Location: Animal Genomics and Improvement Laboratory
2023 Annual Report
Accomplishments
1. Dynamic transcriptome in gastrointestinal tracts at different lactation stages of dairy cattle. To investigate the molecular basis for the gastrointestinal adaption of the dairy cattle to changes in nutrient delivery in response to increased nutrient requirements to support milk production, researchers at Beltsville, Maryland used RNA-seq to profile gene expression patterns in three tissues, including the colon, duodenum, and rumen at eight-time points during the transition from the dry period to lactation and during lactation (dry period, day 3, day 14, day 28, day 45, day 120, day 220, and day 305). The multi-time points sampling allowed direct comparison of expression patterns within and among tissues during different lactation periods. This resource provided comprehensive insight into nutritional efficiency of cattle during lactation and revealed the specific characteristics of gastrointestinal tract tissues for researchers to understand the complexity of genomic activities during lactation.
Review Publications
Cavani, L., Parker Gaddis, K.L., Baldwin, R.L., Santos, J.E., Koltes, J.E., Tempelman, R.J., Vandehaar, M.J., Caputo, M.J., White, H.M., Penagaricano, F., Weigel, K.A. 2023. Impact of parity differences on residual feed intake estimation in Holstein cows. Journal of Dairy Science Communications. https://doi.org/10.3168/jdsc.2022-0307.
Shadpour, S., Chud, T.C., Hailemariam, D., De Oliveira, H.R., Plastow, G., Stothard, P., Lassen, J., Baldwin, R.L., Miglior, F., Baes, C.F., Tulpan, D., Schenkel, F.S. 2022. Predicting dry matter intake in Canadian Holstein dairy cattle using milk mid-infrared reflectance spectroscopy and other commonly available predictors via artificial neural networks. Journal of Dairy Science. 105(10):8257–8271. https://doi.org/10.3168/jds.2021-21297.
Liang, Z., Prakapenka, D., Parker Gaddis, K.L., Vandehaar, M.J., Weigel, K.A., Tempelman, R.J., Koltes, J.E., Santos, J.P., White, H.M., Penagaricano, F., Baldwin, R.L., Da, Y. 2022. Impact of epistasis effects on the accuracy of predicting phenotypic values of residual feed intake in U.S. Holstein cows. Frontiers in Genetics. 13:1017490. https://doi.org/10.3389/fgene.2022.1017490.
Boschiero, C., Gao, Y., Baldwin, R.L., Ma, L., Li, C., Liu, G. 2022. Butyrate induces modifications of the CTCF-binding landscape in cattle cells. Biomolecules. 12(9):1177. https://doi.org/10.3390/biom12091177.
Marceau, A., Gao, Y., Baldwin, R.L., Li, C., Jiang, J., Ma, L., Liu, G. 2022. Investigation of rumen long noncoding RNA before and after weaning in cattle. BMC Genomics. 23:531. https://doi.org/10.1186/s12864-022-08758-4.
Boschiero, C., Gao, Y., Baldwin, R.L., Ma, L., Li, C., Liu, G. 2022. Differentially CTCF-binding sites in cattle rumen tissue during weaning. International Journal of Molecular Sciences. 23(16):9070. https://doi.org/10.3390/ijms23169070.
Liu, S., Gao, Y., Canela-Xandri, O., Wang, S., Yu, Y., Cai, W., Li, B., Pairo-Castineira, E., D'Mellow, K., Rawlik, K., Xia, C., Yao, Y., Li, X., Yan, Z., Li, C., Rosen, B.D., Van Tassell, C.P., Van Raden, P.M., Zhang, S., Ma, L., Cole, J.B., Liu, G., Tenesa, A., Fang, L. 2022. A multi-tissue atlas of regulatory variants in cattle. Nature Genetics. 54(9):1438-1447. https://doi.org/10.1038/s41588-022-01153-5.
Yao, Y., Liu, S., Xia, C., Gao, Y., Pan, Z., Canela-Xandri, O., Khamesh, A., Rawlik, K., Wang, S., Li, B., Zhang, Y., Pairo-Castineira, E., D'Mellow, K., Li, X., Yan, Z., Li, C., Yu, Y., Zhang, S., Ma, L., Cole, J.B., Ross, P.J., Zhou, H., Haley, C., Liu, G., Fang, L., Tenesa, A. 2022. Comparative transcriptome in large-scale human and cattle populations. Genome Biology. 23:176. https://doi.org/10.1186/s13059-022-02745-4.
