12747.</li> <li>Steyn, Y., T. Lawlor, D. Lourenco, and I. Misztal. (2023) The importance of historically popular sires on the accuracy of genomic predictions of young animals in the US Holstein population. J. Dairy Sci. Comm. doi: 10.3168/jdsc.2022-0299.</li> <li>Steyn, Y., T. Lawlor, Y. Masuda, S. Tsuruta, D. Lourenco, and I. Misztal. (2023) Non-parallel genome changes within sub-populations over time contribute to genetic diversity within the U.S. Holstein population. J. Dairy Sci. doi: 10.3168/jds.2022-21914.</li> <li>Wilson, R.A., B.J. Johnson, J.O. Sarturi, W.L. Crossland, K.E. Hales, R.J. Rathmann, C.L. Bratcher, M.E. Theurer, R.G. Amachawadi, T.G. Nagaraja, S.E. Speidel, R.M. Enns, M.G. Thomas, B.A. Foraker, M.A. Cleveland, and D.R. Woerner. (2023) Identification of blood-based biomarkers for detection of liver abscess in beef x dairy heifers. Applied Animal Science. (submitted).</li> </ol>   Abstracts and proceedings <ol> <li>Adams, S., N. Aluthge, W. Abbas, M.L. Spangler, J. Wells, K. Hales, L. Kuehn, T. Burkey, P. Miller, and S.C. Fernando. 2023. Microbiomes from the theory to application. J. Anim. Sci. 101: Suppl. 2.</li> <li>Alvarez Munera, A., D. Lourenco, I. Misztal, I. Aguilar, J. Bauer, J. &Scaron;plíchal and M. Bermann. 2023. Improving the efficiency of genomic evaluations with random regression models. In: 74th EAAP – European Association for Animal Production, Lyon, France.</li> <li>Baty, S.K., R.M. Enns, T.N. Holt, and S.E. Speidel. Genetic correlations between systolic and diastolic pulmonary arterial pressure in Beef Cattle.  J. Anim. Sci.  101:Suppl. 3.</li> <li>Bermann, M., I. Aguilar, D. Lourenco, and I. Misztal. 2023. Approximation of reliabilities for random-regression single-step genomic best linear unbiased predictor. American Dairy Science Association Annual Meeting, Ottawa, Canada.</li> <li>Bermann, M., D. Lourenco, and I. Misztal. 2023. Large-scale single-step genome wide association studies with the algorithm for proven and young. PAG XXX– Plant and Animal Genome Conference, San Diego, CA.</li> <li>Bussiman, F., C. Chen, J. Holl, A. Legarra, I. Misztal and D. Lourenco. 2023. Improving computing performance of genomic evaluations by genotype and phenotype truncation. In: 74th EAAP – European Association for Animal Production, Lyon, France.</li> <li>Bussiman, F., C.Y. Chen, J. Holl, A. Legarra, I. Misztal, and D. Lourenco. 2023. Data truncation as a tool for increasing computing efficiency in genomic predictions. PAG XXX– Plant and Animal Genome Conference, San Diego, CA.</li> <li>Croucamp, C., D.M. Stock, M.W. Semler, A.R. Hartman, D.M. Grieger, J.P. Martins, R.L. Weaber, J.M. Bormann, and M.M. Rolf.   The application of GWAS in selection signature analysis of beef bull fertility traits.  Beef Improvement Federation Genetic Prediction Workshop.  Kansas City, MO.</li> <li>Dressler, E.A., J.M. Bormann, R.L. Weaber, and M.M. Rolf.   Spot sample protocol for gas quantification of grazing beef cattle using a GreenFeed.  American Society of Animal Science Annual meeting. Albuquerque, NM.</li> <li>Dressler, E.A., J.M. Bormann, R.L. Weaber, and M.M. Rolf.   Characterization of the number of visits required for quantification of gas fluxes and metabolic heat production using a GreenFeed.  Beef Improvement Federation Genetic Prediction Workshop.  Kansas City, MO.</li> <li>Dressler, E.A., W.R. Shaffer, C.R. Krehbiel, M.S. Calvo-Lorenzo, C.J. Richards, S.E. Place, U. DeSilva, L.A. Kuehn, J.M. Bormann, R.L. Weaber, and M.M. Rolf.   Genetic evaluation of feed and water intake behavior traits for feedlot cattle.  American Society of Animal Science Annual meeting.  Albuquerque, NM.</li> <li>Dressler, E.A., W.R. Shaffer, C.R. Krehbiel, M.S. Calvo-Lorenzo, C.J. Richards, S.E. Place, U. DeSilva, L.A. Kuehn, J.M. Bormann, R.L. Weaber, and M.M. Rolf.   Genetic evaluation of feed and water intake behavior traits for feedlot cattle.  Beef Improvement Federation Genetic Prediction Workshop.  Kansas City, MO.</li> <li>Dodds, G., C. Gondro, T. Kendrick, M. Young, and B. Fragomeni 2023. Identifying educational resources and gaps in AG2P data science across plant and animal agriculture genomics. Agricultural Genome to Phenome Initiative Conference. (Virtual)</li> <li>Engle, B., G. Moser, K.S. Villiers, M. Suarez, E. Grey, B.J. Hayes, and M.J. Kelly. 2023. Using digital twin simulations to optimize genetic selection in an admixed beef herd. American Society of Animal Science Annual meeting. Albuquerque, NM.</li> <li>Galoro Leite, N., M. Bermann, S. Tsuruta, I. Misztal and D. Lourenco. 2023. Expanding the capabilities of single-step GWAS with P-values for large genotyped populations. In: 74th EAAP – European Association for Animal Production, Lyon, France.</li> <li>Giess, L.K., S.E. Speidel, R.J. Boldt, W.R. Shafer, M.G. Thomas, and R.M. Enns.   Variance components for age at first calving and yearling weight when accounting for age differences at fixed breeding dates in a contemporary group.  J. Anim. Sci. 101:Suppl. 3.</li> <li>Gonzalez-Murray, R.A., M.G. Thomas, R.M. Enns, and S.E. Speidel. Heterosis effects on reproductive traits in a multibreed beef cattle herd in Panama.  J. Anim. Sci.  101:Suppl. 3. </li> <li>Hess, M., G. Erickson, and M. Spangler. 2023. Genomic analysis of liver abscesses in feedlot beef cattle. Advances in Genome Biology and Technology Agriculture Conference, San Antonio, TX.</li> <li>Hidalgo, J., S. Tsuruta, D. Gonzalez, G. de Oliveira, M. Sanchez, A. Kulkarni, C. Przybyla, G. Vargas, N. Vukasinovic, I. Misztal, and D. Lourenco. 2023. Converting linear breeding values to probabilities for health traits in dairy cattle. American Dairy Science Association Annual Meeting, Ottawa, Canada.</li> <li>Hollifield, M.K., J. Hidalgo, F. Bussiman, D. Lourenco, and I. Misztal. 2023. Improving the efficiency of heritability estimation with genomic information—Method R. In: American Dairy Science Association Annual Meeting, Ottawa, Canada.</li> <li>Hurst, C.W., R.M. Enns, C. Huffhines, K.R. Stackhouse-Lawson, and S.E. Speidel. Sire differences for blood urea nitrogen (BUN) in Hereford cattle.  J. Anim. Sci. 101:Suppl. 3.</li> <li>Kinghorn, M.S., D.M. Stock, A.R. Hartman, M.W. Semler, G.M. Grieger, J.P. Martins, J.M. Bormann, R.L. Weaber, and M.M. Rolf.   Methods to predict bull fertility:  Connecting the dots.  Beef Improvement Federation Genetic Prediction Workshop.  Kansas City, MO.</li> <li>Kukor, I., R.M. Enns, T.N. Holt, M.A. Cleveland, B.P. Holland, A.B. Word, G. Ellis, M. Theurer, and S.E. Speidel. Prevalence of right sided heart failure in Angus influenced and beef on dairy fattening feedlot cattle.  J. Anim. Sci. 101:Suppl. 3.</li> <li>Lakamp, A.D., A.C. Neujahr, M.M. Hille, J.D. Loy, S.C. Fernando, and M.L. Spangler. 2023. Longitudinal heritability of ocular microbiota in preweaned beef cattle. J. Anim Sci. 101: Suppl. 3.</li> <li>Leite, N., M. Bermann, S. Tsuruta, I. Misztal, D. Lourenco. 2023. Marker effect p-value for large genotype populations with the algorithm for proven and young. American Society of Animal Science Annual Meeting, Albuquerque, NM.</li> <li>Leite, N.G., M. Bermann, S. Tsuruta, I. Misztal, and D. Lourenco. 2023. Single-step genome-wide association analysis with P-values for large genotyped populations. American Dairy Science Association Annual Meeting, Ottawa, Canada.</li> <li>Lourenco, D., A. Cesarani, S. Tsuruta, A. Legarra, E. Nicolazzi, P. VanRaden, and I. Misztal. 2023. Big Data Genomic Analysis in Dairy Cattle. PAG XXX– Plant and Animal Genome Conference, San Diego, CA.</li> <li>Lourenco, D., F. Guinan, G. Wiggans, J. Dürr, S. Tsuruta, and I. Misztal. 2023. Sometimes we win, sometimes we lose: the consequences of genomic selection. In: 74th EAAP – European Association for Animal Production, Lyon, France.</li> <li>Lourenco, D., S. Jang, R. Ros-Freixedes, J. Hickey, C.Y. Chen, J. Holl, W. Herring, and I. Misztal. 2023. Large-Scale Genomic Predictions with Sequence Data. PAG XXX– Plant and Animal Genome Conference, San Diego, CA.</li> <li>Miztal, I., V. Breen, D. Lourenco. 2023. Using theoretical and realized accuracies to estimate changes in heritabilities. American Society of Animal Science Annual Meeting, Albuquerque, NM.</li> <li>Misztal, I., A. Cesarani, A. Legarra, D. Lourenco, S. Tsuruta, M. Bermann, E. Nicolazzi, and P. VanRaden. 2023. Integrating foreign information into single-step evaluations in US Holsteins. American Dairy Science Association Annual Meeting, Ottawa, Canada.</li> <li>Nawaz, M.Y., H. Ostrovski, R.P. Savegnago, L.K. Ackerson, and C. Gondro 2023. Breed identification by mobile sequencing technology. Plant and Animal Genome Conference XXX, San Diego, CA.</li> <li>Place, S.E., M. Swenson, E.J. Raynor, K.R. Stackhouse-Lawson, S.E. Speidel, R.M. Enns, and P.H.V. Carvalho. 2023. Evaluation of methane emissions predictions from observed methane emissions date in beef steers, heifers, and bulls. Anim. Sci. 101: Suppl. 3.</li> <li>Ramos, P.V.B., A. Garcia, K. Retallick, M. Bermann, I. Misztal, D. Lourenco. 2023. Comparison of algorithms for approximation of accuracies for single-step genomic best linear unbiased predictor models. American Society of Animal Science Annual Meeting, Albuquerque, NM.</li> <li>Rosa, G.J.M., D. Lourenco, T.N. Rowan, L.F. Brito, C. Gondro, J. Huang, and S. Valle de Souza 2023. Integrating enviromics, genomics, and machine learning for precision breeding of resilient livestock. American Society of Animal Science Annual Meeting, Albuquerque, NM.</li> <li>Rovere, G., B.C.D. Cuyabano, B. Makanjuola, and C. Gondro. 2023. Longitudinal study of environmental effects for American Angus beef cattle over 30 years. Joint International Congress on Animal Science Conference, Lyon, France.</li> <li>Shaffer, W., K. Bruno, C. Krehbiel, M.S. Calvo-Lorenzo, C.J. Richards, S.E. Place, U. DeSilva, L.A. Kuehn, J.M. Bormann, R.L. Weaber, and M.M. Rolf.   Combining GWAS and miRNA analysis.  Beef Improvement Federation Genetic Prediction Workshop.  Kansas City, MO.</li> <li>Shaffer, W., J.A.H. Moreno, N.M. Bello, R. Noland, K. Bruno, C. Krehbiel, M.S. Calvo-Lorenzo, C.J. Richards, S.E. Place, U. DeSilva, L.A. Kuehn, J.M. Bormann, R.L. Weaber, and M.M. Rolf.   Characterization of Dry Matter Intake Genetic Parameters with Respect to a Temperature Humidity Index: Insights into Environmental Sensitivity and Genetic-by-Environment Interactions.  American Society of Animal Science Annual meeting.  Albuquerque, NM.</li> <li>Spangler, M.L., B.L. Golden, and S. Newman. 2023. Genetic selection for improved profit conditioned on enterprise-specific circumstances. J. Anim. Sci. 101: Suppl. 3.</li> <li>Speidel, S.E., R.M. Enns, and C.N. Cadaret. 2023. Preliminary investigations into developmental origins of pulmonary arterial pressure in Beef Cattle. Anim. Sci. 101:Suppl. 3.</li> <li>Stock, D.M., J.M. Bormann, and M.M. Rolf. Male fertility in beef cattle.  In:  2023 Applied Reproductive Strategies in Beef Cattle Proceedings.  Cheyenne, WY.</li> <li>Stock, D.M., A.R. Hartman, M.W. Semler, G.M. Grieger, J.P. Martins, J.M. Bormann, R.L. Weaber, and M.M. Rolf.   Genetic parameter estimation for breeding soundness examination traits in Angus bulls.  Beef Improvement Federation Genetic Prediction Workshop.  Kansas City, MO.</li> <li>Stohlmann, M., M.K. Hess, S. Ference, S.R. Nafziger, J.A. Keane, A. Fuller, S.G. Kurz, M.L. Spangler, J.L. Petersen, A.S. Cupp. 2023. Puberty classifications in beef heifers are moderate to highly heritable with nucleotide polymorphisms (SNPs) from candidate genes highly associated to their cyclicity and timing of puberty. Gil Greenwald Reproductive Symposia, Kansas City, KS.</li> <li>Torres-Quijada, I.F., S.E. Speidel, M.L. Zuvich, E.J. Raynor, P.H.V. Carvalho, S.E. Place, S.E. Speidel, M.L. Zuvich, E.J. Raynor, P.H.V. Carvalho, S.E. Place, K.R. Stackhouse-Lawson, and R.M. Enns. 2023. The relationship of methane emissions with stayability in Angus cattle. Anim. Sci. 101:Suppl. 3.</li> <li>Zuvich, M.L., S.E. Speidel, I.F. Torres-Quijada, E.J. Raynor, P.H.V. Carvalho, S.E. Place, K.R. Stackhouse-Lawson, and R.M. Enns. 2023. The relationship between pulmonary arterial expected progeny differences and methane emissions. Anim. Sci. 101:Suppl. 3.</li> </ol>   Presentations <ol> <li>Engle, B. Introduction to the USMARC Germplasm Evaluation Program. Presented to Fort Hayes State University students. Clay Center, NE, 2023.</li> <li>Engle, B. Developing resources to improve genetic selection in beef cattle. University of Nebraska-Lincoln. Lincoln, NE, 2023.</li> <li>Enns, R.M. and S.E. Speidel. Interpreting and using the new PAP EPD. University of Wyoming Bull Sale Dinner, 2023.</li> <li>Enns, R.M., S.E. Speidel, and T.N. Holt. Genetic prediction for pulmonary arterial pressure. Presented at the American Simmental Association Fall Focus. Denver, CO, 2023.</li> <li>Enns, R.M., S.E. Speidel, and T.N. Holt. Selecting Sires to use at high elevation. Applied Reproductive Strategies in Beef Cattle (ASRBC). Cheyenne, WY, 2023. </li> <li>Enns, R.M., S.E. Speidel, and C. Hurst. Breeding and Genetics Research Update. Presented at the Leachman Cattle of Colorado-URUS CSU Facilities Tour. Fort Collins, CO, 2023.</li> <li>Enns, R.M., S.E. Speidel, K. Stackhouse-Lawson, S. Place, M.G. Thomas, C. Huffhines, and C. Hurst. Evaluating the genetic components of greenhouse gas emissions and reactive nitrogen produced by Hereford seedstock for deriving systems, selection tools, and documented trends to achieving carbon neutral in the US beef industry. Young Hereford Breeder Tour.  Fort Collins, CO, 2023.</li> <li>Gondro, C. Imputation and genetic evaluation with sequence data (and a bit of AI). BIF 12th Genetic Prediction Workshop, Kansas City, MO, 2023.</li> <li>Hulsman-Hanna, L.L. Breed and Animal Improvements + Genomics, Heartland Highland Association Annual Meeting, Branson, MO, 2023.</li> <li>Hulsman-Hanna, L.L. Interplay of Cow Size in the Production System, NDSU Dickinson Research Extension Center Field Day, Fargo, ND, 2023.</li> <li>Hulsman-Hanna, L.L. Interplay of Cow Size in the Production System, NDSU Fall Extension Conference, Fargo, ND, 2023.</li> <li>Lourenco, D. Big data analysis in animal breeding. 10th Animal Science Congress of Iran. Tehran, Iran, 2023.</li> <li>Lourenco, D. Single-step GWAS with p-values for large genotyped populations. Animal and Dairy Science Association. Ottawa, Canada, 2023.</li> <li>Lourenco, D. Are there benefits in using sequence data for genomic predictions?. Animal Production Science Congress. Bari, Italy, 2023.</li> <li>Lourenco, D. Updates in the BLUPF90 software suite. Plemdat Workshop. Prague, Czech Republic, 2023.</li> <li>Lourenco, D. Understanding Genomic Selection. Genomic Breeding Workshop. Dunedin, New Zealand, 2023.</li> <li>Lourenco, D. Implementing Genomic Selection. Genomic Breeding Workshop. Dunedin, New Zealand, 2023.</li> <li>Lourenco, D. Large multibreed genomic evaluation in dairy cattle. Genomic Breeding Workshop. Dunedin, New Zealand, 2023.</li> <li>Lourenco, D. Efficient approximation of GEBV reliability (a measure of precision). Genomic Breeding Workshop. Dunedin, New Zealand, 2023.</li> <li>Lourenco, D. Use of sequence data and other sources of information for genomic predictions. Genomic Breeding Workshop. Dunedin, New Zealand, 2023.</li> <li>Lourenco, D. SNP-BLUP vs. GBLUP based models. Genomic Breeding Workshop. Dunedin, New Zealand, 2023.</li> <li>Lourenco, D. Simple vs. Complex models. Genomic Breeding Workshop. Dunedin, New Zealand, 2023.</li> <li>Lourenco, D. Making genomic evaluations for millions of animals possible. University of Queensland Seminar. Brisbane, Australia, 2023.</li> <li>Lourenco, D. Decoding Genomic Predictions in Large Populations. Benchmark Genetics Workshop. Bergen, Norway, 2023.</li> <li>Lourenco, D., and I. Misztal. Decoding Genomic Predictions in Large Populations. Gordon Conference - Quantitative Genetics. Ventura, CA, 2023.</li> <li>Spangler, M.L. Value of Genetic Data Beyond Seedstock and Geneticists, UNL Beef Group meeting, Lincoln, NE, 2023.</li> <li>Spangler, M.L. Why Genotype? National Salers Show and Sale, Oklahoma City, OK, 2023.</li> <li>Spangler, M.L. Genomic EPDs, Eastern NE Cattle Conference, Syracuse, NE, 2023.</li> <li>Spangler, M.L. Impact of Genomics on EPDs (panelist), Cattlemens Conference—Blueprint for the Future, Stillwater, OK, 2023.</li> <li>Spangler, M.L. Utilizing U.S. Beef Cattle Genetics to Improve Quality in Mexican Beef: A Case Study from Nebraska (given by interpreter), International Meat Congress, Leon, Guanajuato, Mexico, 2023.</li> <li>Spangler, M.L. Genetic Selection for Enterprise Profit, American Simmental Association STYLE Conference, Oklahoma City, OK, 2023.</li> <li>Spangler, M.L. Genetic selection for improved profit conditioned on enterprise-specific circumstances, American Society of Animal Science meetings (Invited), Albuquerque, NM, 2023.</li> <li>Spangler, M.L. Tools for selecting U.S. beef genetics, Argentine trade group, Lincoln, NE, 2023.</li> <li>Spangler, M.L. Genetic considerations for the cowherd, UNL Ranch practicum (virtual), 2023.</li> <li>Spangler, M.L. Genomics: Improving the U.S. Cowherd, American Gelbvieh Association webinar series (virtual), 2023.</li> <li>Spangler, M.L. iGENDEC—Next generation decision support, Wulf/Riverview webinar (virtual), 2023.</li> <li>Spangler, M.L. Current and Future Use of Genomics in Beef Cattle, Iowa Vet Med Association annual meeting, Ames, IA, 2023.</li> <li>Spangler, M.L. Profit Focused? Make Sure Your Selection Decisions Are Too, NBCEC Brown Bagger webinar series (virtual), 2023.</li> <li>Spangler, M.L. Here in the middle with you: modern quantitative animal genetics, Complex Biosystems seminar, Lincoln, NE, 2023.</li> <li>Spangler, M.L. Impacting the Quality of EPDs for You and Your Customers, Beef Seedstock Symposium, Lexington, KY, 2023.</li> <li>Spangler, M.L. Putting Selection Tools to Work (EPDs and Indices), Beef Seedstock Symposium, Lexington, KY, 2023.</li> <li>Spangler, M.L. Impacting the Quality of EPDs for You and Your Customers, Beef Seedstock Symposium, Glasgow, KY, 2023.</li> <li>Spangler, M.L. Putting Selection Tools to Work (EPDs and Indices), Beef Seedstock Symposium, Glasgow, KY, 2023.</li> <li>Spangler, M.L. Impacting the Quality of EPDs for You and Your Customers, Beef Seedstock Symposium, Spring Hill, TN, 2023.</li> <li>Spangler, M.L. Putting Selection Tools to Work (EPDs and Indices), Beef Seedstock Symposium, Spring Hill, TN, 2023.</li> <li>Kuehn, L.A., and Spangler, M.L. A Genetics Primer and Vision for Fed Cattle Phenotypic Prediction and Data Utilization, Genetic Merit Pricing Task Force meeting, Denver, CO, 2023</li> <li>Spangler, M.L. Genetic tools for the cow/calf producer (panel moderator), Nebraska Beef Industry Scholars Beef Summit, Mead, NE, 2023</li> <li>Spangler, M.L. Making genetic progress and why end product quality matters to Seedstock producers, American Gelbvieh Association annual convention, Omaha, NE, 2023.</li> <li>Spangler, M.L. Increasing the accuracy of selection decisions, ISU Genetics Symposium, Ames, IA, 2023.</li> <li>Spangler, M.L. Leveraging commercial data to improve selection and management decisions, BIF Genetic Prediction Workshop, Kansas City, MO, 2023.</li> <li>Speidel, S.E., R.M. Enns, M.G. Thomas, I.M. Kukor, and T.N. Holt. Genetics of heart score and relationships with performance.  Presented in the Cowherd Efficiency Subcommittee meeting at the Annual Beef Improvement Federation Meeting. Calgary, AB, Canada, 2023.</li> <li>Speidel, S.E., R.M. Enns, M.G. Thomas, I.M. Kukor, and T.N. Holt. Genetic prediction for bovine congestive heart failure. Presented at the American Simmental Fall Focus. Denver, CO, 2023.</li> <li>Thallman, R.M. Maternal composites for terminal crossing. Presented to representatives from Maddux Ranches. Clay Center, NE, 2023.</li> <li>Thallman, R.M. The Germplasm Evaluation Project. USDA-ARS Grazinglands Research Laboratory. El Reno, OK, 2023.</li> <li>Thallman, R.M. The Germplasm Evaluation Project. Junior American Braunvieh Association. Kearney, NE, 2023.</li> <li>Thallman, R.M. Rewarding high-quality data with higher accuracies, Beef Improvement Federation Annual Research Symposium. Calgary, AB, Canada, 2023.</li> <li>Thallman, R.M. The Germplasm Evaluation Project. Presented to visiting beef producers from New Zealand. Clay Center, NE, 2023.</li> <li>Thallman, R.M. The Germplasm Evaluation Project. American Gelbvieh Association. Clay Center, NE, 2023.</li> <li>Thallman, R.M. Recent developments in the Germplasm Evaluation Project, U.S. Meat Animal Research Center Beef Focus Group. Clay Center, NE, 2023.</li> <li>Thallman, R.M. A vision for the future of low-pass sequencing. Beef Improvement Federation Genetic Prediction Workshop. Kansas City, MO, 2023.</li> </ol>   Extension   <ol> <li>Hulsman Hanna, L.L. Fence Post: Have you thought about cow size lately? North Dakota Stockman Magazine. May/June 2023: 20-21. 2023.</li> <li>Sanglard, L.P., G.M. See, and M.L. Spangler. Including Gene Edited Sires in Genetic Evaluation. NE Beef Report. 2023.</li> <li>Spangler, M.L. The impact of genomics on EPDs. Proc. Beef Cattle Congress—Blueprint for the Future. 2023.</li> <li>Valasek, H.F., B.L. Golden, and M.L. Spangler. Impact of Planning Horizon Length on Breeding Objectives and Resulting Selection Decisions. NE Beef Report. 2023.</li> </ol>