Research Project: Genomes to Phenomes in Beef Cattle Research

Location: Genetics and Animal Breeding

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

Leveraging data from commercial cattle for genetic improvement– an international perspective - (Peer Reviewed Journal)

Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 buffalo genomes project - (Peer Reviewed Journal)
Pineda, P.S., Flores, E.B., Villamor, L.P., Parac, C.J.M., Khatkar, M.S., Thu, H.T., Smith, T.P.L., Rosen, B.D., Ajmone-Marsan, P., Colli, L., Williams, J.L., Low, W. et al. 2024. Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 buffalo genomes project. Gigascience. 13. Article giae053. https://doi.org/10.1093/gigascience/giae053.

Ultra-long sequencing experiences with a variety of mammalian sample types - (Other)

Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology - (Peer Reviewed Journal)
Beiki, H., Murdoch, B.M., Park, C.A., Kern, C., Kontechy, D., Becker, G., Rincon, G., Jiang, H., Zhou, H., Thorne, J., Koltes, J.E., Michal, J.J., Davenport, K.G., Rijnkels, M., Ross, P.J., Hu, R., Corum, S., McKay, S., Smith, T.P.L., Liu, W., Ma, W., Zhang, X., Xu, X., Han, X., Jiang, Z., Hu, Z., Reecy, J.M. 2024. Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology. Gigascience. 13. Article giae019. https://doi.org/10.1093/gigascience/giae019.

Genetic parameters for carcass traits of progeny of beef bulls mated to dairy cows - (Peer Reviewed Journal)

Probiotics in milk replacer affect the microbiome of the lung in neonatal dairy calves - (Peer Reviewed Journal)
McDaneld, T.G., Eicher, S.D., Dickey, A.M., Kritchevsky, J.E., Bryan, K.A., Chitko-McKown, C.G. 2024. Probiotics in milk replacer affect the microbiome of the lung in neonatal dairy calves. Frontiers in Microbiology. 14. Article 1298570. https://doi.org/10.3389/fmicb.2023.1298570.

Imputation strategies for genomic prediction using nanopore sequencing - (Peer Reviewed Journal)
Lamb, H.J., Nguyen, L.T., Copley, J.P., Engle, B.N., Hayes, B.J., Ross, E.M. 2023. Imputation strategies for genomic prediction using nanopore sequencing. BMC Biology. 21. Article 286. https://doi.org/10.1186/s12915-023-01782-0.

Heritability and variance component estimation for feed and water intake behaviors of feedlot cattle - (Peer Reviewed Journal)

Variance component estimates for growth traits in beef cattle using selected variants from imputed low-pass sequence data - (Peer Reviewed Journal)
Russell, C.A., Kuehn, L.A., Snelling, W.M., Kachman, S.D., Spangler, M.L. 2023. Variance component estimates for growth traits in beef cattle using selected variants from imputed low-pass sequence data. Journal of Animal Science. 101. Article skad274. https://doi.org/10.1093/jas/skad274.

Variance component estimation and genome-wide association of predicted methane production in crossbred beef steers - (Peer Reviewed Journal)
Lakamp, A.D., Ahlberg, C.M., Allwardt, K., Broocks, A., Bruno, K., McPhillips, L., Taylor, A., Krehbiel, C.R., Calvo-Lorenzo, M.S., Richards, C., Place, S.E., DeSilva, U., Kuehn, L.A., Weaber, R.L., Bormann, J.M., Rolf, M.M. 2023. Variance component estimation and genome-wide association of predicted methane production in crossbred beef steers. Journal of Animal Science. 101. Article skad179. https://doi.org/10.1093/jas/skad179.

Use of overlapping DNA pools to discern genetic differences despite pooling error - (Peer Reviewed Journal)
Keele, J.W., McDaneld, T.G., Kuehn, L.A. 2023. Use of overlapping DNA pools to discern genetic differences despite pooling error. Journal of Animal Science. 101. Article skad166. https://doi.org/10.1093/jas/skad166.

Integrating genome-wide association and expression quantitative trait loci (eQTL) analyses identifies genes affecting fertility in cattle and suggests a common set of genes regulating fertility in mammals - (Pre-print Publication)
Forutan, M., Engle, B.N., Chamberlain, A.J., Ross, E.M., Nguyen, L.T., D'Occhio, M., Collins Sr, A., Kho, E.A., Fordyce, G., Speight, S., Goddard, M.E., Hayes, B.J. 2023. Integrating genome-wide association and expression quantitative trait loci (eQTL) analyses identifies genes affecting fertility in cattle and suggests a common set of genes regulating fertility in mammals. Research Square. Article 283935. https://doi.org/10.21203/rs.3.rs-2839305/v1.

Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies - (Peer Reviewed Journal)
Ren, Y., Tseng, E., Smith, T.P.L., Hiendleder, S., Williams, J.L., Low, W. 2023. Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies. BMC Genomics. 24. Article 108. https://doi.org/10.1186/s12864-023-09212-9.

Irish genome sequence of ungulate tetraparvovirus 1 from a nasal swab of a beef- suckler calf - (Research Notes)

Genetic diversity and connectivity of moose (Alces americanus americanus) in eastern North America - (Peer Reviewed Journal)
Rosenblatt, E., Gieder, K., Donovan, T., Murdoch, J., Smith, T.P.L., Heaton, M.P., Kalbfleisch, T.S., Murdoch, B.M., Bhattarai, S., Pacht, E., Verbist, E., Basnayake, V., McKay, S. 2023. Genetic diversity and connectivity of moose (Alces americanus americanus) in eastern North America. Conservation Genetics. 24:235-248. https://doi.org/10.1007/s10592-022-01496-w.

Detection of Mycoplasma bovirhinis and bovine coronavirus in an outbreak of bovine respiratory disease in nursing beef calves - (Peer Reviewed Journal)
McDaneld, T.G., Workman, A.M., Chitko-McKown, C.G., Kuehn, L.A., Dickey, A.M., Bennett, G.L. 2022. Detection of Mycoplasma bovirhinis and bovine coronavirus in an outbreak of bovine respiratory disease in nursing beef calves. Frontiers in Microbiomes. 1. Article 1051241. https://doi.org/10.3389/frmbi.2022.1051241.

Complete genome sequence of bovine coronavirus variants from the nasal virome of Irish beef-suckler and pre-weaned dairy calves clinically diagnosed with bovine respiratory disease - (Research Notes)