Publications

2025

Ma, X.^#, Wang, H.^#, Yan, S.^#, Zhou, C.^#, Zhou, K., Zhang, Q., Li, M., Yang, Y., Li, D., Song, P., Tang, C., Geng, L., Sun, J., Ji, Z., Sun, X., Zhou, Y., Zhou, P., Cui, D., Han, B., Jing, X.*, He, Q.*, Fang, W.*, Han, L.* 2025. Large-scale genomic and phenomic analyses of modern cultivars empower future rice breeding design. Molecular Plant. DOI: 10.1016/j.molp.2025.03.007.

Zhang, H.^#, Liang, H.^#, Zhi, H., Yuan, D., Yao, Q., Zhang, R., Xing, L., Yang, B., Sang, L., Zhao, L., Tang, S., Wang, L., Wang, H., Ren, Y., Zhang, H., Zhang, Y., Wang, E., Man, X., Xu, G., Zhang, L., He, Q.^*, Diao, X.^* & Jia, G.^*. 2025. An efficient target-mutant screening platform of model variety Ci846 facilitates genetic studies of Setaria. Plant Biotechnology Journal. DOI: 10.1111/pbi.14594.

Wang, L.^#, Tian, B.^#, He, Q.^#, Jia, G., Liu, B., Lu, Q., Zhi, H. & Diao, X.^*. 2025. SiPRR37 exerts dual functions in the regulation of photoperiodic flowering and contributes to the ecological adaptation of foxtail millet. The Crop Journal. DOI: 10.1016/j.cj.2024.12.004.

2024

Deng, Y.^#, Zhou, P.^#, Li, F.^#, Wang, J.^#, Xie, K.^#, Liang, H., Wang, C., Liu, B., Zhu, Z., Zhou, W., Dun, B., Lu, X.*, Diao, X.* & He, Q.*. 2024. A complete assembly of the sorghum BTx623 reference genome. Plant Communications. Doi: 10.1016/j.xplc.2024.100977.

He, Q.^*,#, Wang, C^#., He, Q.^#, Zhang, J., Liang, H., Lu, Z., Xie, K., Tang, S., Zhou, Y., Liu, B., Zhi, H., Jia, G., Guo, G., Du, H.*, & Diao, X.* 2024. A complete reference genome assembly for foxtail millet and Setaria-db, a comprehensive database for Setaria. Molecular Plant. Doi: 10.1016/j.molp.2023.12.017.

Wang, H., Yan, S., Wang, W., Cheng, Y., Hong, J., He, Q., ... & Fang, W.* 2024. Cropformer: An Interpretable Deep Learning Framework for Crop Genome Prediction. Plant Communications. Doi: 10.1016/j.xplc.2024.101223.

2023

He, Q.^#, Tang, S.^#, Zhi, H.^#, Chen, J., Zhang, J., Liang, H., Alam, O., Li, H., Zhang, H., Xing, L., Li, X., Zhang, W., Wang, H., Shi, J., Du, H., Wu, H., Wang, L., Yang, P., Xing, L., Yan, H., … Diao, X.* 2023. A graph-based genome and pan-genome variation of the model plant Setaria. Nature Genetics. Doi: 10.1038/s41588-023-01423-w.

Li, N.^#, He, Q.^#, Wang, J., Wang, B., Zhao, J., Huang, S., Yang, T., Tang, Y., Yang, S., Aisimutuola, P., Xu, R., Hu, J., Jia, C., Ma, K., Li, Z., Jiang, F., Gao, J., Lan, H., Zhou, Y., Zhang, X., … Yu, Q.* & Yu, Q.* 2023. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nature Genetics. Doi: 10.1038/s41588-023-01340-y.

Chen, J.^#, Liu, Y.^#, Liu, M.^#, Guo, W.^#, Wang, Y.^#, He, Q.^#,... & Yu, Q.* 2023. Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet. Nature Genetics. Doi: 10.1038/s41588-023-01571-z.

Liang, H.^#, He, Q.^#, Zhang, H., Zhi, H., Tang, S., Wang, H., Meng, Q., Jia, G., Chang, J., & Diao, X.* 2023. Identification and haplotype analysis of SiCHLI: a gene for yellow-green seedling as morphological marker to accelerate foxtail millet (Setaria italica) hybrid breeding. Theoretical and Applied Genetics. Doi: 10.1038/s41588-023-01571-z.

Zhu, M.^#,He, Q.^#, Lyu, M.^#, Shi, T., Gao, Q., Zhi, H., ... & Gao, Y.* 2023. Integrated genomic and transcriptomic analysis reveals genes associated with plant height of foxtail millet. The Crop Journal. Doi: 10.1038/s41588-023-01571-z.

Before

He, Q.^#, Zhi, H.^#, Tang, S., Xing, L., Wang, S., Wang, H., Zhang, A., Li, Y., Gao, M., Zhang, H., Chen, G., Dai, S., Li, J., Yang, J., Liu, H., Zhang, W., Jia, Y., Li, S., Liu, J., Qiao, Z., … Diao, X.* 2021. QTL mapping for foxtail millet plant height in multi-environment using an ultra-high density bin map. Theoretical and Applied Genetics. Doi: 10.1007/s00122-020-03714-w.

Zhi, H.^#,He, Q.^#, Tang, S., Yang, J., Zhang, W., Liu, H., Jia, Y., Jia, G., Zhang, A., Li, Y., Guo, E., Gao, M., Li, S., Li, J., Qin, N., Zhu, C., Ma, C., Zhang, H., Chen, G., Zhang, W., … Diao, X.* 2021. Genetic control and phenotypic characterization of panicle architecture and grain yield-related traits in foxtail millet (Setaria italica). Theoretical and Applied Genetics. Doi: 10.1007/s00122-021-03875-2.

Cheng, X.^#,He,Q.^#, Tang, S., Wang, H., Zhang, X., Lv, M., Liu, H., Gao, Q., Zhou, Y., Wang, Q., Man, X., Liu, J., Huang, R., Wang, H., Chen, T., & Liu, J.* 2021. The miR172/IDS1 signaling module confers salt tolerance through maintaining ROS homeostasis in cereal crops. New Phytologist. Doi: 10.1111/nph.17211.

Kan, J.^#, Gao, G.^#, He,Q.^#, Gao, Q.^#, Jiang, C., Ahmar, S., Liu, J., Zhang, J., & Yang, P.* 2021. Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley. International Journal of Molecular Sciences. Doi: 10.3390/ijms22105354.

He, Q., Xu, F., Min, M. H., Chu, S. H., Kim, K. W., & Park, Y. J.* 2019. Genome-wide association study of vitamin E using genotyping by sequencing in sesame (Sesamum indicum). Genes & genomics. Doi: 10.1007/s13258-019-00837-3.

Tong, W.^#, He, Q.^#, & Park, Y. J.* 2017. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice. Scientific Reports. Doi: 10.1038/srep43327.

He, Q., Kim, K. W., & Park, Y. J.* 2017. Population genomics identifies the origin and signatures of selection of Korean weedy rice. Plant Biotechnology Journal. Doi: 10.1111/pbi.12630.

He, Q., Park, Y.* 2015. Discovery of a novel fragrant allele and development of functional markers for fragrance in rice. Molecular Breeding. Doi: 10.1007/s11032-015-0412-4.

He, Q., Yu, J., Kim, T. S., Cho, Y. H., Lee, Y. S., & Park, Y. J.* 2015. Resequencing reveals different domestication rate for BADH1 and BADH2 in Rice (Oryza sativa). PLoS One. Doi: 10.1371/journal.pone.0134801.

He, Q., & Park, Y.* 2013 Evaluation of genetic structure of amaranth accessions from the United States. Weed&Turfgrass Science. Doi: 10.5660/WTS.2013.2.3.230.

Li, X., Gao, J., Song, J., Guo, K., Hou, S., Wang, X., He, Q., Zhang, Y., Zhang, Y., Yang, Y., Tang, J., Wang, H., Persson, S., Huang, M., Xu, L., Zhong, L., Li, D., Liu, Y., Wu, H., Diao, X., … Han, Y.* 2022. Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects. Molecular Plant. Doi: 10.1016/j.molp.2022.07.003.

Shi, L., Jiang, C., He, Q., Habekuß, A., Ordon, F., Luan, H., Shen, H., Liu, J., Feng, Z., Zhang, J., & Yang, P.* 2019. Bulked segregant RNA-sequencing (BSR-seq) identified a novel rare allele of eIF4E effective against multiple isolates of BaYMV/BaMMV. Theoretical and Applied Genetics. Doi: 10.1007/s00122-019-03314-33.

Yu, J., Zao, W., He, Q., Kim, T. S., & Park, Y. J.* (2017). Genome-wide association study and gene sets analysis for understanding candidate genes involved in salt tolerance at the rice seedling stage. Molecular Genetics and Genomics. Doi: 10.1007/s00438-017-1354-9.

Xu, F., Bao, J., He, Q., & Park, Y. J.* 2016. Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.). BMC Genomics. Doi: 10.1186/s12864-016-3000-z.

Kim, T. S.,He, Q., Kim, K. W., Yoon, M. Y., Ra, W. H., Li, F. P., Tong, W., Yu, J., Oo, W. H., Choi, B., Heo, E. B., Yun, B. K., Kwon, S. J., Kwon, S. W., Cho, Y. H., Lee, C. Y., Park, B. S., & Park, Y. J.* 2016. Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era. BMC Genomics. Doi: 10.1186/s12864-016-2734-y.

Wei, T., He, Q., Wang, XQ., Yoon, MY., Ra, WH., Li, F., Yu, J., Win Htet Oo, Min, SK., Choi, BW., Heo, EB., Yun, BK., Kim, KW., Kim, TS., Lee, CY., & Park, YJ.* 2015. A chloroplast variation map generated using whole genome re‐sequencing of Korean landrace rice reveals phylogenetic relationships among Oryza sativa subspecies. Biological Journal of the Linnean Society. Doi: 10.1111/bij.12564.

Wang, X. Q., Yoon, M. Y., He, Q., Kim, T. S., Tong, W., Choi, B. W., Lee, Y. S., & Park, Y. J. 2015. Natural variations in OsγTMT contribute to diversity of the α-tocopherol content in rice. Molecular Genetics and Genomics. Doi: 10.1007/s00438-015-1059-x.