Research Project: Developing a Systems Biology Approach to Enhance Efficiency and Sustainability of Beef and Lamb Production

Location: Genetics and Animal Breeding

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Mitochondrial DNA copy number as a potential genetic indicator of growth and carcass traits in beef cattle - (Proceedings)
Sanglard, L.P., Kuehn, L.A., Snelling, W.M., Spangler, M.L. 2023. Mitochondrial DNA copy number as a potential genetic indicator of growth and carcass traits in beef cattle [abstract]. In: Proceedings of the World Congress of Genetics Applied in Livestock Production. Session 40. p. 47.

Genetic prediction for growth traits in beef cattle using selected variants from imputed low-pass sequence data - (Proceedings)
Russell, C.C., Kuehn, L.A., Snelling, W.M., Spangler, M.L. 2023. Genetic prediction for growth traits in beef cattle using selected variants from imputed low-pass sequence data [abstract]. In: Proceedings of the World Congress of Genetics Applied in Livestock Production, July 3-8, 2022, Rotterdam, The Netherlands. Session 40. p. 47.

iGENDEC: A web-based decision support tool for economic index construction - (Proceedings)
Spangler, M.L., Golden, B.L., Newman, S., Kuehn, L.A., Snelling, W.M., Thallman, R.M., Weaber, R.L. 2023. iGENDEC: A web-based decision support tool for economic index construction [abstract]. In: Proceedings of the World Congress of Genetics Applied in Livestock Production. Session 51. p. 53-54.

Genomic prediction of wool shedding in a composite sheep flock using pooled allele frequencies and individual genotypes - (Proceedings)
Vargas, J.N., Keele, J.W., Kuehn, L.A., Lewis, R.M. 2023. Genomic prediction of wool shedding in a composite sheep flock using pooled allele frequencies and individual genotypes [abstract]. In: Proceedings of the World Congress of Genetics Applied in Livestock Production, July 3-8, 2022, Rotterdam, The Netherlands. Session 25. p.35.

The bovine pangenome consortium: Democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species - (Peer Reviewed Journal)
Smith, T.P.L., Bickhart, D.M., Boichard, D., Chamberlain, A.J., Djikeng, A., Jiang, Y., Low, W., Pausch, H., Demyda-Peyras, S., Prendergast, J., Schnabel, R.D., Rosen, B.D. 2023. The bovine pangenome consortium: Democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species. Genome Biology. 24. Article 139. https://doi.org/10.1186/s13059-023-02975-0.

Genetic and phenotypic associations of mitochondrial DNA copy number, SNP, and haplogroups with growth and carcass traits in beef cattle - (Peer Reviewed Journal)
Sanglard, L.P., Snelling, W.M., Kuehn, L.A., Thallman, R.M., Freetly, H.C., Wheeler, T.L., Shackelford, S.D., King, D.A., Spangler, M.L. 2022. Genetic and phenotypic associations of mitochondrial DNA copy number, SNP, and haplogroups with growth and carcass traits in beef cattle. Journal of Animal Science. 101. Article skac415. https://doi.org/10.1093/jas/skac415.

Breeding sustainable beef cows: Reducing weight and increasing productivity - (Peer Reviewed Journal)
Snelling, W.M., Thallman, R.M., Spangler, M.L., Kuehn, L.A. 2022. Breeding sustainable beef cows: Reducing weight and increasing productivity. Animals. 12(14). Article 1745. https://doi.org/10.3390/ani12141745.

Bacterial communities of the uterus and rumen during heifer development with protein supplementation - (Peer Reviewed Journal)
Ault-Seay, T.B., Brandt, K.J., Henniger, M.T., Payton, R.R., Mathew, D.J., Moorey, S.E., Schrick, F.N., Pohler, K.G., Smith, T.P.L., Rhinehart, J.D., Schneider, L.G., McLean, K.J., Myer, P.R. 2022. Bacterial communities of the uterus and rumen during heifer development with protein supplementation. Frontiers in Animal Science. 3. Article 903909. https://doi.org/10.3389/fanim.2022.903909.

Using pooled data for genomic prediction in a bivariate framework with missing data - (Peer Reviewed Journal)
Baller, J.L., Kachman, S.D., Kuehn, L.A., Spangler, M.L. 2022. Using pooled data for genomic prediction in a bivariate framework with missing data. Journal of Animal Breeding and Genetics. Article 12727. https://doi.org/10.1111/jbg.12727.

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies - (Peer Reviewed Journal)
Leonard, A.S., Crysnanto, D., Fang, Z., Heaton, M.P., Vander Ley, B.L., Herrera, C., Bollwein, H., Bickhart, D.M., Kuhn, K.L., Smith, T.P.L., Rosen, B.D., Pausch, H. 2022. Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies. Nature Communications. 13. Article 3012. https://doi.org/10.1038/s41467-022-30680-2.

Discrete distributions of simple sequence repeat lengths in DNA template vary at individual loci in Mannheimia haemolytica isolates - (Proceedings)

Variations in antibody repertoires correlate with vaccine responses - (Peer Reviewed Journal)
Safonova, Y., Shin, S.B., Kramer, L., Reecy, J., Watson, C.T., Smith, T.P.L., Pevzner, P.A. 2022. Variations in antibody repertoires correlate with vaccine responses. Genome Research. 32:791-804. https://doi.org/10.1101/gr.276027.121.

Influence of environmental factors and genetic variation on mitochondrial DNA copy number - (Peer Reviewed Journal)
Sanglard, L.P., Kuehn, L.A., Snelling, W.M., Spangler, M.L. 2022. Influence of environmental factors and genetic variation on mitochondrial DNA copy number. Journal of Animal Science. 100(5). Article skac059. https://doi.org/10.1093/jas/skac059.

Defining the caprine ¿d T cell WC1 multigenic array and evaluation of its expressed sequences and gene structure conservation among goat breeds and relative to cattle - (Peer Reviewed Journal)

Genetic parameters, heterosis, and breed effects for body condition score and mature cow weight in beef cattle - (Peer Reviewed Journal)
Ribeiro, A.F., Sanglard, L.P., Snelling, W.M., Thallman, R.M., Kuehn, L.A., Spangler, M.L. 2022. Genetic parameters, heterosis, and breed effects for body condition score and mature cow weight in beef cattle. Journal of Animal Science. 100(2). Article skac017. https://doi.org/10.1093/jas/skac017.

Estimation of pool construction and technical error - (Peer Reviewed Journal)
Keele, J., McDaneld, T., Lawrence, T., Jennings, J., Kuehn, L. 2021. Estimation of pool construction and technical error. Agriculture. 11(11). Article 1091. https://doi.org/10.3390/agriculture11111091.

A conserved Histophilus somni 23S intervening sequence yields functional, fragmented 23S rRNA - (Peer Reviewed Journal)
Harhay, G.P., Harhay, D.M., Brader, K.D., Smith, T.P.L. 2021. A conserved Histophilus somni 23S intervening sequence yields functional, fragmented 23S rRNA. Microbiology Spectrum. 9(3). Article e0143121. https://doi.org/10.1128/Spectrum.01431-21.

Characterization of the respiratory microbiome and virome associated with bovine respiratory disease - (Abstract Only)
McDaneld, T., Earley, B., Cosby, L., McGee, M., Duffy, K., Cuevas-Gomez, I., Kuehn, L., Workman, A., Conant, G., Cormican, P., McCabe, M., Duffy, C., Lemon, K., McMenamy, M., Smyth, V., Smith, T. 2021. Characterization of the respiratory microbiome and virome associated with bovine respiratory disease [abstract]. In proceedings: Conference of Research Workers in Animal Diseases, December 4-7, 2021, Chicago, Illinois. V-P048. Available: https://crwad.org/wp-content/uploads/CRWAD-2021/

Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes - (Peer Reviewed Journal)
Ren, Y., MacPhillamy, C., To, T., Smith, T.P.L., Williams, J.L., Low, W.Y. 2021. Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes. Genomics. 113(6):3599-3609. https://doi.org/10.1016/j.ygeno.2021.08.021.

Revealing how variations in antibody repertoires correlate with vaccine responses - (Pre-print Publication)
Safonova, Y., Shin, S.B., Kramer, L., Reecy, J., Watson, C.T., Smith, T.P.L., Pevzner, P.A. 2021. Revealing how variations in antibody repertoires correlate with vaccine responses. bioRxiv. Article 454618. https://doi.org/10.1101/2021.08.06.454618.

Breed and heterotic effects for mature weight in beef cattle - (Peer Reviewed Journal)
Zimmermann, M.J., Kuehn, L.A., Spangler, M.L., Thallman, R.M., Snelling, W.M., Lewis, R.M. 2021. Breed and heterotic effects for mature weight in beef cattle. Journal of Animal Science. 99(8). Article skab209. https://doi.org/10.1093/jas/skab209.

Using genomics to measure phenomics: Repeatability of bull prolificacy in multiple-bull pastures - (Peer Reviewed Journal)
Bennett, G.L., Keele, J.W., Kuehn, L.A., Snelling, W.M., Dickey, A.M., Light, D.E., Cushman, R.A., McDaneld, T.G. 2021. Using genomics to measure phenomics: Repeatability of bull prolificacy in multiple-bull pastures. Agriculture. 11(7). Article 603. https://doi.org/10.3390/agriculture11070603.

Using genomics to measure phenomics: Repeatability of bull prolificacy in multiple-bull pastures - (Pre-print Publication)
Bennett, G.L., Keele, J.W., Kuehn, L.A., Snelling, W.M., Dickey, A.M., Light, D.E., Cushman, R.A., McDaneld, T.G. 2021. Using genomics to measure phenomics: Repeatability of bull prolificacy in multiple-bull pastures. Agriculture. 11(7). Article 603. https://doi.org/10.3390/agriculture11070603.

Accuracy of GEBV of sires based on pooled allele frequency of their progeny - (Peer Reviewed Journal)
Vargas Jurado, N., Kuehn, L.A., Keele, J.W., Lewis, R.M. 2021. Accuracy of GEBV of sires based on pooled allele frequency of their progeny. G3, Genes/Genomes/Genetics. 11(11). Article jkab231. https://doi.org/10.1093/g3journal/jkab231.

Ruminal protozoal populations of Angus steers differing in feed efficiency - (Peer Reviewed Journal)
Clemmons, B.A., Shin, S.B., Smith, T.P.L., Embree, M.M., Voy, B.H., Schneider, L.G., Donohoe, D.R., McLean, K.J., Myer, P. 2021. Ruminal protozoal populations of Angus steers differing in feed efficiency. Animals. 11(6). Article 1561. https://doi.org/10.3390/ani11061561.

Use of advanced reproductive technologies and inclusion of these records in genetic evaluation - (Proceedings)
Thallman, R.M., Snider, A.P. 2021. Use of advanced reproductive technologies and inclusion of these records in genetic evaluation. In: Proceedings of the Beef Improvement Federation Symposium, June 22-25, 2021, Des Moines, Iowa. p. 42-50.

Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species - (Peer Reviewed Journal)
Liu, R., Tearle, R., Low, W., Chen, T., Thomsen, D., Smith, T.P.L., Hiendleder, S., Williams, J.L. 2021. Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species. Biomed Central (BMC) Genomics. 22. Article 410. https://doi.org/10.1186/s12864-021-07667-2.

Association between clinical respiratory signs, lung lesions detected by thoracic ultrasonography and growth performance in pre-weaned dairy calves - (Peer Reviewed Journal)
Cuevas-Gomes, I., McGee, M., Sanchez, J., O'Riordan, E., Byrne, N., McDaneld, T.G., Earley, B. 2021. Association between clinical respiratory signs, lung lesions detected by thoracic ultrasonography and growth performance in pre-weaned dairy calves. Irish Veterinary Journal. 74. Article 7. https://doi.org/10.1186/s13620-021-00187-1.

De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification - (Peer Reviewed Journal)
Dobson, L.K., Zimin, A., Bayles, D., Fritz-Waters, E., Alt, D., Olsen, S., Blanchong, J., Reecy, J., Smith, T.P.L., Derr, J.N. 2021. De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification. Animal Genetics. 52(3):263-274. https://doi.org/10.1111/age.13060.

Relationships among intramammary health, udder and teat characteristics, and productivity of extensively managed ewes - (Peer Reviewed Journal)
Knuth, R.M., Stewart, W.C., Taylor, J.B., Bisha, B., Yeoman, C.J., Van Emon, M.L., Murphy, T.W. 2021. Relationships among intramammary health, udder and teat characteristics, and productivity of extensively managed ewes. Journal of Animal Science. 99(4):1-10. https://doi.org/10.1093/jas/skab059.

Genetic changes in beef cow traits following selection for calving ease - (Peer Reviewed Journal)
Bennett, G.L., Thallman, R.M., Snelling, W.M., Keele, J.W., Freetly, H.C., Kuehn, L.A. 2021. Genetic changes in beef cow traits following selection for calving ease. Translational Animal Science. 5(1):1-10. https://doi.org/10.1093/tas/txab009.

Evaluating accuracy of DNA pool construction based on white blood cell counts - (Peer Reviewed Journal)
Abrams, A.N., McDaneld, T.G., Keele, J.W., Chitko-McKown, C.G., Kuehn, L.A., Gonda, M.G. 2021. Evaluating accuracy of DNA pool construction based on white blood cell counts. Frontiers in Livestock Genomics. 12. Article 635846. https://doi.org/10.3389/fgene.2021.635846.

Characterization of the domestic goat yd T cell receptor gene loci and gene usage - (Peer Reviewed Journal)
Gillespi, A., Yirsaw, A., Gunasekaran, K.P., Smith, T.P., Bickhart, D.M., Turley, M., Connelley, T., Telfer, J.C., Baldwin, C.L. 2021. Characterization of the domestic goat yd T cell receptor gene loci and gene usage. Immunogenetics. 73:187-201. https://doi.org/10.1007/s00251-021-01203-y.

Comparison of performance of F1 Romanov crossbred ewes with wool and hair breeds during fall lambing and body weight and longevity through six production years - (Peer Reviewed Journal)
Murphy, T.W., Freking, B.A. 2021. Comparison of performance of F1 Romanov crossbred ewes with wool and hair breeds during fall lambing and body weight and longevity through six production years. Journal of Animal Science. 99(1):1-7. https://doi.org/10.1093/jas/skaa400.

Comparison of performance of F1 Romanov crossbred ewes with wool and hair breeds during spring lambing under intensive and extensive production systems - (Peer Reviewed Journal)
Freking, B.A., Murphy Jr, T.W. 2020. Comparison of performance of F1 Romanov crossbred ewes with wool and hair breeds during spring lambing under intensive and extensive production systems. Journal of Animal Science. 99(1):1-10. https://doi.org/10.1093/jas/skaa397.

Development and validation of a neural network for the automated detection of horn flies on cattle - (Peer Reviewed Journal)
Psota, E.T., Luc, E.K., Pighetti, G.M., Schneider, L.G., Trout Fryxell, R.T., Keele, J.W., Kuehn, L.A. 2021. Development and validation of a neural network for the automated detection of horn flies on cattle. Computers and Electronics in Agriculture. 180. Article 105927. https://doi.org/10.1016/j.compag.2020.105927.

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C - (Peer Reviewed Journal)
Kronenberg, Z.N., Rhie, A., Koren, S., Concepcion, G., Peluso, P., Munson, K.M., Porubsky, D., Kuhn, K.L., Mueller, K.A., Low, W., Hiendleder, S., Fedrigo, O., Liachko, I., Hall, R.J., Phillippy, A.M., Eichler, E.E., Williams, J.L., Smith, T.P.L., Jarvis, E.D., Sullivan, S.T., Kingan, S.B. 2021. Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nature Communications. 12. Article 1935. https://doi.org/10.1038/s41467-020-20536-y.

Assessment of imputation from low-pass sequencing to predict merit of beef steers - (Peer Reviewed Journal)
Snelling, W.M., Hoff, J.L., Li, J.H., Kuehn, L.A., Keel, B.N., Lindholm-Perry, A.K., Pickrell, J.K. 2020. Assessment of imputation from low-pass sequencing to predict merit of beef steers. Genes. 11(11). Article 1312. https://doi.org/10.3390/genes11111312.

Anthelmintic resistance in gastrointestinal nematodes and associated management factors in Intermountain West sheep flocks - (Peer Reviewed Journal)
Stewart, W.C., Scott, D.M., Howell, S.B., Kaplan, R.M., Roeder, B.L., Murphy, T.W. 2020. Anthelmintic resistance in gastrointestinal nematodes and associated management factors in Intermountain West sheep flocks. Sheep and Goat Research Journal. 35:30-37.

Growth performance and hematological changes of weaned beef calves diagnosed with respiratory disease using respiratory scoring and thoracic ultrasonography - (Peer Reviewed Journal)
Cuevas-Gomez, I., McGee, M., McCabe, M., Cormican, P., O'Riordan, E., McDaneld, T.G., Earley, B. 2020. Growth performance and hematological changes of weaned beef calves diagnosed with respiratory disease using respiratory scoring and thoracic ultrasonography. Journal of Animal Science. 98(11):1-11. https://doi.org/10.1093/jas/skaa345.

Using pooling to capture commercial data for inclusion in genetic evaluations - (Research Notes)
Baller, J.L., Kachman, S.D., Kuehn, L.A., Spangler, M.L. 2021. Using pooling to capture commercial data for inclusion in genetic evaluations. Nebraska Beef Reports. p. 11-13. Available: https://beef.unl.edu/documents/2021-beef-report/mp110-2021-03.pdf.

Genetic parameter estimates for age at slaughter and days to finish in a multibreed population - (Research Notes)
Upperman, L.R., Kuehn, L.A., Spangler, M.L. 2021. Genetic parameter estimates for age at slaughter and days to finish in a multibreed population. Nebraska Beef Reports. p. 16-17. Available: https://beef.unl.edu/documents/2021-beef-report/mp110-2021-05.pdf.

Assessment of alternative models for genetic analysis of worm and tick infestation in nellore cattle - (Peer Reviewed Journal)
Passafaro, T.L., Lopes, F.B., Murphy Jr, T.W., Valente, B.D., Leite, R.C., Rosa, G.J., Toral, F.L. 2021. Assessment of alternative models for genetic analysis of worm and tick infestation in nellore cattle. Livestock Science. 244. Article 104276. https://doi.org/10.1016/j.livsci.2020.104276.

Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0) - (Peer Reviewed Journal)
Salavati, M., Caulton, A., Clark, R., Gazova, I., Smith, T.P.L., Worley, K.C., Cockett, N.E., Archibald, A.L., Clarke, S., Murdoch, B.M., Clark, E.L. 2020. Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0). Frontiers in Genetics. Article e580580. https://doi.org/10.3389/fgene.2020.580580.

Effect of increasing dietary zinc sulfate fed to primiparous ewes: I. Effects on serum metabolites, mineral transfer efficiency, and animal performance - (Peer Reviewed Journal)
Stewart, W.C., Murphy Jr, T.W., Page, C.M., Rule, D.C., Taylor, J.B., Austin, K., Pankey, C. 2020. Effect of increasing dietary zinc sulfate fed to primiparous ewes: I. Effects on serum metabolites, mineral transfer efficiency, and animal performance. Applied Animal Science. 36(6):839-850. https://doi.org/10.15232/aas.2020-02057.

Genetic and nongenetic factors influencing ewe prolificacy and lamb body weight in a closed Romanov flock - (Peer Reviewed Journal)
Murphy Jr, T.W., Keele, J.W., Freking, B.A. 2020. Genetic and nongenetic factors influencing ewe prolificacy and lamb body weight in a closed Romanov flock. Journal of Animal Science. 98(9):1-8. https://doi.org/10.1093/jas/skaa283.

Influence of host genetics in shaping the rumen bacterial community in beef cattle - (Peer Reviewed Journal)
Abbas, W., Howard, J.T., Paz, H.A., Hales, K.E., Wells, J., Kuehn, L.A., Erickson, G.E., Spangler, M.L., Fernando, S.C. 2020. Influence of host genetics in shaping the rumen bacterial community in beef cattle. Scientific Reports. 10. Article 15101. https://doi.org/10.1038/s41598-020-72011-9.

Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing - (Peer Reviewed Journal)
Myer, P.R., McDaneld, T.G., Kuehn, L.A., Dedonder, K.D., Apley, M.D., Capik, S.F., Lubbers, B.V., Harhay, G.P., Harhay, D.M., Keele, J.W., Henniger, M.T., Clemmons, B.A., Smith, T.P.L. 2020. Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing. PLoS One. 15(7):e0235498. https://doi.org/10.1371/journal.pone.0235498.

Genomic prediction using pooled data in a single-step genomic best linear unbiased prediction framework - (Peer Reviewed Journal)
Baller, J.L., Kachman, S.D., Kuehn, L.A., Spangler, M.L. 2020. Genomic prediction using pooled data in a single-step genomic best linear unbiased prediction framework. Journal of Animal Science. 98(6):1-12. https://doi.org/10.1093/jas/skaa184.

Estimated breeding values for enhanced flock productivity - (Other)

Development, selection criteria, and performance of Composite IV sheep at the U.S. Meat Animal Research Center - (Proceedings)
Murphy, T., Freking, B., Bennett, G.L., Keele, J.W. 2020. Development, selection criteria, and performance of Composite IV sheep at the U.S. Meat Animal Research Center [abstract]. Journal of Animal Science. 98(Supplement 4):207. https://doi.org/10.1093/jas/skaa278.381.

Phenotypic and genetic differences in Rambouillet lines divergently selected for reproductive rate over 50 yr - (Abstract Only)
Murphy, T., Thomson, J.M., Berardinelli, J., Roeder, B. 2020. Phenotypic and genetic differences in Rambouillet lines divergently selected for reproductive rate over 50 yr [abstract]. Journal of Animal Science. 98(supplement 4):206. https://doi.org/10.1093/jas/skaa278.379.

Effects of dietary Zn on ewe milk minerals and somatic cell count - (Proceedings)
Page, C.M., Murphy, T., Taylor, B., Julian, A., Whaley, J., Woodruff, K., Hummel, G., DeMarco, C., Laverell, D., Cunningham, H., Rule, D., Stewart, W. 2020. Effects of dietary Zn on ewe milk minerals and somatic cell count [abstract]. Journal of Animal Science. 98(Supplement 4):213-214. https://doi.org/10.1093/jas/skaa278.394.

Harvest season, carcass weight, and fat measurements effects on lamb carcass characteristics and economic comparison of moderate and heavy weight lamb carcasses in the Western lamb processing industry - (Proceedings)
Whaley, J., Means, W., Ritten, J., Murphy, T., Gifford, C., Cunningham, H., Woodruff, K., McKibben, H., Page, C.M., Stewart, W.C. 2020. Harvest season, carcass weight, and fat measurements effects on lamb carcass characteristics and economic comparison of moderate and heavy weight lamb carcasses in the Western lamb processing industry [abstract]. Journal of Animal Science. 98(4):190-191. https://doi.org/10.1093/jas/skaa278.351.

Fleece and fiber characteristics of Rambouillet, Targhee, and their reciprocal-crosses at first shearing - (Proceedings)
Murphy, T., Stewart, W.C., Notter, D., Knuth, R., Feagler, T., Taylor, B. 2020. Fleece and fiber characteristics of Rambouillet, Targhee, and their reciprocal-crosses at first shearing [abstract]. Journal of Animal Science. 98(supplement 4):206-207. https://doi.org/10.1093/jas/skaa278.380.

Current progress in the Agricultural Research Service Beef Grand Challenge: A large-scale genetics by environment by management evaluation project - (Abstract Only)
Kuehn, L.A., Casperson, S.L., Derner, J.D., Gunter, S.A., Hay, E., Moffet, C., Neel, J.P., Picklo, M.J., Petersen, M.K., Roemmich, J.N., Turner, K.E., Waterman, R.C., Wheeler, T.L., Boggess, M.V. 2020. Current progress in the Agricultural Research Service Beef Grand Challenge: A large-scale genetics by environment by management evaluation project [abstract]. Journal of Animal Science. 98(Supplement 4):13-14. https://doi.org/10.1093/jas/skaa278.025.

Genetic parameter estimates for days on feed, age at slaughter, and carcass traits in a multi-breed beef cattle population - (Abstract Only)
Upperman, L.R., Kuehn, L.A., Spangler, M.L. 2020. Genetic parameter estimates for days on feed, age at slaughter, and carcass traits in a multi-breed beef cattle population. Journal of Animal Science. 98(Supplement 4):21-22. https://doi.org/10.1093/jas/skaa278.040.

Using pooled data for single-step genomic prediction: Impact of within-pool variance and size - (Abstract Only)
Baller, J.L., Kachman, S.D., Kuehn, L.A., Spangler, M.L. 2020. Using pooled data for single-step genomic prediction: Impact of within-pool variance and size [abstract]. Journal of Animal Science. 98(Supplement 4):9. https://doi.org/10.1093/jas/skaa278.017.

Methods of determining the presence or absence of a plurality of target polynucleotides in a sample - (Pct (patent Cooperation Treaty))
Curry, J.D., Koshinsky, H., Lindholm-Perry, A.K., Thallman, R.M. 2020. Methods of determining the presence or absence of a plurality of target polynucleotides in a sample. U.S. Patent and Trademark Office. Patenet #10/648,030 B2.

Mature size and other trait differences in cows selected for calving ease and growth - (Abstract Only)
Bennett, G.L., Keele, J.W., Thallman, R.M., Snelling, W.M., Freetly, H.C., Kuehn, L.A. 2020. Mature size and other trait differences in cows selected for calving ease and growth [abstract]. Journal of Animal Science Supplement. 98(Supplement 4):22. https://doi.org/10.1093/jas/skaa278.041.

Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle - (Peer Reviewed Journal)
Rice, E.S., Koren, S., Rhie, A., Heaton, M.P., Kalbfleisch, T., Hardy, T., Hackett, P., Bickhart, D.M., Rosen, B.D., Vander Ley, B., Maurer, N.W., Green, R.E., Phillippy, A.M., Petersen, J.L., Smith, T.P. 2020. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. GigaScience. 9(4):1-9. https://doi.org/10.1093/gigascience/giaa029.

Assessing the potential of low-pass sequencing and imputation to genotype sequence variants in beef cattle - (Abstract Only)
Snelling, W.M., Kuehn, L.A., Li, J.H., Hoff, J.L., Pickrell, J.K. 2020. Assessing the potential of low-pass sequencing and imputation to genotype sequence variants in beef cattle [abstract]. In: Plant and Animal Genome Conference Proceedings, January 11-15, 2020, San Diego, California. Paper No. PE0330.

Characterization of water intake and water efficiency in beef cattle - (Peer Reviewed Journal)
Ahlberg, C.M., Allwardt, K., Broocks, A., Bruno, K., Taylor, A., McPhillips, L., Krehbiel, C.R., Calvo-Lorenzo, M.S., Richards, C.J., Place, S.E., DeSilva, U., VanOverbeke, D.L., Mateescu, R.G., Kuehn, L.A., Weaber, R., Bormann, J., Rolf, M.M. 2019. Characterization of water intake and water efficiency in beef cattle. Journal of Animal Science. 97(12):4770-4782. https://doi.org/10.1093/jas/skz354.

Development of a low-pass sequencing platform to support genomic selection in livestock - (Abstract Only)
Pickrell, J., Li, J.H., Hoff, J.L., Kuehn, L.A., Snelling, W.M. 2020. Development of a low-pass sequencing platform to support genomic selection in livestock [abstract]. International Plant & Animal Genome XXVIII Conference, January 11-15, 2020, San Diego, California. Abstract Number W218. Available at: https://plan.core-apps.com/pag_2020/abstracts

Genome assemblies of global cattle breeds to create a cattle Pangenome - (Abstract Only)
Smith, T.P.L, Bickhart, D.M., Rosen, B.D. 2020. Genome assemblies of global cattle breeds to create a cattle Pangenome [abstract]. International Plant & Animal Genome XXVIII Conference, January 11-15, 2020, San Diego, California. Poster Number PE0318. Available at: https://plan.core-apps.com/pag_2020/abstracts

Pipelines, workflows and virtualization to build institutional informatics capacity - (Abstract Only)
Dickey, A.M., Nonneman, D.J., Freetly, H.C., Workman, A.M., Kuehn, L.A. 2019. Pipelines, workflows and virtualization to build institutional informatics capacity [abstract]. In: Proceedings of Rocky 2019, December 5-7, 2019, Aspen/Snowmass, Colorado. Paper No. P22.

Implications of cryptic correlations caused by interacting traits for quantitative genetics - (Abstract Only)

Lamb wool shedding is a good predictor of ewe wool shedding - (Peer Reviewed Journal)
Vargas Jurado, N., Kuehn, L.A., Lewis, R.M. 2019. Lamb wool shedding is a good predictor of ewe wool shedding. Journal of Animal Breeding and Genetics. 137(4):365-373. https://doi.org/10.1111/jbg.12449.

Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid - (Research Notes)
Rice, E.S., Koren, S., Rhie, A., Heaton, M.P., Kalbfleisch, T.S., Hardy, T., Hackett, P.H., Bickhart, D.M., Rosen, B.D., Vander Ley, B., Maurer, N.W., Green, R.E., Phillippy, A.M., Petersen, J.L., Smith, T.P.L. 2019. Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid. bioRxiv. 737171. https://doi.org/10.1101/737171.

Characterization of the respiratory microbiome and virome associated with bovine respiratory disease complex - (Abstract Only)
McDaneld, T.G., Earley, B., McGee, M., Kuehn, L.A., Workman, A.M., Conant, G., Cormican, P., McCabe, M., Duffy, C., Lemon, K., McMenamy, M., Smyth, V., Smith, T.P., Cosby, L. 2019. Characterization of the respiratory microbiome and virome associated with bovine respiratory disease complex [abstract]. Conference of Research Workers in Animal Diseases Conference, November 2-5, 2019, Chicago, Illinois. P213. Available: https://crwad.org/crwad-2019/

Uterine and vaginal bacterial community diversity prior to artificial insemination between pregnant and nonpregnant postpartum cows - (Peer Reviewed Journal)
Ault, T.B., Clemmons, B.A., Reese, S.T., Dantas, F.G., Franco, G.A., Smith, T.P.L., Edwards, J.L., Myer, P.R., Pohler, K.G. 2019. Uterine and vaginal bacterial community diversity prior to artificial insemination between pregnant and nonpregnant postpartum cows. Journal of Animal Science. 97(10):4298-4304. https://doi.org/10.1093/jas/skz210.

Bacterial taxonomic composition of the postpartum cow uterus and vagina prior to artificial insemination - (Peer Reviewed Journal)
Ault, T.B., Clemmons, B.A., Reese, S.T., Dantas, F.G., Franco, G.A., Smith, T.P.L., Edwards, J.L., Myer, P.R., Pohler, K.G. 2019. Bacterial taxonomic composition of the postpartum cow uterus and vagina prior to artificial insemination. Journal of Animal Science. 97(10):4305-4313. https://doi.org/10.1093/jas/skz212.

Association of a nucleotide variant in Tenascin X with objective milk production traits in US dairy sheep - (Abstract Only)
Hemmerling, K.M., Murphy, T.W., Herndon, M.K., Massa, A.T., Cinar, M.U., Thomas, D.L., White, S.N., Mousel, M.R. 2019. Association of a nucleotide variant in Tenascin X with objective milk production traits in US dairy sheep [abstract]. International Society for Animal Genetics (ISAG). Abstract #P65 (Abstract Book p. 81). Available: https://www.isag.us/Docs/Proceedings/ISAG2019_Proceedings.pdf

Effects of feeding juniper as a roughage on feedlot performance, carcass measurements, meat sensory attributes, and volatile aroma compounds of yearling Rambouillet wethers - (Peer Reviewed Journal)
Kerth, C.R., Wall, K.R., Miller, R.K., Whitney, T.R., Stewart, W.C., Boles, J.A., Murphy Jr, T.W. 2019. Effects of feeding juniper as a roughage on feedlot performance, carcass measurements, meat sensory attributes, and volatile aroma compounds of yearling Rambouillet wethers. Journal of Animal Science. 97(7):2816-2830. https://doi.org/10.1093/jas/skz174.

Relationship of molecular breeding value for beef tenderness on heifer traits through weaning their first calf - (Abstract Only)
Bennett, G.L., Cushman, R.A., McNeel, A.K., Casas, E., Smith, T.P.L. 2019. Relationship of molecular breeding value for beef tenderness on heifer traits through weaning their first calf [abstract]. Journal of Animal Science. 97(Suppl3):266-267. https://doi.org/10.1093/jas/skz258.542.

Genomics in animal agriculture: current technologies and applications - (Abstract Only)
Smith, T.P.L. 2019. Genomics in animal agriculture: current technologies and applications [abstract}. Journal of Animal Science. 97(Supplement 3):55-56. https://doi.org/10.1093/jas/skz258.113.

Influence of microRNAs from semen on bovine fertility - (Abstract Only)
Perkins, S.D., Keel, B.N., Northrop, E.J., McDaneld, T.G., Cushman, R.A., Harstine, B.R., DeJarnette, J.M., Utt, M.D., Perry, G.A. 2019. Influence of microRNAs from semen on bovine fertility [abstract]. Society for the Study of Reproduction Annual Meeting. Abstract Program, p. 181-182. Available: https://community.ssr.org/news-events/past-meetings/annual-meetings575

Validation of SNP associations with bovine ovulation and twinning rate - (Peer Reviewed Journal)
Kirkpatrick, B.W., Thallman, R.M., Kuehn, L.A. 2019. Validation of SNP associations with bovine ovulation and twinning rate. Animal Genetics. 50:259-261. https://doi.org/10.1111/age.12793.

Structural diversity of ultralong CDRH3s in seven bovine antibody heavy chains - (Peer Reviewed Journal)
Dong, J., Finn, J.A., Larsen, P.A., Smith, T.P.L., Crowe, J.E. 2019. Structural diversity of ultralong CDRH3s in seven bovine antibody heavy chains. Frontiers in Immunology. 10:558. https://doi.org/10.3389/fimmu.2019.00558.

Comparison of different functions to describe growth from weaning to maturity in crossbred beef cattle - (Peer Reviewed Journal)
Zimmerman, M.J., Kuehn, L.A., Spangler, M.L., Thallman, R.M., Snelling, W.M., Lewis, R.M. 2019. Comparison of different functions to describe growth from weaning to maturity in crossbred beef cattle. Journal of Animal Science. 97(4):1523-1533. https://doi.org/10.1093/jas/skz045.

Rambouillet and Romanov reciprocal breed effects on survival and growth traits of F1 lambs and on reproductive traits of F1 ewes - (Peer Reviewed Journal)
Freking, B.A., Bennett, G.L. 2019. Rambouillet and Romanov reciprocal breed effects on survival and growth traits of F1 lambs and on reproductive traits of F1 ewes. Journal of Animal Science. 97:578-586. https://doi.org/10.1093/jas/sky474.

Host genetics help shape the rumen microbiome in beef cattle - (Abstract Only)
Abbas, W., Howard, J.T., Paz, H.A., Hales, K.E., Wells, J., Kuehn, L.A., Spangler, M.L., Erickson, G.E., Fernando, S.C. 2019. Host genetics help shape the rumen microbiome in beef cattle. Journal of Animal Science. 97(Supplement 2):51. https://doi.org/10.1093/jas/skz122.093.

Enhanced estimates of carcass and meat quality effects for polymorphisms in myostatin and mu-calpain genes - (Peer Reviewed Journal)
Bennett, G.L., Tait, R.G., Shackelford, S.D., Wheeler, T.L., King, D.A., Casas, E., Smith, T.P.L. 2019. Enhanced estimates of carcass and meat quality effects for polymorphisms in myostatin and mu-calpain genes. Journal of Animal Science. 97(2):569-577. https://doi.org/10.1093/jas/sky451.

Evaluating accuracy of DNA pool construction based on white blood cell counts versus two common DNA quantification methods - (Abstract Only)
Abrams, A., Keele, J.W., McDaneld, T.G., Chitko-McKown, C.G., Gonda, M.G., Kuehn, L.A. 2019. Evaluating accuracy of DNA pool construction based on white blood cell counts versus two common DNA quantification methods [abstract]. International Plant & Animal Genome XXVII Conference, January 12-16, 2019, San Diego, California. Abstract PE0160. Available: https://plan.core-apps.com/pag_2019/abstracts

Genetic correlations among weight and cumulative productivity of crossbred beef cows - (Peer Reviewed Journal)
Snelling, W.M., Kuehn, L.A., Thallman, R.M., Bennett, G.L., Golden, B.L. 2018. Genetic correlations among weight and cumulative productivity of crossbred beef cows. Journal of Animal Science. 97:63-77. https://doi.org/10.1093/jas/sky420.

Status of evaluation of three maternal lines under pasture lambing management conditions at USMARC - (Other)
Freking, B.A. 2018. Status of evaluation of three maternal lines under pasture lambing management conditions at USMARC. World Wide Web [online]. Available: http://dasnr.adobeconnect.com/ag_coffee_shop/.

Environmental effects on water intake and water intake prediction in growing beef cattle - (Peer Reviewed Journal)
Ahlberg, C.M., Allwardt, K., Broocks, A., Bruno, K., McPhillips, L., Taylor, A.A., Krehbiel, C.R., Calvo-Lorenzo, M.S., Richards, C.J., Place, S.E., Desilva, U., Vanoverbeke, D.L., Mateescu, R.G., Kuehn, L.A., Weaber, R.L., Bormann, J.M., Rolf, M.M. 2018. Environmental effects on water intake and water intake prediction in growing beef cattle. Journal of Animal Science. 96:4368-4384. https://doi.org/10.1093/jas/sky267.

Test duration for water intake, ADG, and DMI in beef cattle - (Peer Reviewed Journal)
Ahlberg, C.M., Allwardt, K., Broocks, A., Bruno, K., McPhillips, L., Taylor, A., Krehbiel, C.R., Calvo-Lorenzo, M., Richards, C.J., Place, S.E., Desilva, U., VanOverbeke, D.L., Mateescu, R.G., Kuehn, L.A., Weaber, R.L., Bormann, J.M., Rolf, M.M. 2018. Test duration for water intake, ADG, and DMI in beef cattle. Journal of Animal Science. 96(8):3043-3054. https://doi.org/10.1093/jas/sky209.

Extended haplotype phasing of de novo genome assemblies with FALCON-Phase - (Pre-print Publication)
Kronenberg, Z.N., Rhie, A., Koren, S., Concepcion, G.T., Peluso, P., Munson, K.M., Hiendleder, S., Fedrigo, O., Jarvis, E.D., Phillippy, A.M., Eichler, E.E., Williams, J.L., Smith, T.P.L, Hall, R.J., Sullivan, S.T., Kingan, S.B. 2019. Extended haplotype phasing of de novo genome assemblies with FALCON-Phase. bioRxiv. 327064. https://doi.org/10.1101/327064.

Comparison of genomic relationship matrices using differing number of SNP in pooled DNA analyses - (Abstract Only)
Boldt, R.J., Keele, J.W., Kuehn, L.A., McDaneld, T.G., Smith, T.P.L., Enns, R.M. 2018. Comparison of genomic relationship matrices using differing number of SNP in pooled DNA analyses. Journal of Animal Science. 96(Supplement 3):124. https://doi.org/10.1093/jas/sky404.273.

Incorporation of genomic information into genetic evaluation: U. S. beef industry as a model - (Other)
Kuehn, L.A. 2018. Incorporation of genomic information into genetic evaluation: U. S. beef industry as a model [abstract]. American Sheep Industry 2018 Convention, San Antonio, TX, Jan. 31-Feb. 3, 2018. Available: http://www.sheepusa.org/Events_2018Convention.

Status of evaluation of three maternal lines under pasture lambing experiment at USMARC - (Other)
Freking, B.A. 2018. Status of evaluation of three maternal lines under pasture lambing experiment at USMARC [abstact]. American Sheep Industry 2018 Convention, San Antonio, TX, Jan. 31-Feb. 3, 2018. Available: http://www.sheepusa.org/Events_2018Convention.