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Principal Investigator
Researcher
Email:dlyang@cemps.ac.cn
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Research Direction

Disease resistance, epigenetics


Research Unit

State Key laboratory of Plant Trait Design

Donglei Yang

Personal Profile

• Education:

 1999.09-2003.06, Life Science College, Shandong University, Bachelor

 2003.08-2009.11, The Institute of Plant Physiology and Ecology, Chinese Academy of Science, Ph.D


• Working experience:

2009.12-2010.12, College of Agriculture and Life Science, Cornell University, Postdoctor;

2011.01-2011.12, College of Agriculture, Purdue University, Postdoctor;

2012.01-2014.12, Shanghai Institute of Biological Science, Chinese Academy of Science; Associate Investigator;

2015.01-2024.12, College of Agriculture, Nanjing Agricultural University, Professor;

2025.01-present, Center for Excellence in Molecular Plant Science, Chinese Academy of Science, Principal Investigator



Research Work

& GA negatively regulates rice immunity through repressing JA signaling.

Gibberellic acid is one important phytohormone promoting rice growth. We demonstrated that GA negatively regulate disease resistance against bacterial blight and blast disease. More importantly, the “Green Revolution” gene, semi-dwarf 1 (sd1) significantly enhanced disease resistance. GA negatively regulate disease resistance through repressing jasmonic acid (JA) signaling via DELLA-JAZ interaction and mutual interference.


& MicroRNA156-IPA1 integrate GA and SA signaling to enhance disease resistance.

Ideal Plant Architecture 1 (IPA1, also named OsSPL14) reduces inefficient tiller number, increases panicle branching, and strength culm. We found that microRNA156 reduces disease resistance, while its two target genes, IPA1 and OsSPL7 enhance disease resistance against bacterial blight. IPA1 and OsSPL7 physically interact with SLR1 (Slender Rice 1), the solely DELLA protein in rice, and stabilizes SLR1. Finally, IPA1 and OsSPL7 increase disease resistance and reduced growth through repressing GA signaling.

The salicylic acid receptor, OsNPR1 physically interact with IPA1 and facilitate the binding of IPA1 on defense-related genes. OsNPR1 enhance the transcriptional activity of IPA1 on both down-regulated genes and up-regulated genes. In the nucleus, IPA1 stabilize OsNPR1 through interfering the interaction between OsNPR1 and OsCullin3a, the E3 ligase for OsNPR1. The mutual enhancement between IPA1 and OsNPR1 boosts rice immunity.


& The molecular mechanism of RNA-directed DNA methylation

We identified the 24-nt siRNA precursors, which range from 25-nt to 50-nt in length. Without four DCLs, the precursors of 24-nt siRNAs could direct DNA methylation at most RdDM loci on whole genome scale. We also demonstrated that four CLASSY genes, encoding chromatin remodeling proteins, is collectively required for Pol IV-RDR2 generating 24-nt siRNAs. In addition, mutation in single or two CLASSY could result in DNA hypermethylation.

Our study found that overexpression of OsGA2ox1, encoding a GA deactivating enzyme, driven by constitutive 35S promoter largely reduces bioactive GA levels and results in dwarfism. The 35S::OsGA2ox1 transgenic rice plants were autonomously silenced and rescued GA levels and plant height. We isolated dozens of five elements mountain (fem) mutants that restored OsGA2ox1 overexpression. Map-based cloning demonstrated that FEM1 encodes OsRDR2, FEM2 encodes a chromatin remodeler (CLSY homologue), FEM3 encodes OsNRPE1b (the largest subunit of RNA polymerase V). Using these fem mutants, we found that RdDM activity is substantially enhanced in reproductive organs and is required for reproductive development. The difference between Pol V-dependent and -independent 24-nt siRNAs is associated with epigenetic modifications (DNA methylation in three contexts, histone modifications).



Main Achievements

    Multiple diseases threaten yield production and food safety. Our laboratory focus on rice diseases including bacterial blight, blight leaf streak, and sheath blight. We are dedicated to clone new resistance genes against these diseases, and reveal the underlying mechanism of these genes mediated-immunity. On particular, the trade-off of immunity on yield-related traits is under investigated. Using technology such as molecular marker assistant selection, genome editing and transgene, the disease resistance genes will be applied in rice breeding.

    Transgene is the technology to quickly utilize disease resistance genes in crop breeding. Transgenes often be silenced by genomic immunity in rice. The mechanism of gene silencing in Arabidopsis is well demonstrated. In crops, however, the gene silencing machinery is largely unknown. We are cloning the genes that are essential for gene silencing and created new germplasm of suppressing gene silencing.



Publications

1. Wang Z(#), Liu M, Yan R, Zhang X, Song X, Xiong G, Li J, He Z, Yang D-L(*). Mutual potentiation of IPA1 and OsNPR1 enhances rice immunity.The Plant Cell. 2026,38(5):koag122.

2. Chen X(#), Yao X(#), Yan F(#), Li S(#), Wang ZD(#), Yin FY(#), Zhou M, Wang Z, Qin L, Zhao B, Lu K, Zhang L, Li X, Mu X, Zhang Y, Lu T, Ma JB, Zhao YK, Lin D, Wang M, Li Q, Qi S, Long J, Bai B, Ma JY, Liu Y, Feng Y, Yang XB, Zhang J, Xu Y, Chen L, Zou S, Ding X, Zhang MX(*), Yang DL(*), Cheng Z(*), Zhou H(*), Dong H(*). Alternative splicing of OsNPR3 promoted by the bacterial TAL effectors-targeted splicing regulator OsRBP11 antagonizes OsNPR1 function and enhances disease susceptibility in rice. Molecular Plant. 2025 Sep 1;18(9):1505-1525.

3. Xu D(#), Zeng L(#), Wang L, Yang D-L(*) Rice requires a chromatin remodeler for Polymerase IV-small interfering RNA production and genomic immunity. Plant Physiology. 2024, 194(4): 2149-2164

4. Yang D-L(#)(*), Huang K, Deng D, Zeng Y, Wang Z(*), Zhang Y(*). DNA-dependent RNA polymerases in plants. The Plant Cell. 2023, 35(10): 3641-3661

5. Wang L(#), Xu D, Zeng L, Yang D-L(*). The rise and fall of billionaire siRNAs during reproductive development in rice. Plants. 2022,11(15): 1957

6. Wang L(#), Zheng K, Zeng L, Xu D, Zhu T, Yin Y, Zhan H, Wu Y, Yang D-L(*). Reinforcement of CHH methylation through RNA-directed DNA methylation ensures sexual reproduction in rice. Plant Physiology. 2022, Feb 4; 188(2):1189-1209

7. Zheng K(#), Wang L(#), Zeng L(#), Xu D, Guo Z, Gao X, Yang D-L(*). The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice. PNAS. 2021, Jul 27;118(30):e2100709118.

8. Deng Y(#), Ning Y(#), Yang D-L(#), Zhai K, Wang GL(*),He Z(*) Molecular Basis of Disease Resistance and Perspectives on Breeding Strategies for Resistance Improvement in Crops. Molecular Plant. 2020, Oct 5;13(10):1402-1419.

9. 殷雨萌，曾龙军，王莉莉，郑克志，徐大超，杨东雷.水稻中的“伥鬼”：不同表观遗传学状态的同一转基因之间的相互作用。植物生理学报.2020, 56 (9): 1784–1794

10. 杨东雷. 人们对水杨酸受体的认知再次深入。 植物生理学报，2020, 56 (11): 2329–2331

11. Liu M(#), Shi Z(#), Zhang X, Wang M, Zhang L, Zheng K, Liu J, Hu X, Di C, Qian Q, He Z, Yang D-L(*). Inducible overexpression of Ideal Plant Architecture1 improves both yield and disease resistance in rice. Nature Plants. 2019, Apr; 5(4):389-400. (ESI highly cited paper)

12. Yang D-L(#)(*), Zhang G, Wang L, Li J, Xu D, Di C, Tang K, Yang L, Zeng L, Miki D, Duan CG, Zhang H, Zhu JK(*). Four putative SWI2/SNF2 chromatin remodelers have dual roles in regulating DNA methylation in Arabidopsis. Cell Discovery. 2018, Oct 16;4:55. doi: 10.1038/s41421-018-0056-8.

13. Li Y(#), Guo J, Yang Z, Yang D-L(*). Plasma Membrane-Localized Calcium Pumps and Copines Coordinately Regulate Pollen Germination and Fertility in Arabidopsis. International Journal of Molecular Science. 2018, 19(6). pii: E1774. doi: 10.3390/ijms19061774.

14. Yang D-L(#)(*), Shi Z(#), Bao Y(#), Yan J(#), Yang Z, Yu H, Li Y, Gou M, Wang S, Zou B, Xu D, Ma Z, Kim J, Hua J(*). Calcium pumps and interacting BON1 protein modulate calcium signature, stomatal closure, and plant immunity. Plant Physiology. 2017, 175(1): 424-437.

15. Li X(#), Yang D-L(#), Sun L(#), Li Q, Mao B, He Z(*).The Systemic Acquired Resistance Regulator OsNPR1 Attenuates Growth by Repressing Auxin Signaling through Promoting IAA-Amido Synthase Expression. Plant Physiology. 2016, 172(1):546-558.

16. Yang D-L(#),Zhang G(#), Tang K, Li J, Yang L, Huang H, Zhang H, Zhu JK(*). Dicer-independent RNA-directed DNA methylation in Arabidopsis. Cell Research. 2016, 26(1): 66-82.

17. Zou B(#), Yang D-L(#), Shi Z(#), Dong H, Hua J(*). Monoubiquitination of Histone 2B at the disease resistance gene locus regulates its expression and impacts immune responses in Arabidopsis. Plant Physiology. 2014, 165(1):309-318.

18. Sun L(#), Yang D-L(#),Kong Y, Chen Y, Li XZ, Zeng LJ, Li Q, Wang ET, He ZH(*). Sugar homeostasis mediated by cell wall invertase GRAIN INCOMPLETE FILLING 1 (GIF1) plays a role in pre-existing and induced defence in rice. Molecular Plant Pathology. 2014, 15(2):161-173.

19. Yang D-L(#), Yang Y, He Z(*). Roles of plant hormones and their interplay in rice immunity. Molecular Plant 2013, 6(3):675-685. (ESI highly cited paper)

20. Yang D-L(#), Dong WX(#), Zhang YY, He ZH(*). Gibberellins modulate abiotic stress tolerance in plants. Scientia Sinica. 2013, 43(12): 1119-1126

21. Yang D-L(#), Yao J(#), Mei CS(#),Tong XH, Zeng LJ, Li Q, Xiao LT, Sun TP, Li J, Deng XW, Lee CM, Thomashow MF, Yang Y(*), He Z(*), He SY(*). Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade. PNAS 2012, 109(19):E1192-1200. (ESI highly cited paper，F1000 recommended)

22. Yang D-L(#), Li Q, Deng YW, Lou YG, Wang MY, Zhou GX, Zhang YY, He ZH(*). Altered disease development in the eui mutants and Eui overexpressors indicates that gibberellins negatively regulate rice basal disease resistance. Molecular Plant. 2008, 1:528-537.

23. Lin H, Chen F, Cheng G, Yan B, Yuan M, Qiu J, Lu Y, Suo M, Chen Y, Wang Y, Cui K, Gong X, Liu S, Liu B, Liu J, Wang J, Li R, Mao B, Xu J, Jeon JS, Huang X, Han B, Yang DL, Gao Q, Xu H, Deng Y, Chen G, He Z. Asymmetric selection of a rice immune module and rebuild of disease resistance. Nature. 2026, 653(8115):840-849.

24. Dong Y, An Q, He Y, Zhang Y, Guo G, Zhang C, Zhang Y, Xia X, Wang Y, Zhang S, Yang DL, Ma W, Whitford R, Yang X, Zhang Z, Li G. The metacaspase-Peps-PEPR immune module confers resistance to Fusarium head blight in wheat. The Plant Cell. 2025, 37(8):koaf177.

25. Dong K(#), Wu F(#), Cheng S(#), Li S, Zhang F, Xing X, Jin X, Luo S, Feng M, Miao R, Chang Y, Zhang S, You X, Wang P, Zhang X, Lei C, Ren Y, Zhu S, Guo X, Wu C, Yang DL, Lin Q(*), Cheng Z(*), Wan J(*). OsPRMT6a-mediated arginine methylation of OsJAZ1 regulates jasmonate signaling and spikelet development in rice. Molecular Plant. 2024,17(6):900-919.

26. Yan W(#), Zhu Y, Liu W, Zou C, Jia B, Chen Z-Q, Han Y, Wu J, Yang D-L, Zhang Z, Xie L, Chen B, Li R, Ding S-W, Wu Q, Guo Z(*). Discovery of aphid-transmitted Rice tiller inhibition virus from native plants through metagenomic sequencing. PLoS Pathogen 2023, 19 (3)：e1011238

27. Ai G(#), Yang D-L, Dou D(*). The warfare for plant highway: vascular plant–microbe interaction pinpoints lignin. Stress Biology. 2022. 2:24

28. Fang Q(#), Zhang J, Yang D-L, Huang CF(*). The SUMO E3 ligase SIZ1 partially regulates STOP1 SUMOylation and stability in Arabidopsis thaliana. Plant Signal Behavior. 2021, 16:1899487

29. Wan K(#), Lu K, Gao M, Zhao T, He Y, Yang D-L, Tao X, Xiong G, Guan X(*). Functional analysis of the cotton CLE polypeptide signaling gene family in plant growth and development. Scientific Reports. 2021, Mar 3;11(1):5060.

30. Li J(#), Yang D-L, Huang H, Zhang G, He L, Pang J, Lozano-Durán R, Lang Z, Zhu JK(*). Epigenetic memory marks determine epiallele stability at loci targeted by de novo DNA methylation. Nature Plants. 2020, Jun;6(6):661-674.

31. Zhong Y(#), Wang W, Huang X, Liu M, Hebelstrup KH, Yang D, Cai J, Wang X, Zhou Q, Cao W, Dai T, Jiang D(*).Nitrogen topdressing timing modifies the gluten quality and grain hardness related protein levels as revealed by iTRAQ. Food Chemistry. 2019, Mar 30;277:135-144.

32. Zhang Q(#), Liang Z, Cui X, Ji C, Li Y, Zhang P, Liu J, Riaz A, Yao P, Liu M, Wang Y, Lu T, Yu H, Yang D, Zheng H, Gu X(*).N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development and Stress Responses. Molecular Plant. 2018, Dec 3;11(12):1492-1508.

33. Zhong Y(#), Xu D, Hebelstrup KH, Yang D, Cai J, Wang X, Zhou Q, Cao W, Dai T, Jiang D(*). Nitrogen topdressing timing modifies free amino acids profiles and storage protein gene expression in wheat grain. BMC Plant Biology. 2018, Dec 13;18(1):353.

34. Zhao K(#), Xiao J, Liu Y, Chen S, Yuan C, Cao A, You FM, Yang D, An S, Wang H, Wang X(*). Rht23 (5Dq') likely encodes a Q homeologue with pleiotropic effects on plant height and spike compactness. Theor Appl Genet. 2018, 131(9):1825-1834.

35. Niu D(#), Zhang X, Song X, Wang Z, Li Y, Qiao L, Wang Z, Liu J, Deng Y, He Z, Yang D, Liu R, Wang Y, Zhao H(*). Deep sequencing uncovers rice long siRNAs and its involvement in immunity against Rhizoctonia solani. Phytopathology. 2018, 108(1):60-69.

36. Wang L(#), Yuan J, Ma Y, Jiao W, Ye W, Yang D-L, Yi C, Chen ZJ(*). Rice Interploidy Crosses Disrupt Epigenetic Regulation, Gene Expression, and Seed Development. Molecular Plant. 2018, 11: 300-314.

37. Zou B(#), Sun Q, Zhang W, Ding Y, Yang D-L, Shi Z, Hua J(*). The Arabidopsis Chromatin-Remodeling Factor CHR5 Regulates Plant Immune Responses and Nucleosome Occupancy. Plant Cell Physiology. 2017, 58(12):2202-2216.

38. Yuan J(#), Chen S(#), Jiao W(#), Wang L, Wang L, Ye W, Lu J, Hong D, You S, Cheng Z, Yang D-L, Chen ZJ(*). Both maternally and paternally imprinted genes regulate seed development in rice. New Phytologist. 2017, 216(2):373-387.

39. You Q(#), Zhai K(#), Yang D, Yang W, Wu J, Liu J, Pan W, Wang J, Zhu X, Jian Y, Liu J, Zhang Y, Deng Y, Li Q, Lou Y, Xie Q, He Z(*). An E3 Ubiquitin Ligase-BAG Protein Module Controls Plant Innate Immunity and Broad-Spectrum Disease Resistance. Cell Host & Microbe. 2016, 20(6):758-769.

40. Zhang Q(#), Li Y, Xu T, Srivastava AK, Wang D, Zeng L, Yang L, He L, Zhang H, Zheng Z, Yang D-L, Zhao C, Dong J, Gong Z, Liu R, Zhu JK(*). The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism. Cell Discovery. 2016, 2:16027.

41. Wan Q(#), Guan X(#), Yang N, Wu H, Pan M, Liu B, Fang L, Yang S, Hu Y, Ye W, Zhang H, Ma P, Chen J, Wang Q, Mei G, Cai C, Yang D, Wang J, Guo W, Zhang W, Chen X(*), Zhang T(*). Small interfering RNAs from bidirectional transcripts of GhMML3_A12 regulate cotton fiber development. New Phytologist. 2016, 210(4):1298-1310.

42. Xu J(#), Zhang L, Yang D-L, Li Q, He Z(*). Thymidine kinases share a conserved function for nucleotide salvage and play an essential role in Arabidopsis thaliana growth and development. New Phytologist. 2015, 208(4): 1089-1103.

43. Feng Z(#), Mao Y, Xu N, Zhang B, Wei P, Yang D-L, Wang Z, Zhang Z, Zheng R, Yang L, Zeng L, Liu X, Zhu JK(*).Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. PNAS. 2014, 111(12):4632-4637.

44. Feng Z(#), Zhang B(#), Ding W, Liu X, Yang D-L, Wei P, Cao F, Zhu S, Zhang F, Mao Y, Zhu JK(*). Efficient genome editing in plants using a CRISPR/Cas system. Cell Research. 2013, 23(10):1229-1232.

45. Yan W(#), Ye S(#),, Jin Q, Zeng L, Peng Y, Yan D, Yang W, Yang D-L, He Z(*), Dong Y(*), Zhang X(*). Characterization and mapping of a novel mutant sms1 (senescence and male sterility 1) in rice. J Genet Genomics. 2010, 37(1):47-55.

46. Yuan Y(#), Zhong S, Li Q, Zhu Z, Lou Y, Wang L, Wang J, Wang M, Li Q, Yang D-L, He Z(*).Functional analysis of rice NPR1-like genes reveals that OsNPR1/NH1 is the rice orthologue conferring disease resistance with enhanced herbivore susceptibility. Plant Biotechnology Journal. 2007, 5(2):313-324.