Functional Omics and Systems Biology

Tian, Z., Nepomuceno, A. L., Song, Q., Stupar, R. M., Liu, B., Kong, F., Ma, J., Lee, S. H., and Jackson, S. A. (2025). Soybean2035: A decadal vision for soybean functional genomics and breeding. Mol. plant 18: 245–271.

Zhu, Z., Wang, Y., Liu, S., Wang, S., Li, J., Fang, C., Liu, Y., Yang, X., Tian, D., Song, S., and Tian, Z. (2025). Genomic atlas of 8,105 accessions reveals stepwise domestication, global dissemination, and improvement trajectories in soybean. Cell 188: 6519–6535.e15.

Liu, Y., Zhang, Y., Liu, X., Shen, Y., Tian, D., Yang, X., Liu, S., Ni, L., Zhang, Z., Song, S., and Tian, Z. (2023). SoyOmics: A deeply integrated database on soybean multi-omics. Mol. Plant 16: 794-797.

Liu, S., Zhang, M., Feng, F., and Tian, Z. (2020). Toward a ‘green revolution’ in soybean. Mol. Plant 13: 688–697.

Liu, Y., Du, H., Li, P., Shen, Y., Peng, H., Liu, S., Zhou, G.A., Zhang, H., Liu, Z., Shi, M., Huang, X., Li, Y., Zhang, M., Wang, Z., Zhu, B., Han, B., Liang, C., and Tian, Z. (2020). Pan-genome of wild and cultivated soybeans. Cell 182: 162–176.

Lu, S., Dong, L., Fang, C., Liu, S., Kong, L., Cheng, Q., Chen, L., Su, T., Nan, H., Zhang, D., Zhang, L., Wang, Z., Yang, Y., Yu, D., Liu, X., Yang, Q., Lin, X., Tang, Y., Zhao, X., Yang, X., Tian, C., Xie, Q., Li, X., Yuan, X., Tian, Z., Liu, B., Weller, J.L., and Kong, F. (2020). Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication. Nat. Genet. 52: 428–436.

Wang, M., Li, W., Fang, C., Xu, F., Liu, Y., Wang, Z., Yang, R., Zhang, M., Liu, S., Lu, S., Lin, T., Tang, J., Wang, Y., Wang, H., Lin, H., Zhu, B., Chen, M., Kong, F., Liu, B., Zeng, D., Jackson, S., Chu, C., and Tian, Z. (2018). Parallel selection on a dormancy gene during domestication of crops from multiple families. Nat. Genet. 50: 1435–1441.

Lu, S., Zhao, X., Hu, Y., Liu, S., Nan, H., Li, X., Fang, C., Cao, D., Shi, X., Kong, L., Su, T., Zhang, F., Li, S., Wang, Z., Yuan, X., Cober, E., Weller, J., Liu, B., Hou, X., Tian, Z., and Kong, F. (2017). Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield. Nat. Genet. 49: 773–779.

Zhou, Z., Jiang, Y., Wang, Z., Gou, Z., Lyu, J., Li, W., Yu, Y., Shu, L., Zhao, Y., Ma, Y., Fang, C., Shen, Y., Liu, T., Li, C., Li, Q., Wu, M., Wang, M., Wu, Y., Dong, Y., Wan, W., Wang, X., Ding, Z., Gao, Y., Xiang, H., Zhu, B., Lee, S.H., Wang, W., and Tian, Z. (2015). Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol. 33: 408-414.