Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

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

New insights into transcriptome variation during cattle adipocyte adipogenesis by direct RNA sequencing - (Peer Reviewed Journal)
Peng, L., Zhang, X., Du, Y., Li, F., Han, J., Liu, O., Dai, S., Zhang, X., Liu, G., Yang, L., Zhou, Y. 2023. New insights into transcriptome variation during cattle adipocyte adipogenesis by direct RNA sequencing. iScience. 26(10):107753. https://doi.org/10.1016/j.isci.2023.107753.

The African Goat Improvement Network: A scientific group empowering smallholder farmers - (Peer Reviewed Journal)
Van Tassell, C.P., Rosen, B.D., Woodward Greene, M.J., Silverstein, J., Huson, H.J., Solkner, J., Boettcher, P., Rothschild, M.F., Meszaros, G., Nakimbugwe, H., Gondwe, T., Muchadeyi, F.C., Nandolo, W., Mulindwa, H.A., Banda, L.J., Kaumbata, W., Getachew, T., Haile, A., Soudre, A., Ouedraogo, D., Rischkowsky, B.A., Mwai, A.O., Dzomba, E.F., Nash, O., Abegaz, S., Masiga, C.W., Wurzinger, M., Sayre, B.L., Stella, A., Tosser-Klopp, G., Sonstegard, T.S. 2023. The African Goat Improvement Network: A scientific group empowering smallholder farmers. Frontiers in Genetics. 14:1183240. https://doi.org/10.3389/fgene.2023.1183240.

Using the community-based breeding program (CBBP) model as a collaborative platform to develop the African Goat Improvement Network—Image collection protocol (AGIN-ICP) with mobile technology for data collection - (Peer Reviewed Journal)
Woodward Greene, M.J., Kinser, J.M., Huson, H.J., Sonstegard, T.S., Solkner, J., Vaisman, I.I., Boettcher, P., Masiga, C., Mukasa, C., Abegaz, S., Agaba, M., Ahmed, S.S., Fridolin, M., Getachew, T., Gondowe, T., Haile, A., Hassan, Y., Kihara, A., Kouriba, A., Mruttu, H.A., Mujibi, D., Nandolo, W., Rischkowsky, B., Rosen, B.D., Sayre, B., Van Tassell, C.P. 2023. Using the community-based breeding program (CBBP) model as a collaborative platform to develop the African Goat Improvement Network—Image collection protocol (AGIN-ICP) with mobile technology for data collection and management of livestock phenotypes. Frontiers in Genetics. 14:1200770. https://doi.org/10.3389/fgene.2023.1200770.

The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese Holstein cattle - (Peer Reviewed Journal)
Wang, X., Gao, Y., Li, C., Fang, L., Liu, G., Zhao, X., Zhang, Y., Cai, G., Xue, G., Liu, Y., Wang, L., Zhang, F., Wang, K., Zhang, M., Li, R., Gao, Y., Li, J. 2023. The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese Holstein cattle. BMC Genomic Data. 24:39. https://doi.org/10.1186/s12863-023-01139-0.

Morphometric characterization of local goat breeds in two agroecological zones of Burkina Faso, West Africa - (Peer Reviewed Journal)
Akounda, B., Ouedraogo, D., Soudre, A., Burger, P.A., Rosen, B.D., Van Tassell, C.P., Solkner, J. 2023. Morphometric characterization of local goat breeds in two agroecological zones of Burkina Faso, West Africa. Animals. 13(12):1931. https://doi.org/10.3390/ani13121931.

Harnessing male germline epigenomics for the genetic improvement in cattle - (Peer Reviewed Journal)
Wang, X., Li, W., Feng, X., Li, J., Liu, G., Fang, L., Yu, Y. 2023. Harnessing male germline epigenomics for the genetic improvement in cattle. Journal of Animal Science and Biotechnology. 14:76. https://doi.org/10.1186/s40104-023-00874-9.

Characterization and localization of within and across breed as indications of inbreeding depression and heterosis - (Abstract Only)

The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology - (Peer Reviewed Journal)
Ballard, J.O., Field, M.A., Edwards, R.J., Wilson, L.A., Koungoulos, L.G., Rosen, B.D., Chernoff, B., Dudchenko, O., Omer, A., Keilwagen, J., Skvortsova, K., Bogdanovic, O., Chan, E.K., Zammit, R.A., Hayes, V., Aiden, E.L. 2023. The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. GigaScience. https://doi.org/10.1093/gigascience/giad018.

A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes - (Peer Reviewed Journal)
Li, R., Gong, M., Zhang, X., Wang, F., Liu, Z., Zhang, L., Yang, Q., Xu, Y., Xu, M., Zhang, H., Zhang, Y., Dai, X., Zhang, Z., Fang, W., Yang, Y., Fu, W., Cao, C., Yang, P., Ghanatsaman, Z.A., Negari, N.J., Nanaei, H.A., Yue, X., Song, Y., Lan, X., Deng, W., Wang, X., Pan, C., Xiang, R., Ibeagha-Awemu, E.M., Heslop-Harrison, P.J., Rosen, B.D., Lenstra, J.A., Gan, S., Jiang, Y. 2023. A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes. Genome Research. 33:463-477. https://doi.org/10.1101/gr.277372.122.

Cis-eQTL analysis and functional validation of candidate genes for carcass yield traits in beef cattle - (Peer Reviewed Journal)
Wang, T., Niu, Q., Zhang, T., Zheng, X., Li, H., Gao, X., Chen, Y., Gao, H., Zhang, L., Liu, G., Li, J., Xu, L. 2022. Cis-eQTL analysis and functional validation of candidate genes for carcass yield traits in beef cattle. International Journal of Biological Sciences. 23(23):15055. https://doi.org/10.3390/ijms232315055.

Characterization and localization within and across breed measures of dominance as observed in inbreeding depression and heterosis - (Abstract Only)

The conservation of human functional variants and their effects across livestock species - (Peer Reviewed Journal)
Zhao, R., Talenti, A., Fang, L., Liu, S., Liu, G., Chue Hong, N.P., Tenesa, A., Hassan, M., Prendergast, J.G. 2022. The conservation of human functional variants and their effects across livestock species. Communications Biology. 5:1003. https://doi.org/10.1038/s42003-022-03961-1.

Favored single nucleotide variants identified using whole genome re-sequencing of Austrian and Chinese cattle breeds - (Peer Reviewed Journal)
Naji, M.M., Jiang, Y., Utsunomiya, Y.T., Rosen, B.D., Solkner, J., Wang, C., Jiang, L., Zhang, Q., Zhang, Y., Ding, X., Meszaros, G. 2022. Favored single nucleotide variants identified using whole genome re-sequencing of Austrian and Chinese cattle breeds. Frontiers in Genetics. https://doi.org/10.3389/fgene.2022.974787.