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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Research Project #424177

Research Project: Genomic and Metagenomic Approaches to Enhance Efficient and Sustainable Production of Beef Cattle

Location: Genetics and Animal Breeding

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

Microbiome of the upper nasal cavity of beef calves prior to weaning Reprint Icon - (Peer Reviewed Journal)
McDaneld, T.G., Kuehn, L.A., Keele, J.W. 2019. Microbiome of the upper nasal cavity of beef calves prior to weaning. Journal of Animal Science. 97:2368–2375. https://doi.org/10.1093/jas/skz119.

Evaluating the microbiome of two sampling locations in the nasal cavity of cattle with bovine respiratory disease complex (BRDC) Reprint Icon - (Peer Reviewed Journal)
McDaneld, T.G., Kuehn, L.A., Keele, J.W. 2018. Evaluating the microbiome of two sampling locations in the nasal cavity of cattle with bovine respiratory disease complex (BRDC). Journal of Animal Science. 96:1281-1287. https://doi.org/10.1093/jas/sky032.

Third time’s a charm: Into “the Genomics Era” once more - (Abstract Only)
Smith, T.P.L. 2018. Third time’s a charm: Into “the Genomics Era” once more [abstract]. International Plant & Animal Genome XXVI Conference, January 13-17, 2018, San Diego, California. Abstract W169. Available: https://plan.core-apps.com/pag_2018/abstract

Evaluation of a functional variant assay for selecting beef cattle - (Proceedings)
Snelling, W.M., McDaneld, T.G., Kuehn, L.A., Dickey, A.M., Bennett, G.L. 2018. Evaluation of a functional variant assay for selecting beef cattle. In: Proceedings World Congress of Genetics Applied in Livestock Production. 11-16 Feb 2018. Auckland, New Zealand. Volume Technologies - Genotyping p.589. Available: www.wcgalp.org.

DNA pooling strategies for categorical (ordinal) traits - (Proceedings)
Vargas-Jurado, N., Kuehn, L.A., Keele, J.W., Lewis, R.M. 2018. DNA pooling strategies for categorical (ordinal) traits. In: Proceedings World Congress of Genetics Applied in Livestock Production. 11-16 Feb 2018. Auckland, New Zealand. Volume Electronic Poster Session - Theory to Application 3, p. 717. Available: www.wcgalp.org.

Quantification of genomic relationship from DNA pooled samples - (Proceedings)
Kuehn, L.A., McDaneld, T.G., Keele, J.W. 2018. Quantification of genomic relationship from DNA pooled samples. In: Proceedings World Congress of Genetics Applied in Livestock Production. 11-16 Feb 2018. Auckland, New Zealand. Volume Electronic Poster Session - Theory to Application 2, p. 631. Availabe: www.wcgalp.org.

A high-quality annotated transcriptome of swine peripheral blood Reprint Icon - (Peer Reviewed Journal)
Liu, H., Smith, T.P., Nonneman, D.J., Dekkers, J.C., Tuggle, C.K. 2017. A high-quality annotated transcriptome of swine peripheral blood. BMC Genomics. 18:479.. https://doi.org/10.1186/s12864-017-3863-7.

Vaginal and uterine bacterial communities in postpartum lactating cows Reprint Icon - (Peer Reviewed Journal)
Clemmons, B.A., Reese, S.T., Dantas, F.G., Franco, G.A., Smith, T.P., Adeyosoye, O.I., Pohler, K.G., Myer, P.R. 2017. Vaginal and uterine bacterial communities in postpartum lactating cows. Frontiers in Microbiology. 8:1047. https://doi.org/10.3389/fmicb.2017.01047.

Evaluating the metagenome of two sampling locations in the nasal cavity of cattle with bovine respiratory disease complex - (Abstract Only)
McDaneld, T.G., Kuehn, L.A., Keele, J.W. 2017. Evaluating the metagenome of two sampling locations in the nasal cavity of cattle with bovine respiratory disease complex [abstract]. Journal of Animal Science. 95(Supplement 4):21. doi:10.2527/asasann.2017.42.

Vaginal and uterine bacterial communities in postpartum lactating cows - (Abstract Only)
Clemmons, B.A., Dantas, F.G., Franco, G.A., Reese, S.T., Adeyosoye, O.I., Smith, T.P., Myer, P.R., Pohler, K.G. 2017. Vaginal and uterine bacterial communities in postpartum lactating cows [abstract]. Journal of Animal Science. 95(Suppl. 2):112. doi:10.2527/asasmw.2017.112.

Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers - (Peer Reviewed Journal)
Myer, P.R., Kim, M.S., Freetly, H.C., Smith, T.P. 2016. Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers. Data in Brief. 8:1048-1053. doi: 10.1016/j.dib.2016.07.027.

Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers - (Peer Reviewed Journal)
Myer, P.R., Kim, M.S., Freetly, H.C., Smith, T.P. 2016. Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers. Journal of Microbiological Methods. 127:132-140. doi: 10.1016/j.mimet.2016.06.004.

Identification and expression analysis of bovine X degenerate YcChromosome genes - (Abstract Only)
Ponce De Leon, F.A., Guo, Y., Crooker, B.A., McDaneld, T.G., Smith, T.P.L. 2016. Identification and expression analysis of bovine X degenerate YcChromosome genes [abstract]. International Society for Animal Genetics (35th ISAG). Abstract Book. p. 75 (Abstract #P3045). Available: https://www.isag.us.Docs/Proceedings/ISAG_Proceedings_2016.pdf

Evaluating the metagenome of nasal samples from cattle with bovine respiratory disease complex (BRDC) - (Abstract Only)
McDaneld, T.G., Kuehn, L.A., Keele, J.W. 2016. Evaluating the metagenome of nasal samples from cattle with bovine respiratory disease complex (BRDC) [abstract]. International Society for Animal Genetics (35th ISAG). Abstract Book. p. 148-149 (Abstract #P6002). Available: https://www.isag.us.Docs/Proceedings/ISAG_Proceedings_2016.pdf

A reduced panel to determine beef cattle breed composition - (Abstract Only)
Kuehn, L.A., Snelling, W.M., Lindholm-Perry, A.K. 2016. A reduced panel to determine beef cattle breed composition [abstract]. International Society for Animal Genetics (ISAG). Abstract Book. p. 32 (Abstract #P1036). Available: https://www.isag.us/Docs/Proceedings/ISAG_proceedings_2016.pdf.

Inferring genotypes of functional variants in crossbred beef cattle - (Abstract Only)
Snelling, W.M., Kuehn, L.A., Lindholm-Perry, A.K. 2016. Inferring genotypes of functional variants in crossbred beef cattle [abstract]. International Society for Animal Genetics (35th ISAG). Abstract Book. p. 26 (Abstract #P1024). Available: https://www.isag.us.Docs/Proceedings/ISAG_Proceedings_2016.pdf

A comprehensive porcine blood transcriptome - (Abstract Only)
Liu, H., Smith, T.P.L., Nonneman, D.J., Dekkers, J.C.M., Tuggle, C.K. 2016. A comprehensive porcine blood transcriptome [abstract]. In: Proceedings of 35th International Society for Animal Genetics (ISAG) Conference, 23-17 July 2016, Salt Lake City, UT. pg. 69. P3033. Available: https://www.isag.us/docs/Proceedings/ISAG_Proceedings_2016.pdf

Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe - (Peer Reviewed Journal)
Massilamany, C., Mohammed, A., Loy, J.D., Purvis, T., Krishnan, B., Basavalingappa, R.H., Kelley, C.M., Guda, C., Barletta, R.G., Moriyama, E.N., Smith, T.P.L., Reddy, J. 2016. Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe. Biomed Central (BMC) Genomics. 17(Suppl. 7):511. doi: 10.1186/s12864-016-2900-2.

Genomewide association study of liver abscess in beef cattle Reprint Icon - (Peer Reviewed Journal)
Keele, J.W., Kuehn, L.A., McDaneld, T.G., Tait Jr, R.G., Jones, S., Keel, B.N., Snelling, W.M. 2016. Genomewide association study of liver abscess in beef cattle. Journal of Animal Science. 94(2):490-499.

A survey of polymorphisms detected from sequences of popular beef breeds - (Peer Reviewed Journal)
Snelling, W.M., Bennett, G.L., Keele, J.W., Kuehn, L.A., McDaneld, T.G., Smith, T.P., Thallman, R.M., Kalbfleisch, T.S., Pollak, E.J. 2015. A survey of polymorphisms detected from sequences of popular beef breeds. Journal of Animal Science. 93(11):5128-5143. doi:10.2527/jas2015-9356.

Historical overview and current status of genomic technology and marker assisted selection in beef cattle - (Proceedings)
Pollak, E.J., Smith, T.P., Snelling, W.M. 2015. Historical overview and current status of genomic technology and marker assisted selection in beef cattle. In Proceedings of the American Meat Science Association. 68th Annual Reciprocal Meat Conference, June 14 - 17, 2015, Lincoln, NE. pg. 32-36.

Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle Reprint Icon - (Peer Reviewed Journal)
Rolf, M.M., Garrick, D.J., Fountain, T., Ramey, H.R., Weaber, R.L., Decker, J.E., Pollak, E.J., Schnabel, R.D., Taylor, J.F. 2015. Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle. Genetics Selection Evolution. 47:23. DOI 10.1186/s12711-015-0106-8.

Evaluation of single nucleotide polymorphisms in chromosomal regions impacting pregnancy status in cattle Reprint Icon - (Peer Reviewed Journal)
Psaros, K.M., McDaneld, T.G., Kuehn, L.A., Snelling, W.M., Keele, J.W. 2015. Evaluation of single nucleotide polymorphisms in chromosomal regions impacting pregnancy status in cattle. Journal of Animal Science. 93(3):978-987. doi: 10.2527/jas2014-8509.

Genomewide association study of lung lesions in cattle using sample pooling - (Peer Reviewed Journal)
Keele, J.W., Kuehn, L.A., McDaneld, T.G., Tait Jr., R.G., Jones, S., Smith, T.P., Shackelford, S.D., King, D.A., Wheeler, T.L., Lindholm-Perry, A.K., McNeel, A.K. 2015. Genomewide association study of lung lesions in cattle using sample pooling. Journal of Animal Science. 93(3):956-964. DOI: 10.2527/jas.2014-8492.

Multi-tissue omics analyses reveal molecular regulatory networks for puberty in composite beef cattle - (Peer Reviewed Journal)
Canovas, A., Reverter, A., DeAtley, K.L., Ashley, R.L., Colgrave, M.L., Fortes, M.R., Islas-Trejo, A., Lehnert, S.A., Porto-Neto, L.R., Rincon, G., Silver, G.A., Snelling, W.M., Medrano, J.F., Thomas, M.G. 2014. Multi-tissue omics analyses reveal molecular regulatory networks for puberty in composite beef cattle. PLoS One. 9(7):e102551. DOI: 10.1371/journal.pone.0102551.

Evaluation of anthelmintic resistance of intestinal parasitic nematodes in heifers in south central Nebraska - (Abstract Only)
Jones, S., Chase, C.C., Cortinas, R., Griffin, D., Kuehn, L.A., Shuck, K., Whitman, K., Tait Jr, R.G., Keele, J.W. 2014. Evaluation of anthelmintic resistance of intestinal parasitic nematodes in heifers in south central Nebraska [abstract]. Journal of Animal Science Supplement. 92(E-Supplement 2):462.

Filling the knowledge gap: Integrating quantitative genetics and genomics in graduate education and outreach - (Proceedings)
Lewis, R.M., Spangler, M.L., Lockee, B.B., Enns, R.M., Enns, K.J., Dekkers, J.C., Maltecca, C., Cassady, J.P., MacNeil, M.D., Gould, C.A., Boggs, D.L., Misztal, I., Pollak, E.J. 2014. Filling the knowledge gap: Integrating quantitative genetics and genomics in graduate education and outreach. In: Proceedings of the 10th World Congress on Genetics Applied to Livestock Production, August 17-22, 2014, Vancouver, BC, Canada. Paper No. 222. Available: https://asas.org/wcgalp-proceedings.

Genomewide association study of reproductive efficiency in female cattle Reprint Icon - (Peer Reviewed Journal)
McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Snelling, W.M., Smith, T.P.L., Pollak, E.J., Cole, J.B., Keele, J.W. 2014. Genomewide association study of reproductive efficiency in female cattle. Journal of Animal Science. 92(5):1945-1957.

Utilization of sequence on relatives to improve analysis of individuals' low-coverage NGS data - (Abstract Only)

Deletion on chromosome 5 associated with decreased reproductive efficiency in female cattle - (Peer Reviewed Journal)
McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Pollak, E.J., Keele, J.W. 2014. Deletion on chromosome 5 associated with decreased reproductive efficiency in female cattle. Journal of Animal Science. 92:1378-1384.

Microbiome characterization using SMRT sequencing on 16S rRNA genes across a range of amplicon sizes and variable region content - (Abstract Only)

Characterization of microbiomes related to respiratory disease in cattle - (Abstract Only)
Smith, T.P., Kim, M.S., Myer, P.R., McDaneld, T.G., Kuehn, L.A., Clawson, M.L., Harhay, D.M., Harhay, G.P. 2014. Characterization of microbiomes related to respiratory disease in cattle [Abstract]. Proceedings of the Plant and Animal Genome XXII Conference, January 11-15, 2014, San Diego, CA. Poster W759.

Deep sequencing of immune repertoires during bovine development and in response to respiratory pathogen challenge - (Abstract Only)
Smith, T.P.L., and Larsen, P.A. 2013. Deep sequencing of immune repertoires during bovine development and in response to respiratory pathogen challenge [Abstract]. Advances in Genome Biology and Technology Conference, February 20-23, 2013, Marco Island, FL. Page 126.

Complete genome assemblies and methylome characterization in infectious diseases - (Abstract Only)
Smith, T.P. 2013. Complete genome assemblies and methylome characterization in infectious diseases [Abstract]. Plant & Animal Genome XXI Conference, January 12-16, 2013, San Diego, CA. Paper No. W483.