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.)

Beef cattle phenotypic plasticity and stability of dry matter intake and respiration rate across varying levels of temperature humidity index - (Peer Reviewed Journal)

Breed-specific heterosis for growth and carcass traits in 18 U.S. cattle breeds - (Peer Reviewed Journal)
Engle, B.N., Thallman, R.M., Snelling, W.M., Wheeler, T.L., Shackelford, S.D., King, D.A., Kuehn, L.A. 2025. Breed-specific heterosis for growth and carcass traits in 18 U.S. cattle breeds. Journal of Animal Science. Article skaf048. https://doi.org/10.1093/jas/skaf048.

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

Investigating genotype by environment interaction for beef cattle fertility traits in commercial herds in northern Australia with multi-trait analysis - (Peer Reviewed Journal)
Copley, J.P., Hayes, B.J., Ross, E.M., Speight, S., Fordyce, G., Wood, B.J., Engle, B.N. 2024. Investigating genotype by environment interaction for beef cattle fertility traits in commercial herds in northern Australia with multi-trait analysis. Genetic Selection Evolution. 56. Article 70. https://doi.org/10.1186/s12711-024-00936-0.

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.

Genome-wide association and expression quantitative trait loci in cattle reveals common genes regulating mammalian fertility - (Peer Reviewed Journal)
Forutan, M., Engle, B.N., Chamberlain, A.J., Ross, E.M., Nguyen, L.T., D'Occhio, M.J., Collins Sr, A., Kho, E.A., Fordyce, G., Speight, S., Goddard, M.E., Hayes, B.J. 2024. Genome-wide association and expression quantitative trait loci in cattle reveals common genes regulating mammalian fertility. Communications Biology. 7(1). Article 724. https://doi.org/10.1038/s42003-024-06403-2.

Genetics: How long does it take for genetics to improve carcass characteristics? - (Abstract Only)
Engle, B.N., Thallman, R.M., Snelling, W.M., Wheeler, T.L., Shackelford, S.D., King, D.A., Kuehn, L.A. 2024. Genetics: How long does it take for genetics to improve carcass characteristics? [abstract]. American Society of Animal Science Annual Meeting. 102(Supplement 3):94-95. https://doi.org/10.1093/jas/skae234.108.

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

Chromosome-scale genome assembly of the rough periwinkle Littorina saxatilis - (Peer Reviewed Journal)
De Jode, A., Faria, R., Formenti, G., Sims, Y., Smith, T.P., Tracey, A., Wood, J.M.D., Zagrodzka, Z.B., Johannesson, K., Butlin, R.K., Leder, E.H. 2024. Chromosome-scale genome assembly of the rough periwinkle Littorina saxatilis. Genome Biology and Evolution. 16(4). Article evae076. https://doi.org/10.1093/gbe/evae076.

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)
Keele, J.W., Foraker, B.A., Boldt, R.J., Kemp, C., Kuehn, L.A., Woerner, D.R. 2024. Genetic parameters for carcass traits of progeny of beef bulls mated to dairy cows. Journal of Animal Science. 102. Article skae075. https://doi.org/10.1093/jas/skae075.

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)
Dressler, E.A., Shaffer, W., Bruno, K., Krehbiel, C.R., Calvo-Lorenzo, M., Richards, C.J., Place, S.E., DeSilva, U., Kuehn, L.A., Weaber, R.L., Bormann, J.M., Rolf, M.M. 2023. Heritability and variance component estimation for feed and water intake behaviors of feedlot cattle. Journal of Animal Science. 101. Article skad386. https://doi.org/10.1093/jas/skad386.

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.

Genome sequence of ungulate tetraparvovirus 1 from a nasal swab of an Irish beef- suckler calf - (Research Notes)
Dhufaigh, K.N., McCabe, M., Cormican, P., Cuevas-Gomez, I., McGee, M., McDaneld, T., Earley, B. 2023. Genome sequence of ungulate tetraparvovirus 1 from a nasal swab of an Irish beef- suckler calf. Microbiology Resource Announcements. 12(2). Article e00911-22. https://doi.org/10.1128/mra.00911-22.

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.

Use of heterosis and breed differences in crossbreeding systems or composite populations to improve efficiency of beef production - (Book / Chapter)
Cundiff, L.V., Kuehn, L.A., Thallman, R.M. 2024. Use of heterosis and breed differences in crossbreeding systems or composite populations to improve efficiency of beef production. In: Dikeman, M., Encyclopedia of Meat Sciences. 3rd edition. Elsevier. p.601-628. https://doi.org/10.1016/B978-0-323-85125-1.00152-6.

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.

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)
Dhufaigh, K.N., McCabe, M., Cormican, P., Cuevas-Gomez, I., McGee, M., McDaneld, T., Earley, B. 2022. 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. Microbiology Resource Announcements. 11(11). Article e00821-22. https://doi.org/10.1128/mra.00821-22.