本课题组从基因组学的角度研究农作物抗病性状的遗传机制。综合使用生物信息学、基因组学、分子生物学、遗传学等手段研究小麦与真菌病害协同进化的基本原理。

0710J3-生物信息学

农作物与病原菌的协同进化
小麦群体遗传学
农作物病原真菌的基因组进化

2006-09--2011-06   中国农业大学   理学博士 （生物信息学）
2002-09--2006-06   西南大学   理学学士 （生物学）

   

2016-06~2021-06,堪萨斯州立大学 （美国）, 博士后 (Postdoc Follow)
2015-07~2016-06,伊利诺伊大学厄巴纳-香槟分校 （美国）, 访问学者 (Visiting scholar)
2012-08~2016-06,布鲁克海文国家实验室（美国）, 博士后 (Research Associate)
2011-07~2012-07,纪念斯隆凯特琳癌症中心 （美国）, 博士后 （Research Fellow）

   

[1] []. Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement. biorxiv. 2025, https://biorxiv.org/content/10.1101/2025.02.18.638840v1.
[2] Shengwei Ma, Jianqing Niu, Yaoqi Si, Shusong Zheng, Yaru Lu, Shuiquan Tian, Xiaoli Shi, Zedong Chen, Cong Sun, Ziyi Qin, Xiaolin Liu, Huilan Wu, Mengjun Gu, Man Cui, Qiao Lu, Wenjuan Zhou, Weiming He, Chi Zhang, Fei He, HongQing Ling. A comprehensive map of DNA-segment copy number variation in 491 genomes of common wheat uncovers genes associated with multiple agronomic traits. Plant Communications[J]. 2025, 第 19 作者6(3): 101226, http://www.sciencedirect.com/science/article/pii/S2590346224006473.
[3] Xinyu Zhao, Zhimeng Zhang, Jiarui Ding, Chunfei Wu, Yunfeng Qu, Anning Song, Haibin Zhao, Weiwei Song, Meng Liu, Donghe Yang, Yizhuo Liu, Miao He, Qianyu Xing, Huixin Zhang, Lei Cui, Xinling Li, Jingzhong Xie, Hongjie Li, Fei He, Yanming Zhang. Cytogenetics and genomics analysis of cold-hardy perennial wheatgrass: insights into agronomic performance, chromosome composition, and gene expression. The Plant Journal[J]. 2025, 第 19 作者122(3): e70179, https://onlinelibrary.wiley.com/doi/10.1111/tpj.70179.
[4] []. A biGWAS strategy reveals the genetic architecture of the interaction between wheat and Blumeria graminis f. sp. tritici. biorxiv. 2025, https://biorxiv.org/content/10.1101/2025.04.09.647224v1.
[5] []. Reshaping epistatic network modules enhances wheat yield potential. biorxiv. 2025, https://biorxiv.org/content/10.1101/2025.04.01.646715v1.
[6] Luo, Qiaoling, Zheng, Qi, Tong, Chunyan, Jia, Hongwei, Liu, Liqin, Yin, Mou, Xie, Jingzhong, Li, Hongwei, Wang, Hongxin, Chen, Zeyang, Li, Bin, He, Fei, Li, Zhensheng. The location and genome origin of alien chromatin in wheat founder parent Xiaoyan 6. THEORETICAL AND APPLIED GENETICS[J]. 2025, 第 12 作者138(2): 1-15, http://dx.doi.org/10.1007/s00122-025-04826-x.
[7] Wei, Wenxin, Liu, Nannan, Zhang, Shengnan, Zhang, Jing, Pan, Wei, Xie, Xiaoming, Yang, Zuhuan, Sun, Junna, Ma, Jun, Hu, Zhaorong, Guo, Weilong, Luo, Qiaoling, Xie, Jingzhong, He, Fei, Li, Yinghui, Xie, Chaojie, Sun, Qixin. Mapping of powdery mildew resistance genes transferred to common wheat from wild emmer wheat revealed three functional Pm60 haplotypes. CROP JOURNAL[J]. 2024, 第 14 作者12(2): 540-548, http://lib.cqvip.com/Qikan/Article/Detail?id=7111926727.
[8] []. Two divergent haploid nuclei shaped the landscape of population diversity in wheat stripe rust. biorxiv. 2024, https://biorxiv.org/content/10.1101/2024.12.10.627719v1.
[9] Zhu, Mo, Bai, Hongxia, Zhang, Wanwan, Zhao, Sujing, Qiu, Zongbo, He, Fei. Identification and Biocontrol of Cladosporium Mold Caused by Cladosporium cladosporioides on Wheat Spikes in Central China. AGRONOMY-BASEL[J]. 2024, 第 6 作者  通讯作者  14(10): http://dx.doi.org/10.3390/agronomy14102330.
[10] 肖军, 鲁非, 邓娴, 宋显伟, 贺飞, 蒋才富, 刘倩, 赵玉胜, 姜丹华, 傅向东. 植物基因组与表观遗传学研究进展. 植物生理学报[J]. 2023, 第 5 作者59(9): 1665-1693, http://lib.cqvip.com/Qikan/Article/Detail?id=7110724235.
[11] Niu，Jianqing, Ma，Shengwei, Zheng，Shusong, Zhang，Chi, Lu，Yaru, Si, Yaoqi, Tian，Shuiquan, Shi，Xiaoli, Liu，Xiaolin, M. Kashif Naeem, Sun，Hua, Hu，Yafei, Wu， Huilan, Cui，Yan, Chen，Chunlin, Long，Wenbo, Zhang，Yue, Gu，Mengjun, Cui，Man, Lu，Qiao, Zhou，Wenjuan, Peng，Junhua, Akhunov，Eduard, He，Fei, Zhao，Shancen, Ling，Hong-Qing. Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States. The Plant Cell[J]. 2023, 第 24 作者  通讯作者  
[12] Jordan, Katherine W, He, Fei, de Soto, Monica Fernandez, Akhunova, Alina, Akhunov, Eduard. Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes. GENOME BIOLOGY[J]. 2020, 第 2 作者21(1): http://dx.doi.org/10.1186/s13059-020-02093-1.
[13] He, Fei, Pasam, Raj, Shi, Fan, Kant, Surya, KeebleGagnere, Gabriel, Kay, Pippa, Forrest, Kerrie, Fritz, Allan, Hucl, Pierre, Wiebe, Krystalee, Knox, Ron, Cuthbert, Richard, Pozniak, Curtis, Akhunova, Alina, Morrell, Peter L, Davies, John P, Webb, Steve R, Spangenberg, German, Hayes, Ben, Daetwyler, Hans, Tibbits, Josquin, Hayden, Matthew, Akhunov, Eduard. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. NATURE GENETICS[J]. 2019, 第 1 作者51(5): 896-+, http://dx.doi.org/10.1038/s41588-019-0382-2.
[14] Xiao, Long, Zhao, Zhiguang, He, Fei, Du, Zhuo. Multivariable regulation of gene expression plasticity in metazoans. OPEN BIOLOGY[J]. 2019, 第 3 作者  通讯作者  9(12): https://doaj.org/article/3e246e053795463481feb3c5f5c8784a.
[15] Jordan, Katherine W, Wang, Shichen, He, Fei, Chao, Shiaoman, Lun, Yanni, Paux, Etienne, Sourdille, Pierre, Sherman, Jamie, Akhunova, Alina, Blake, Nancy K, Pumphrey, Michael O, Glover, Karl, Dubcovsky, Jorge, Talbert, Luther, Akhunov, Eduard D. The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. PLANT JOURNAL[J]. 2018, 第 3 作者95(6): 1039-1054, http://dx.doi.org/10.1111/tpj.14009.
[16] Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, MurphyOlson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, JohnMarc, Chia, JerMing, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, Jose P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel M D, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong. KBase: The United States Department of Energy Systems Biology Knowledgebase. NATURE BIOTECHNOLOGY. 2018, 第 49 作者36(7): 566-569, https://www.webofscience.com/wos/woscc/full-record/WOS:000438082000010.
[17] Qi, Huan, Jiang, Zhenhong, Zhang, Kang, Yang, Shiping, He, Fei, Zhang, Ziding. PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. GENOMICS PROTEOMICS & BIOINFORMATICS[J]. 2018, 第 5 作者  通讯作者  16(4): 283-293, https://doaj.org/article/0170c3d29aed417aaaf7411146f55f37.
[18] He, Fei, Yoo, Shinjae, Wang, Daifeng, Kumari, Sunita, Gerstein, Mark, Ware, Doreen, Maslov, Sergei. Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis. PLANT JOURNAL[J]. 2016, 第 1 作者86(6): 472-480, https://www.webofscience.com/wos/woscc/full-record/WOS:000380214500003.
[19] Jiang, Zhenhong, Dong, Xiaobao, Li, ZhiGang, He, Fei, Zhang, Ziding. Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection. SCIENTIFIC REPORTS[J]. 2016, 第 4 作者  通讯作者  6: http://dx.doi.org/10.1038/srep35064.
[20] He, Fei, Maslov, Sergei. Pan- and core- network analysis of co-expression genes in a model plant. SCIENTIFIC REPORTS[J]. 2016, 第 1 作者  通讯作者  6: http://dx.doi.org/10.1038/srep38956.
[21] He, Fei, Karve, Abhijit A, Maslov, Sergei, Babst, Benjamin A. Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis. FRONTIERS IN PLANT SCIENCE[J]. 2016, 第 1 作者  通讯作者  7: https://doaj.org/article/1d32427ecdb84b12a340fa2a44e1ad2f.
[22] Wang, Daifeng, He, Fei, Maslov, Sergei, Gerstein, Mark. DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks. PLOS COMPUTATIONAL BIOLOGY[J]. 2016, 第 2 作者12(10): https://doaj.org/article/309e52bc73054fbab5801d434f060718.
[23] Du, Zhuo, Santella, Anthony, He, Fei, Tiongson, Michael, Bao, Zhirong. De Novo Inference of Systems-Level Mechanistic Models of Development from Live-Imaging-Based Phenotype Analysis. CELL[J]. 2014, 第 3 作者156(1-2): 359-372, http://dx.doi.org/10.1016/j.cell.2013.11.046.
[24] He, Fei, Zhou, Yuan, Zhang, Ziding. Deciphering the Arabidopsis Floral Transition Process by Integrating a Protein-Protein Interaction Network and Gene Expression Data. PLANT PHYSIOLOGY[J]. 2010, 第 1 作者153(4): 1492-1505, https://www.webofscience.com/wos/woscc/full-record/WOS:000280566000005.
[25] He, Fei, Zhang, Yan, Chen, Hao, Zhang, Ziding, Peng, YouLiang. The prediction of protein-protein interaction networks in rice blast fungus. BMC GENOMICS[J]. 2008, 第 1 作者  通讯作者  9(1): 519-519, https://doaj.org/article/9e9f7a68d3274ef09e0532883da88624.

   

（ 1 ） 小麦基因组渗入片段的表达调控规律研究, 负责人, 国家任务, 2025-01--2028-12
（ 2 ） 中英小麦基因组学联合实验室, 负责人, 国家任务, 2024-12--2027-11
（ 3 ） 数据驱动的优异种质鉴定与基因资源精准创制, 负责人, 国家任务, 2023-12--2028-11
（ 4 ） 小麦育种知识数据库, 参与, 国家任务, 2023-12--2025-12

（1）双向GWAS揭示小麦与白粉菌互作的遗传全貌   第三届小麦生物育种大会   2025-05-10
（2）利用双向GWAS策略解析小麦与白粉菌相互作用网络   第二届小麦生物育种高峰论坛   2024-05-19
（3）Dissecting molecular interaction between wheat and powdery mildew through bi-directional GWAS   中英联合研究中心年会   2024-03-20
（4）人工智能在小麦育种领域的应用探讨   第八届全国小麦遗传育种研讨会暨第十一届全国小麦基因组与分子育种大会   2023-08-23
（5）大数据驱动小麦-白粉菌 互作机制解析初探   中国植物病理学会2023年学术年会   2023-08-06
（6）High-throughout phenotyping platform assists understanding the genomic basis of disease resistance in wheat   2023-07-09
（7）Exome sequencing highlights the role of wild relative introgression in shaping the adaptive landscape of the wheat genome   2020-01-11

现指导学生

张志蒙  博士研究生  0710J3-生物信息学  

尹谋  博士研究生  0710J3-生物信息学  

陈昭庚  博士研究生  0710J3-生物信息学  

王豪杰  博士研究生  0710J3-生物信息学  

李轩照  博士研究生  0710J3-生物信息学  

王一波  硕士研究生  071007-遗传学  

赵彩虹  博士研究生  0710J3-生物信息学  

张婧  博士研究生  0710J3-生物信息学  

王世捷  硕士研究生  0710J3-生物信息学  

刘亚苓  博士研究生  071007-遗传学  

侯玥瑄  博士研究生  0710J3-生物信息学  

田阳阳  博士研究生  071007-遗传学  

刘则  博士研究生  071007-遗传学