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.)

Exploring tissue- and sex-specific DNA methylation in cattle using a pan-mammalian infinium array - (Peer Reviewed Journal)
Hu, Z., Boschiero, C., Neupane, M., Bhowmik, N., Yang, L., Kilian, L., DeJarnette, M., Sargolzaei, M., Harstine, B., Li, C., Tuo, W., Baldwin, R.L., Van Tassell, C.P., Sattler, C.G., Liu, G. 2025. Exploring tissue- and sex-specific DNA methylation in cattle using a pan-mammalian infinium array. International Journal of Molecular Sciences. 26(9): 4284. https://doi.org/10.3390/ijms26094284.

Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle - (Peer Reviewed Journal)
Gao, Y., Yang, L., Kuhn, K.L., Li, W., Zanton, G.I., Bowman, M.E., Zhao, P., Zhou, Y., Fang, L., Cole, J.B., Rosen, B.D., Ma, L., Li, C., Baldwin, R.L., Van Tassell, C.P., Zhang, Z., Smith, T.P., Liu, G. 2025. Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle. Journal of Advanced Research. https://doi.org/10.1016/j.jare.2025.04.014.

The farm animal genotype-tissue expression (FarmGTEx) project - (Review Article)
Fang, L., Teng, J., Lin, Q., Bai, Z., Liu, S., Guan, D., Li, B., Gao, Y., Hou, Y., Gong, M., Pan, Z., Yu, Y., Clark, E., Smith, J., Rawlik, K., Xiang, R., Chamberlain, A.J., Goddard, M.E., Littlejohn, M., Larson, G., Machugh, D.E., O’Grady, J.F., Sorensen, P., Sahana, G., Lund, M., Jiang, Z., Pan, X., Gong, W., Zhang, H., He, X., Zhang, Y., Gao, N., He, J., Yi, G., Liu, Y., Zhao, P., Zhou, Y., Wang, X., Young, R.S., Xia, C., Cheng, H., Ma, L., Cole, J.B., Baldwin, R.L., Li, C., Van Tassell, C.P., Lunney, J.K., Liu, W., Guan, L., Zhao, X., Ibeagha-Awemu, E., Luo, O., Lin, L., Canela-Xandri, O., Derks, M., Crooijmans, R., Godia, M., Madsen, O., Groenen, M., Koltes, J.E., Tuggle, C.K., Mccarthy, F.M., Rocha, D., Amills, M., Clop, A., Ballester, M., Tosser-Klopp, G., Li, J., Fang, C., Fang, M., Wang, Q., Hou, Z., Wang, Q., Zhao, F., Jiang, L., Zhao, G., Zhou, Z., Zhou, R., Liu, H., Li, M., Mo, D., Liu, X., Chen, Y., Yuan, X., Li, J., Zhao, S., Ding, X., Sun, D., Sun, H., Li, C., Jiang, Y., Wu, D., Wang, W., Fan, X., Zhang, Q., Li, K., Yang, N., Hu, X., Liu, G. 2025. The farm animal genotype-tissue expression (FarmGTEx) project. Nature Genetics. https://doi.org/10.1038/s41588-025-02121-5.

Profiling genome-wide methylation patterns in cattle infected with Ostertagia ostertagi - (Peer Reviewed Journal)
Boschiero, C., Beshah, E., Zhu, X., Tuo, W., Liu, G. 2024. Profiling genome-wide methylation patterns in cattle infected with Ostertagia ostertagi. International Journal of Molecular Sciences. 26(1):89. https://doi.org/10.3390/ijms26010089.

Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus - (Peer Reviewed Journal)
Azam, S., Sahu, A., Pandey, N.K., Neupane, M., Van Tassell, C.P., Rosen, B.D., Gandam, R.K., Rath, S.N., Majumdar, S.S. 2025. Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus. Journal of Animal Science and Biotechnology. 16. Article 21. https://doi.org/10.1186/s40104-024-01133-1.

Multi-omics analysis reveals signatures of selection and loci associated with complex traits in pigs - (Peer Reviewed Journal)
Liu, L., Yi, G., Yao, Y., Liu, Y., Li, J., Yang, Y., Liu, M., Fang, L., Mo, D., Zhang, L., Liu, Y., Niu, Y., Wang, L., Qu, X., Pan, Z., Wang, L., Chen, M., Fan, X., Chen, Y., Zhang, Y., Li, X., Wang, Z., Tang, Y., Huang, H., Yuan, P., Liao, Y., Li, X., Yin, Z., Liu, D., Zhang, D., Zhou, Q., Wu, W., Jiang, J., Gao, Y., Liu, G., Wang, L., Chen, Y., Li, K., Groenen, M.A., Tang, Z. 2024. Multiomics analysis reveals signatures of selection and loci associated with complex traits in pigs. iMeta. 3(6):e250. https://doi.org/10.1002/imt2.250.

Alternative polyadenylation landscape of longissimus dorsi muscle with high and low intramuscular fat content in cattle - (Peer Reviewed Journal)
Li, C., Xu, J., Zhang, Y., Ding, Y., Zhou, X., Su, Z., Qu, C., Liang, J., Han, Y., Wang, D., Shi, Y., Li, C., Liu, G., Kang, X. 2024. Alternative polyadenylation landscape of longissimus dorsi muscle with high and low intramuscular fat content in cattle. Journal of Animal Science. https://doi.org/10.1093/jas/skae357.

Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations - (Review Article)

Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content - (Peer Reviewed Journal)
Olagunju, T.A., Rosen, B.D., Neibergs, H.L., Becker, G., Davenport, K., Elsik, C., Hadfield, T., Koren, S., Rhie, A., Shira, K., Skibiel, A., Stegemiller, M., Thorne, J.W., Villamediana, P., Cockett, N.E., Murdoch, B.M., Smith, T.P. 2024. Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content. Nature Genetics. 15. Article e8277. https://doi.org/10.1038/s41467-024-52384-5.

A pilot detection and associate study of gene presence-absence variation in Holstein cattle - (Peer Reviewed Journal)
Boschiero, C., Neupane, M., Yang, L., Schroeder, S.G., Tuo, W., Ma, L., Baldwin, R.L., Van Tassell, C.P., Liu, G. 2024. A pilot detection and associate study of gene presence-absence variation in Holstein cattle. Animals. 14(13):1921. https://doi.org/10.3390/ani14131921.

Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans - (Peer Reviewed Journal)
Chang, W., Baker, M., Laritsky, E., Gunasekara, C., Maduranga, U., Galliou, J.C., McFadden, J.W., Waltemyer, J.R., Berggren-Thomas, B., Tate, B.N., Zhang, H., Rosen, B.D., Van Tassell, C.P., Liu, G., Coarfa, C., Yi, A.R., Waterland, R.A. 2024. Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans. Genome Biology. 25(1). Article e185. https://doi.org/10.1186/s13059-024-03307-6.

Variation in a Y-linked single copy gene, AMELY, was shared among modern and lost male Holstein lineages - (Abstract Only)
Yousaf, W., Liu, W., Liu, G., Lewin, H.A., Blackburn, H.D., Dechow, C.D. 2024. Variation in a Y-linked single copy gene, AMELY, was shared among modern and lost male Holstein lineages [abstract]. Journal of Dairy Science. 107(Suppl. 1):406(abstr. 2646).

Whole-genome resequencing reveals genetic diversity and wool trait-related genes in Liangshan Semi-fine Wool Sheep - (Peer Reviewed Journal)
Sun, X., Guo, J., Li, R., Zhang, H., Zhang, Y., Liu, G., Emu, Q., Zhang, H. 2024. Whole-genome resequencing reveals genetic diversity and wool trait-related genes in Liangshan Semi-fine Wool Sheep. Animals. 14(3):444. https://doi.org/10.3390/ani14030444.

Current challenges and future of agricultural genomes to phenomes in the USA - (Peer Reviewed Journal)
Tuggle, C.K., Clarke, J.L., Murdoch, B.M., Lyons, E., Scott, N.M., Mckay, S., Lipka, A., Fulton, J., Hess, A., Lubberstedt, T., Fragomeni, B., Rowan, T., Mccarthy, F., Guadagno, C., Goddard, E., Das Choudhury, S., Sheehan, M., Kramer, L., Feldman, M.J., Daigle, C., Steibel, J.P., Benes, B., Murray, S., Riggs, P., Thompson, A., Hagen, D., Thornton-Kurth, K., Van Tassell, C.P., Campbell, J.D., Dorea, J., Chung, H., Dekkers, J.C., Ertl, D., Lawrence-Dill, C.A., Schnable, P.S. 2024. Current challenges and future of agricultural genomes to phenomes in the USA. Genome Biology. 25:8. https://doi.org/10.1186/s13059-023-03155-w.

Integrated meta-omics reveals the regulatory landscape involved in lipid metabolism between pig breeds - (Peer Reviewed Journal)
Sun, J., Xie, F., Wang, J., Luo, J., Chen, T., Jiang, Q., Xi, Q., Liu, G., Zhang, Y. 2024. Integrated meta-omics reveals the regulatory landscape involved in lipid metabolism between pig breeds. Microbiome. 12. Article e33. https://doi.org/10.1186/s40168-023-01743-3.

Participatory investigation of goat farmers’ breeding practices, trait preference, and selection criteria in Burkina Faso - (Peer Reviewed Journal)
Badjibassa, A., Ouedraogo, D., Burger, P.A., Rosen, B.D., Van Tassell, C.P., Solkner, J., Soudre, A. 2024. Participatory investigation of goat farmers’ breeding practices, trait preference, and selection criteria in Burkina Faso. Tropical Animal Health and Production. 56:35. https://doi.org/10.1007/s11250-023-03869-w.

Unraveling the genetic basis of feed efficiency in cattle through integrated DNA methylation and CcttleGTEx analysis - (Abstract Only)

Unraveling the genetic basis of feed efficiency in cattle through integrated DNA methylation and CattleGTEx analysis - (Peer Reviewed Journal)
Hu, Z., Boschiero, C., Li, C., Connor, E.E., Baldwin, R.L., Liu, G. 2023. Unraveling the genetic basis of feed efficiency in cattle through integrated DNA methylation and CattleGTEx analysis. Genes. 14(12):2121. https://doi.org/10.3390/genes14122121.

A compendium of genetic regulatory effects across pig tissues - (Peer Reviewed Journal)
Teng, J., Gao, Y., Yin, H., Bai, Z., Liu, S., Zeng, H., Consortium, T., Bai, L., Cai, Z., Zhao, B., Li, X., Xu, Z., Lin, Q., Pan, Z., Yang, W., Yu, X., Guan, D., Hou, Y., Keel-Mercer, B.N., Rohrer, G.A., Lindholm-Perry, A.K., Oliver, W.T., Ballester, M., Crespo, D., Quintanilla, R., Canela-Xandri, O., Rawlik, K., Xia, C., Yao, Y., Zhao, Q., Yao, W., Yang, L., Li, H., Zhang, H., Liao, W., Chen, T., Karlskov-Mortensen, P., Fredholm, M., Amills Eras, M., Clop, A., Giuffra, E., Wu, J., Cai, X., Diao, S., Pan, X., Wei, C., Li, J., Cheng, H., Wang, S., Su, G., Sahana, G., Lund, M., Dekkers, J., Kramer, L., Tuggle, C.K., Corbett, R., Groenen, M.A., Madsen, O., Godia, M., Rocha, D., Li, C., Pausch, H., Hu, X., Frantz, L., Luo, Y., Lin, L., Zhou, Z., Zhang, Z., Chen, Z., Cui, L., Xiang, R., Shen, X., Li, P., Huang, R., Tang, G., Li, M., Zhao, Y., Yi, G., Tang, Z., Jiang, J., Zhao, F., Yuan, X., Liu, X., Chen, Y., Xu, X., Zhao, S., Zhao, P., Haley, C., Zhou, H., Wang, Q., Pan, Y., Ding, X., Ma, L., Li, J., Navarro, P., Zhang, Q., Li, B., Tenesa, A., Liu, G. 2024. A compendium of genetic regulatory effects across pig tissues. Nature Genetics. 56:112-123. https://doi.org/10.1038/s41588-023-01585-7.

Genome-wide association analysis of heifer livability and early first calving in Holstein cattle - (Peer Reviewed Journal)
Gao, Y., Marceau, A., Iqbal, V., Torres-Vazquez, J.A., Neupane, M., Jiang, J., Liu, G., Ma, L. 2023. Genome-wide association analysis of heifer livability and early first calving in Holstein cattle. BMC Genomics. 24:628. https://doi.org/10.1186/s12864-023-09736-0.

Investigation of lncRNA in Bos taurus mammary tissue during dry and lactation periods - (Peer Reviewed Journal)
Marceau, A., Wang, J., Iqbal, V., Jiang, J., Liu, G., Ma, L. 2023. Investigation of lncRNA in Bos taurus mammary tissue during dry and lactation periods. Genes. 14(9):1789. https://doi.org/10.3390/genes14091789.

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.

A Chinese indicine pan-genome reveals a wealth of novel structural variants introgressed from other Bos species - (Peer Reviewed Journal)
Dai, X., Bian, P., Hu, D., Luo, F., Huang, Y., Jiao, S., Wang, X., Gong, M., Li, R., Cai, Y., Wen, J., Yang, Q., Deng, W., Nanaei, H.A., Wang, Y., Wang, F., Zhang, Z., Rosen, B.D., Heller, R., Jiang, Y. 2023. A Chinese indicine pan-genome reveals a wealth of novel structural variants introgressed from other Bos species. Genome Research. 33(8):1284–1298. https://doi.org/10.1101/gr.277481.122.

Taming transposable elements in livestock and poultry: a review of their roles and applications - (Peer Reviewed Journal)
Zhao, P., Peng, C., Fang, L., Wang, Z., Liu, G. 2023. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genetic Selection Evolution. 55:50. https://doi.org/10.1186/s12711-023-00821-2.

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.