Yinong Yang, Ph.D.

Areas of Interest

Molecular plant-pathogen interactions; CRISPR/Cas-enabled genome editing, precision breeding and disease diagnostics.

Program Interests

My research program aims to understand the molecular mechanism of plant-pathogen interactions and to advance CRISPR/Cas technologies for genome engineering, precision breeding and disease diagnostics.

1. Unraveling novel mechanisms of host immunity: We have worked on various aspects of molecular plant-pathogen interactions over the past 35 years, including Xanthomonas pathogenicity and avirulence genes that encode transcription activator-like effectors, pathogen-inducible plant transcription factors and protein kinases, rice defense signaling and crosstalk among salicylic acid, jasmonic acid, ethylene and abscisic acid pathways, and fungal effector-host target interactions in the rice blast pathosystem. Our current studies focus on understanding the genetic relationship between rice NLR genes Pi-ta/Pi-42 and the atypical resistance gene Ptr and their roles in mediating broad spectrum resistance against different isolates of the rice blast fungus (Magnaporthe oryzae). The Ptr gene encodes a novel membrane-associated protein with a cytoplasmic armadillo repeat domain and plays a critical role in rice blast resistance in the US and worldwide (Zhao et al. 2018, Nature Comm. 9:2039). We are particularly interested in elucidating the Ptr-mediated immune signal transduction mechanism that leads to the broad-spectrum blast resistance in rice.

2. Advancing genome editing technologies: Our group has conducted pioneering research to improve and apply CRISPR/Cas technologies, particularly in plant systems. We published one of the first CRISPR/Cas plant genome editing papers (Xie and Yang 2013, Mol. Plant 6: 1975), generated the algorithm, database and website for genome-wide prediction of specific guide RNA spacers for model plants and agricultural crops (Xie et al. 2014, Mol. Plant 7: 923; Minkenberg et al. 2019, Plant Biotech J. 17:5), and developed the polycistronic tRNA-gRNA (PTG) technology (Xie et al. 2015, PNAS 112: 3570) that has been widely used for highly efficient multiplex genome editing in plant, human, animal, and microbial systems. Our current research focuses on developing highly efficient systems for advanced prime editing (NSF PGRP Award #2428014) and large DNA fragment replacement in plants.

3. Improving precision breeding and disease diagnostics: With the aid of the mechanistic understanding of plant genetics and advanced CRISPR/Cas technologies, we have generated transgene-free, gene-edited crops with improved agronomic traits. The gene-edited mushroom from our lab was used as the first test case for USDA regulatory approval of gene-edited crops (Waltz 2016, Nature 532: 293). Our current efforts focus on improving commercial rice and tomato cultivars for enhanced quality and disease resistance via multiplex genome editing and allele replacement. In addition, we have developed Cas12a-based diagnostic assays for highly sensitive and specific detection of important bacterial pathogens such as Candidatus Liberibacter asiaticus, Ralstonia solanacearum Race 3 Biovar 2, and various phytoplasmas (Wheatley et al. 2021, Phytopathology 111:2375; Wheatley et al. 2022, Plant Disease 106: 2039).

Teaching

PPATH 505 Fundamentals of Phytopathology (4 credits, 25%, every spring),

PPATH 597 Genome Editing (3 credits, 100%, every fall)

PPATH 533 Molecular Genetics of Plant-pathogen Interaction (3 credits, 50%, every other fall)

PLBIO 513 Plant Communication and Growth Regulation (4 credits, team-taught, every spring)

PLBIO 516 Modern Techniques and Concepts in Plant Molecular Biology (2 credits, 50%, every spring)

Recent Awards and Honors

Fellow, American Phytopathological Society (2023)

Fellow, American Association for the Advancement of Science (2022)

Research Innovator Award, College of Agricultural Sciences, Penn State University (2019)

Recent Publications

Google Scholar (https://scholar.google.com/citations?user=Rgvd2Q8AAAAJ&hl=en)

Wei, W*., Yang, Y*. and Shih, J. 2026. Rapid and sensitive detection of phytoplasma diseases using a CRISPR/Cas12a DETECTR assay combined with isothermal recombinase polymerase amplification. Methods Mol Biol. Phytoplasmas 3008:63-74. doi: 10.1007/978-1-0716-5104-9_6. (*co-corresponding author)

Chen, Y., Yin, S., Yang, Y. and Xie, K. 2025. The dsRNA-binding protein OsDRB1.4 is phosphorylated by OsMPK5 and negatively regulates rice defense against Magnaporthe oryzae. Plant Journal 122: e70285. https://doi.org/10.1111/tpj.70285.

Karmakar, S., Panda, D., Panda, S., Dash, M., Saha, R., Das, P., Avinash, S.P., Shih, J., Yang, Y., Nayak, A.K., Baig, M.J. and Molla, K.A. 2024. A miniature alternative to Cas9 and Cas12: Transposon-associated TnpB mediates targeted genome editing in plants. Plant Biotechnology Journal 22:2950–2953. doi: 10.1111/pbi.14416.

Geiser, D., Martin, F. N., Espindola, A.S., Brown, J. K., Bell, T. H., Yang, Y. and Kang, S. 2023. Knowledge gaps, research needs, and opportunities in plant disease diagnostics assay development and validation. PhytoFrontiers 3:51-63.org/10.1094/PHYTOFR-05-22-0057-FI.

Hu, Y., Zhao, T., Guo, Y., Wang, M., Brachhold, K., Chu, C., Hanson, A., Kumar, S., Lin, R., Long, W., Luo, M., Ma, J. F., Miao, Y., Nie, S., Sheng, Y., Shi, W., Whelan, J., Wu, Q., Wu, Z., Xie, W., Yang, Y., Zhao, C., Lei, L., Zhu, Y.-G. and Zhang, Q. 2023. 100 essential questions for the future of agriculture. Modern Agriculture 1: 4-12.

Li, H., Zhang, Y., Wu, C., Bi, J., Chen, Y., Jiang, C., Cui, M., Chen, Y., Hou, X., Yuan, M., Xiong, L., Yang, Y.* and Xie, K.* 2022. Fine-tuning OsCPK18/OsCPK4 activity via genome editing of phosphorylation motif improves rice yield and immunity. Plant Biotechnol Journal. https://doi.org/10.1111/pbi.13905 (*co-corresponding author)

Wheatley, M. S., Qin Wang, Q., Wei, W., Bottner-Parker, K., Zhao, Y., and Yang, Y. 2022. Cas12a-based diagnostics for potato purple top disease complex associated with infection by ‘Candidatus Phytoplasma trifolii’-related strains. Plant Disease 106: 2039-2045.

Molla K. A.*, Shih, J.*, Wheatley, M. S., and Yang, Y. 2022. Predictable NHEJ insertion and assessment of HDR editing strategies in plants. Front. Genome Editing 4: 825236. doi:10.3389/fgeed. (*co-first author)

Chen, K., Ke, R., Du, M., Yi, Y., Chen, Y., Wang, X., Yao, L., Liu, H., Hou, X., Xiong, L., Yang, Y., and Xie, K. 2022. A FLASH pipeline for arrayed CRISPR library construction and the gene function discovery of rice receptor-like kinases. Molecular Plant 15:243-257.

Zhang, Y. M., Yang, Y., and Xie, K. 2021. CRISPR-Cas12a-based DNA detection for fast pathogen diagnosis and GMO test in plants. In: Islam M.T., Molla K.A. (eds) CRISPR-Cas Methods. Springer Protocols Handbooks. Humana, New York, NY. (doi.org/10.1007/978-1-0716-1657-4_15).

Reeger, J. E., Wheatley, M., Yang, Y., and Brown, K. M. 2021. Targeted mutation of transcription factor genes alters metaxylem vessel size and number in rice roots. Plant Direct 5:e00328 (doi.org/10.1002/pld3.328).

Wheatley, M., Duan, Y.-P., and Yang, Y. 2021. Highly sensitive and rapid detection of citrus Huanglongbing pathogen (Candidatus Liberibacter asiaticus) using Cas12a-based methods. Phytopathology 111:2375-2382.

Li, H., Wu, C., Du, M., Chen, Y., Hou, X., Yang, Y., and Xie, K. 2021. A versatile nanoluciferase toolkit and optimized in-gel detection method for protein analysis in plants. Mol Breeding 41:13 (doi.org/10.1007/s11032-021-01210-7)

Wheatley, M. and Yang, Y. 2021. Versatile applications of the CRISPR/Cas toolkit in plant pathology and disease management. Phytopathology 111:1080-1090.

Yang, X., Medford, J. I., Markel, K., Shih, P. M., De Paoli, H. C., Trinh, C. T., McCormick, A. J., Ployet, R., Hussey, S. G., Myburg, A. A., Jensen, P. E., Hassan, M. M., Zhang, J., Muchero, W., Kalluri, U. C., Yin, H., Zhuo, R., Abraham, P. E., Chen, J.-G., Weston, D. J., Yang, Y., Liu, D., Li, Y., Labbe, J., Yang, B., Lee, J. H., Cottingham, R. W., Martin, S., Lu, M., Tschaplinski, T. J., Yuan, G., Lu, H., Ranjan, P., Mitchell, J. C., Wullschleger, S. D., & Tuskan, G. A. 2020. Plant biosystems design research roadmap 1.0. BioDesign Research (doi.org/10.34133/2020/8051764)

Zeng, Z., Han, N., Liu, C., Buerte, B., Zhou, C., Chen, J., Wang, M., Zhang, Y., Tang, Y., Zhu, M., Wang, J., Yang, Y., and Bian, H. 2020. Functional dissection of HGGT and HPT in barley vitamin E biosynthesis via CRISPR/Cas9-enabled genome editing. Annals of Botany (doi.org/10.1093/aob/mcaa115)

Molla, K.A. and Yang, Y. 2020. CRISPR-Cas-mediated single base editing at more than one locus in rice genome. In: Islam M., Bhowmik P., Molla K. (eds) CRISPR-Cas Methods. Springer Protocols Handbooks. Humana, New York, NY. (doi.org/10.1007/978-1-0716-0616-2_4)

Hsieh-Feng, V. and Yang, Y. 2020. Efficient expression of multiple guide RNAs for CRISPR/Cas genome editing. aBIOTECH 1:123-134. (doi.org/10.1007/s42994-019-00014-w)

Molla, K.A., Shih, J., and Yang, Y. 2020. Single-nucleotide editing for zebra3 and wsl5 phenotypes in rice using CRISPR/Cas9-mediated adenine base editors. aBIOTECH 1:106-118. (doi.org/10.1007/s42994-020-00018-x)

Molla, K.A. and Yang, Y. 2020. Predicting CRISPR/Cas9-induced mutation for precise genome editing. Trends in Biotechnology 38:136-141. (doi.org/10.1016/j.tibtech.2019.08.002)

Osdaghi, E., Martins, S.J., Ramos-Sepulveda, L., Vieira, F.R., Pecchia, J.A., Beyer, D.M., Bell, T.H., Yang, Y., Hockett, K.L., and Bull, C.T. 2019. 100 years since Tolaas: Bacterial blotch of mushrooms in the 21^st century. Plant Disease 103:2714-2732.

Xie, S., Wang, Y., Wei, W., Li, C., Liu, Y., Qu, J., Meng, Q., Lin, Y., Yin, W., Yang,Y., and Luo, C. 2019. The Bax inhibitor UvBI-1, a negative regulator of mycelial growth and conidiation, mediates stress response and is critical for pathogenicity of the rice false smut fungus Ustilaginoidea virens. Current Genetics 65:1185-1197.

Molla, K.A. and Yang, Y. 2019. CRISPR/Cas-mediated base editing: Technical considerations and practical applications. Trends in Biotechnology 37:1121-1142.

Minkenberg, B., Zhang, J., Xie, K., and Yang, Y. 2019. CRISPR-PLANT v2: An online resource for highly specific guide RNA spacers based on improved off-target analysis. Plant Biotechnology J. 17:5-8.

Xie, K. and Yang, Y. 2019. A multiplexed CRISPR-Cas9 editing system based on the endogenous tRNA processing. Methods in Molecular Biology 1917:63-73.

Zhao, H., Wang, X., Jia, Y., Minkenberg, B., Wheatley, M., Fan, J., Jia, M. H., Famoso, A., Edwards, J.D., Wamishe, Y., Valent, B., Wang, G.-L., Yang, Y. 2018. The rice blast resistance gene Ptr encodes a novel protein and confers broad spectrum disease resistance. Nature Communications 9:2039.

Minkenberg, B., Wheatley, M., Yang, Y. 2017. CRISPR/Cas9-enabled multiplex genome editing and its application. In Donald P. Weeks and Bing Yang, editors: Gene Editing in Plants, Vol 149, PMBTS, UK: Academic Press, pp. 111-132.

Minkenberg, B., Xie, K., and Yang, Y. 2017. Discovery of rice essential genes by characterizing a CRISPR-edited mutation of closely related rice MAP kinase genes. Plant J. 89:636-648.

Dong, F., Xie, K., Chen, Y., Yang, Y.*, Mao, Y.* 2017. Polycistronic tRNA and CRISPR guide-RNA enables highly efficient multiplexed genome engineering in human cells. Biochem Biophys Res Commun. 482:889-895. (*co-corresponding author)

Lu, W., Deng, M., Guo, F., Wang, M., Zeng, Z, Han, N., Yang, Y., Zhu, M., Bian, H. 2016. Suppression of OsVPE3 enhances salt tolerance by attenuating vacuole rupture during programmed cell death and affects stomata development in rice. Rice 9:65. 

Helliwell, E.E., Wang, Q., and Yang, Y. 2016. Ethylene biosynthesis and signaling is required for rice immune response and basal resistance against Magnaporthe oryzae infection. Mol. Plant-Microbe Interact. 29:831-843.

Guo, F., Han, N., Xie, Y., Fang, K., Yang, Y., Zhu, M., Wang, J., and Bian, H. 2016. The miR393a/target module regulates seed germination and seedling establishment under submergence in rice (Oryza sativa L.). Plant Cell Environment 39:2288-2302.

Xie, K., Minkenberg, B., and Yang, Y. 2015. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA processing system. Proc. Natl. Acad. Sci. USA 112:3570-3575.

Xie, K., Minkenberg, B., and Yang, Y. 2014. Targeted gene mutation in rice using a CRISPR-Cas9 system. Bio-Protocol 4:e1225.

Xie, K., Chen, J., Wang, Q., and Yang, Y. 2014. Direct phosphorylation and activation of a mitogen-activated protein kinase by a calcium-dependent protein kinase in rice. Plant Cell 26:3077-3089.

Bai, Y., Han, N., Wu, J., Yang, Y., Wang, J., Zhu, M., and Bian, H. 2014. A transient gene expression system using barley protoplasts to evaluate microRNAs for post-transcriptional regulation of their target genes. Plant Cell Tiss Organ Cult 119: 211-219.

Wang, M., Yang, Y., and Bian, H. 2014. New genome targeting modification technology using a CRISPR-Cas system. Chinese J. Biochem Mol. Biol. 30:426-433.

Xie, K., Zhang, J. and Yang, Y. 2014. Genome-wide prediction of highly specific guide RNA spacers for the CRISPR-Cas9 mediated genome editing in model plants and major crops. Mol. Plant 7:923-926.

Xie, K. and Yang, Y. 2013. RNA-guided genome editing in plants using a CRISPR-Cas system. Mol. Plant 6:1975-1983. (Cover story)

Yang, D.L., Yang, Y., and He, Z. 2013. Roles of plant hormones and their interplay in rice immunity. Mol. Plant 6:675-685.

Helliwell, E. H., Wang, Q., and Yang, Y. 2013. Transgenic rice with inducible ethylene production exhibits broad-spectrum disease resistance to the fungal pathogens Maganporthe oryzae and Rhizhoctonia solani. Plant Biotechnology J. 11:33-42.

Yang, Y. (Editor) 2013. Methods in Molecular Biology: Rice Protocols. Humana Press Inc., Springer Science + Business Media.

Jia, Y., Liu, G., Park, D.-S., Correa-Vectoria, F., and Yang, Y. 2013. Inoculation and scoring methods for rice sheath blight disease. Methods in Molecular Biology: Rice Protocols 956:257-268.

Helliwell, E. H. and Yang, Y. 2013. Molecular strategies to improve rice disease resistance. Methods in Molecular Biology: Rice Protocols 956:285-309.

Liu, W., Xie, K., and Yang, Y. 2013. Genomic and bioinformatic resources for rice research. Methods in Molecular Biology: Rice Protocols 956:327-332.

Bian, H., Xie Y., Guo, F., Han, N., Ma, S., Zeng, Z., Wang, J., Yang, Y., and Zhu, M. 2012. Distinctive expression patterns and roles of the miRNA393⁄TIR1 homolog module in regulating flag leaf inclination and primary and crown root growth in rice (Oryza sativa). New Phytologist 196:149–161.

Yang, D.-L., Yao, J., Mei, C.-S., Tong, X.-H., Zeng, L.-J., Li, Q., Xiao, L-T., Sun, T.-P., Li, F., Deng, X.-W., Lee, C.-M., Thomashow, M., Yang, Y.*, He, Z.-H.*, and He, S. Y.* 2012. Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade. Proc. Natl. Acad. Sci. USA 109:7152-7153. (*co-corresponding author)

Patents

Yang, Y. and Xie, K. 2023. Methods and compositions for RNA-guided multiplex genome editing and other RNA technologies. (US Patent 11,702,667)

Yang, Y., Wheatley, M. S. and Wang, Q. 2023. Methods and compositions for supersensitive and specific detection of citrus greening and phytoplasma pathogens. (US Patent Application)

Yang, Y. and Xie, K. 2019. Methods and compositions for RNA-guided multiplex genome editing and other RNA technologies. (US Patents 10,308,947; International patents issued in Brazil, Canada, China, and European Union; Available for licensing in the mamalian, animal and microbial divisions)

Yang, Y. and Xie, K. 2014. Gene targeting and genetic modification of plants via RNA-guided genome editing. PCT WO2014/194190A1 and US2015/0067922A1 (US Patent Application No. 14/291,605; PCT/US2014/040220)

Yang, Y. and Xiong, L. 2008. Mitogen-activated protein kinase and method of use to enhance biotic and abiotic stress tolerance in plants. (US. Patent 7,345,219)

Felton, G., Yang, Y. and Wang, Q. 2004. Apparatus and method for increasing insect resistance in transgenic plants. (U.S. Patent Application: 20040259080).

Klessig, D.F. and Yang, Y. 1999. Novel genes associated with enhanced disease resistance in plants.  (U.S. Patent 5,939,601)