陈永明  作物比较基因组学与调控组学课题组组长

邮箱：yongming.chen@pku-iaas.edu.cn

研究方向：作物多组学、调控组学、比较基因组学、生物信息学

个人简介：

2013年9月-2017年7月，山东农业大学，农学院，学士

2017年9月-2022年6月，中国农业大学，农学院，博士

2022年10月-2024年7月，中国农业大学，农学院，博士后

2024年8月-至今，北京大学现代农业研究院，青年研究员、课题组长（PI）

研究工作：

课题组通过整合多组学、调控组学、比较基因组学、功能基因组学、生物信息学等相关技术手段，开展多组学整合工具开发、表型变异和适应性进化的遗传与调控机制解析、农艺性状关键基因的系统发掘与分子设计育种等方面的系统研究。重点包括：

（1）解析小麦等作物在转录、翻译等多层次的动态调控网络，揭示产量形成与抗逆性复杂性状之间动态平衡与协同调控的遗传与分子机制；

（2）解析作物重要性状的起源、变异及演化规律，阐明基因调控网络的遗传变异与适应性进化的分子基础；

（3）开发多组学数据整合分析平台与基因挖掘工具，建立融合基因进化和调控信息的智能化分子设计育种体系。

研究成果：

已发表29篇论文，其中以第一作者（含共同）在Molecular Plant (3篇)、Plant Cell、Plant Physiology等主流期刊发表7篇论文。主持国家自然科学基金青年科学基金项目（C类）、山东省青年科技人才托举工程、中国博士后科学基金等4项国家及省市级科研和人才项目。担任多个SCI期刊青年编委或审稿人。开发的10余个作物组学分析工具和数据库已被国际同行广泛使用，累计访问量超数十万次。

本课题组长期招聘博士后、助理/副研究员、访问学者，欢迎青年学者加入团队！

发表论文：

（第一作者^*；通讯作者^#)

29. Yongming Chen^*, Yiwen Guo^*, Panfeng Guan, Yongfa Wang, Xiaobo Wang, Zihao Wang, Zhen Qin, Shengwei Ma, Mingming Xin, Zhaorong Hu, Yingyin Yao, Zhongfu Ni, Qixin Sun, Weilong Guo^#, and Huiru Peng^#. (2023) A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement. Molecular Plant, 16(2), 393-414. doi: 10.1016/j.molp.2022.12.019 (Featured article)

28. Yongming Chen, Wanjun Song, Xiaoming Xie, Zihao Wang, Panfeng Guan, Huiru Peng, Yuannian Jiao, Zhongfu Ni, Qixin Sun, and Weilong Guo^#. (2020) A collinearity-incorporating homology inference strategy for connecting emerging assemblies in Triticeae tribe as a pilot practice in the plant pangenomic era. Molecular Plant, 13(12), 1694-1708. doi: 10.1016/j.molp.2020.09.019 (Featured article, On the cover)

27. Yiwen Guo^*, Yongming Chen^*, Yongfa Wang, Xiaojia Wu, Xiaoyu Zhang, Weiwei Mao, Hongjian Yu, Kai Guo, Jin Xu, Liang Ma, Weilong Guo, Zhaorong Hu, Mingming Xin, Yingyin Yao, Zhongfu Ni, Qixin Sun, and Huiru Peng^#. (2023) The translational landscape of bread wheat during grain development. The Plant Cell, 35(6), 1848–1867. doi: 10.1093/plcell/koad075 (Plant Cell News)

26. Yongming Chen, Yiwen Guo, Xiaoming Xie, Zihao Wang, Lingfeng Miao, Zhengzhao Yang, Yuannian Jiao, Chaojie Xie, Jie Liu, Zhaorong Hu, Mingming Xin, Yingyin Yao, Zhongfu Ni, Qixin Sun, Huiru Peng^# and Weilong Guo^#. (2023) Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae. Plant Physiology, 193(1), 578-594. doi: 10.1093/plphys/kiad319

25. Zhichao Yu^*, Yongming Chen^*, Yong Zhou^*, Yulu Zhang, Mengyuan Li, Yidan Ouyang, Dmytro Chebotarov, Ramil Mauleon, Hu Zhao, Weibo Xie, Kenneth L. McNally, Rod A. Wing^#, Weilong Guo^#, Jianwei Zhang^#. (2023) Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice. Molecular Plant, 16(5), 798-801. doi: 10.1016/j.molp.2023.03.012

24. Yongming Chen^*, Wenxi Wang^*, Zhengzhao Yang, Huiru Peng, Zhongfu Ni, Qixin Sun, Weilong Guo^#. (2024) Innovative computational tools provide new insights into the polyploid wheat genome. aBIOTECH, 5, 52-70. doi: 10.1007/s42994-023-00131-7 (Invited review)

23. Weiya Xu^*, Yongming Chen^*, Bin Liu, Qiuyuan Li, Yilan Zhou, Xuanshuang Li, Weilong Guo, Zhaorong Hu, Zhenshan Liu, Mingming Xin, Yingyin Yao, Mingshan You, Huiru Peng, Zhongfu Ni, Jiewen Xing^#. (2023) TaANR1-TaMADS25 module regulates lignin biosynthesis and root development in wheat (Triticum aestivum L.). Journal of Genetics and Genomics, 50(11), 917-920. doi: 10.1016/j.jgg.2023.08.011

22. Yongdong Xu, Yueyao Wang, Yongming Chen, Yunxia Wang, Shicheng Zhang, Gang Luo, Fuhao Cui, Taisheng Du, and Zhidan Liu*. (2025) TCMD: A High-Throughput and Rapid Method for Screening Antimicrobial Ingredients from Renewable Bio-Based Resources. Advanced Science. doi: 10.1002/advs.202502156

21. Hao Wang, Shen Yan, Wenxi Wang, Yongming Chen, Jingpeng Hong, Qiang He, Xianmin Diao, Yunan Lin, Yanqing Chen, Yongsheng Cao, Weilong Guo, Wei Fang. (2024) Cropformer: An Interpretable Deep Learning Framework for Crop Genome Prediction. Plant Communications, 6(3), 101223. doi: 10.1016/j.xplc.2024.101223

20. Renhan Li, Jie Liu, Lingling Chai, Dejie Du, Wen Yang, Jun Zhu, Yaotian Gao, Yunjie Liu, Lingfeng Miao, Long Song, Xiaoming Xie, Yongming Chen, Zhaoheng Zhang, Pei Ni, Yidi Zhao, Zhaoju Li, Lahu Lu, Weilong Guo, Huiru Peng, Qixin Sun, Zhongfu Ni. (2024) A natural variation of TaERF-A1 encoding an AP2/ERF transcription factor confers semidwarf plant architecture and increased lodging resistance in wheat. Plant Communications, 6(3), 101194. doi: 10.1016/j.xplc.2024.101194

19. Xiaoyu Zhang, Yongfa Wang, Yongming Chen, Yazhou Li, Kai Guo, Jin Xu, Panfeng Guan, Tianyu Lan, Mingming Xin, Zhaorong Hu, Weilong Guo, Yingyin Yao, Zhongfu Ni, Qixin Sun, Ming Hao, Huiru Peng. (2024) Partial unidirectional translocation from 5AL to 7BS leads to dense spike in an EMS-induced wheat mutant. BMC Genomics, 25, 1073. doi: 10.1186/s12864-024-11000-y

18. Weiwei Mao^*, Xiaobo Wang^*, Yongming Chen, Yongfa Wang, Liang Ma, Xiaoming Xie, Xiaojia Wu, Jin Xu, Yuqi Zhang, Yue Zhao, Xuejun Tian, Weilong Guo, Zhaorong Hu, Mingming Xin, Yingyin Yao, Zhongfu Ni, Qixin Sun, Huiru Peng^#. (2024) Map-based cloning and characterization reveal that an R2R3 MYB gene confers red glume in wheat. The Crop Journal. doi: 10.1016/j.cj.2024.03.002

17. Yongfa Wang^*, Zihao Wang^*, Yongming Chen, Tianyu Lan, Xiaobo Wang, Gang Liu, Mingming Xin, Zhaorong Hu, Yingyin Yao, Zhongfu Ni, Qixin Sun, Weilong Guo^#, and Huiru Peng^#. (2024) Genomic insights into the origin and evolution of spelt (Triticum spelta L.) as a valuable gene pool for modern wheat breeding. Plant Communications, 5(5), 100883. doi: 10.1016/j.xplc.2024.100883

16. Lingfeng Miao^*, Weiya Xu^*, Yanhong Liu, Xiangyi Huang, Zhe Chen, Huifang Wang, Zihao Wang, Yongming Chen, Qingxin Song, Jing Zhang, Fangpu Han, Huiru Peng, Yingyin Yao, Mingming Xin, Zhaorong Hu, Zhongfu Ni, Qixin Sun, Jiewen Xing^# and Weilong Guo^#. (2024) Reshaped DNA methylation cooperating with homoeolog-divergent expression promotes improved root traits in synthesized tetraploid wheat. New Phytologist, 242(2), 507-523. doi: 10.1111/nph.19593

15. Xiaobo Wang^*, Weiwei Mao^*, Yongfa Wang, Hongyao Lou, Panfeng Guan, Yongming Chen, Huiru Peng^#, Jiankang Wang^#. (2023) Breeding design in wheat by combining the QTL information in a GWAS panel with a general genetic map and computer simulation. The Crop Journal, 11(6), 1816-1827. doi: 10.1016/j.cj.2023.10.001

14. Zihao Wang^*, Lingfeng Miao^*, Yongming Chen, Huiru Peng, Zhongfu Ni, Qixin Sun, Weilong Guo^#. (2023) Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. Journal of Genetics and Genomics, 50(11), 846-860. doi: 10.1016/j.jgg.2023.08.002

13. Zhaoheng Zhang^*, Ruijie Zhang^*, Fengfan Meng, Yongming Chen, Wenxi Wang, Kai Yang, Yujiao Gao, Mingming Xin, Jinkun Du, Zhaorong Hu, Zhongfu Ni, Qixin Sun, Weilong Guo^#, Yingyin Yao^#. (2023) A comprehensive atlas of long non-coding RNAs provides insight into grain development in wheat. Seed Biology, 2, 12. doi: 10.48130/SeedBio-2023-0012

12. Haoran Wang, Man Feng, Yujie Jiang, Dejie Du, Chaoqun Dong, Zhaoheng Zhang, Wenxi Wang, Jing Liu, Xiangqing Liu, Sufang Li, Yongming Chen, Weilong Guo, Mingming Xin, Yingyin Yao, Zhongfu Ni, Qixin Sun, Huiru Peng, Jie Liu^#. (2023) Thermosensitive SUMOylation of TaHsfA1 defines a dynamic ON/OFF molecular switch for the heat stress response in wheat. The Plant Cell, 35(10), 3889-3910. doi: 10.1093/plcell/koad192

11. Xiaobo Wang^*, Jinbo Zhang^*, Weiwei Mao^*, Panfeng Guan, Yongfa Wang, Yongming Chen, Wangqing Liu, Weilong Guo, Yingyin Yao, Zhaorong Hu, Mingming Xin, Zhongfu Ni, Qixin Sun^#, and Huiru Peng^#. (2023) Association mapping identifies loci and candidate genes for grain-related traits in spring wheat in response to heat stress. Plant Science, 331, 11676. doi: 10.1016/j.plantsci.2023.111676

10. Na Song^*, Jingchen Lin^*, Xingbei Liu^*, Zehui Liu, Debiao Liu, Wei Chu, Jinpeng Li, Yongming Chen, Shumin Chang, Qun Yang, Xiaoyu Liu, Weilong Guo, Mingming Xin, Yingyin Yao, Huiru Peng, Zhongfu Ni, Chaojie Xie, Qixin Sun, and Zhaorong Hu^#. (2022) Histone acetyltransferase TaHAG1 interacts with TaPLATZ5 to activate TaPAD4 expression and positively contribute to powdery mildew resistance in wheat. New Phytologist, 236(2), 590-607. doi: 10.1111/nph.18372

9. Jingchen Lin^*, Na Song^*, Debiao Liu, Xingbei Liu, Wei Chu, Jinpeng Li, Shumin Chang, Zehui Liu, Yongming Chen, Qun Yang, Xiaoyu Liu, Yingyin Yao, Weilong Guo, Mingming Xin, Huiru Peng, Zhongfu Ni, Qixin Sun, and Zhaorong Hu^#. (2022) Histone acetyltransferase TaHAG1 interacts with TaNACL to promote heat stress tolerance in wheat. Plant Biotechnology Journal, 20(9), 1645-1647. doi: 10.1111/pbi.13881

8. Qian Chen^*, Changfeng Yang^*, Zhaoheng Zhang, Zihao Wang, Yongming Chen, Vincenzo Rossi, Wei Chen, Mingming Xin, Zhenqi Su, Jinkun Du, Weilong Guo, Zhaorong Hu, Jie Liu, Huiru Peng, Zhongfu Ni, Qixin Sun^#, and Yingyin Yao^#. (2022) Unprocessed wheat γ‐gliadin reduces gluten accumulation associated with the endoplasmic reticulum stress and elevated cell death. New Phytologist, 236(1), 146-164. doi: 10.1111/nph.18316

7. Shengwei Ma, Meng Wang^#, Jianhui Wu, Weilong Guo, Yongming Chen, Guangwei Li, Yanpeng Wang, Weiming Shi, Guangmin Xia, Daolin Fu, Zhensheng Kang, and Fei Ni^#. (2021) WheatOmics: A platform combining multiple omics data to accelerate functional genomics studies in wheat. Molecular Plant, 14(12), 1965-1968. doi: 10.1016/j.molp.2021.10.006

6. 李玲红，张哲，陈永明，尤明山，倪中福，邢界文。（2021）普通小麦颖壳蜡质缺失突变体glossy1的转录组分析。作物学报, 48(1): 48-62。doi: 10.3724/SP.J.1006.2022.11006

5. Lulu Gao^*, Guanghui Yang^*, Yufeng Li, Ying Sun, Ruibin Xu, Yongming Chen, Zihao Wang, Jiewen Xing^#, and Yirong Zhang^#. (2021) A kelch-repeat superfamily gene, ZmNL4, controls leaf width in maize (Zea mays L.). The Plant Journal, 107(3), 817-830. doi: 10.1111/tpj.15348

4. Yujiao Gao^*, Kexin An^*, Weiwei Guo^*, Yongming Chen, Ruijie Zhang, Xue Zhang, Siyuan Chang, Vincenzo Rossi, Fangming Jin, Xinyou Cao, Mingming Xin, Huiru Peng, Zhaorong Hu, Weilong Guo, Jinkun Du, Zhongfu Ni, Qixin Sun, and Yingyin Yao^#. (2021) The endosperm-specific transcription factor TaNAC019 regulates glutenin and starch accumulation and its elite allele improves wheat grain quality. The Plant Cell, 33(3), 603–622. doi: 10.1093/plcell/koaa040

3. Weilong Guo^*, Mingming Xin^*, Zihao Wang^*, Yingyin Yao, Zhaorong Hu, Wanjun Song, Kuohai Yu, Yongming Chen, Xiaobo Wang, Panfeng Guan, Rudi Appels, Huiru Peng^#, Zhongfu Ni^#, and Qixin Sun^#. (2020) Origin and adaptation to high altitude of Tibetan semi-wild wheat. Nature Communications, 33, 5085. doi: 10.1038/s41467-020-18738-5

2. Panfeng Guan, Xueyi Shen, Qing Mu, Yongfa Wang, Xiaobo Wang, Yongming Chen, Yue Zhao, Xiyong Chen, Aiju Zhao, Weiwei Mao, Yiwen Guo, Mingming Xin, Zhaorong Hu, Yingyin Yao, Zhongfu Ni, Qixin Sun, and Huiru Peng^#. (2020) Dissection and validation of a QTL cluster linked to Rht-B1 locus controlling grain weight in common wheat (Triticum aestivum L.) using near-isogenic lines. Theoretical and Applied Genetics, 133, 2639–2653. doi: 10.1007/s00122-020-03622-z

1. Panfeng Guan, Na Di, Qing Mu, Xueyi Shen, Yongfa Wang, Xiaobo Wang, Kuohai Yu, Wanjun Song, Yongming Chen, Mingming Xin, Zhaorong Hu, Weilong Guo, Yingyin Yao, Zhongfu Ni, Qixin Sun, and Huiru Peng^#. (2019) Use of near-isogenic lines to precisely map and validate a major QTL for grain weight on chromosome 4AL in bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 132, 2367–2379. doi: 10.1007/s00122-019-03359-4