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Yiping Qi

Professor


Professor

Plant Science & Landscape Architecture 5121 Plant Sciences Building 4291 Fieldhouse Drive College Park, Maryland 20742
301 405-7682

Expertise

  • Plant genome engineering
  • Plant innate immunity
  • Plant synthetic biology

RESEARCH FOCUS

  • Plant genome engineering
  • CRISPR-Cas systems
  • Novel breeding tools
  • Plant synthetic biology
  • Plant innate immunity

Biography

Biography: 

The Qi Lab is working in the forefront of plant genome engineering and synthetic biology. We develop plant genome editing and transcriptional regulation tools based on different platforms such as TALE, CRISPR-Cas9, Cas12a and Cas12b. We disseminate such tools worldwide through Addgene. These tools not only allow for editing plant genomes, but also enable genome reprogramming at the transcriptome level. We apply these cutting-edge tools in both basic and translational research in plants to ensure food security and safety. First, we use these new genetic tools to answer some basic questions in plant immunity and resilience under stressful environments. Second, we apply multiplex genome editing tools to accelerate crop breeding and de novo crop domestication to make high yield, more nutritious and disease resistant crops. Third, we employ CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) for engineering metabolic pathways, rewiring plant immune responses and developing synthetic switches in plants toward engineering better crops. These goals can not be achieved without collaboration. We are collaborating with other researchers to apply and use these tools in many plant species including rice, maize, wheat, barley, banana, Arabidopsis, Camelina, soybean, cucumber, tomato, potato, carrot, strawberry, poplar, citrus, apple and pear.  Our recent publications can be checked out at Google Scholar. 

Education: 

Ph.D., Plant Biological Sciences, University of Minnesota-Twin cities, 2009. 

[PhD thesis: Purification and characterization of protein complexes containing the Arabidopsis disease resistance protein RPS2 (Advised by Fumiaki Katagiri)]

M.S., Biochemistry and Molecular Biology, Shanghai Jiao Tong University, 2003

B.S., Microbiology, Nankai University, 2000

Awards and Honors: 

2024, 2023, 2022, 2021, 2020Web of Science Highly Cited Researcher
2025, 2024, 2023, 2022, 2021AGNR Dean's Grantsmanship Award
2021AGNR Faculty Research Award
2021UMD Invention of the Year Award in the Life Science category
2021Blue Flame Award, Addgene
2020SIVB 2020 Young Scientist Award
2020UMD Invention of the Year Finalist
2018FFAR New Innovator in Food and Agriculture Research Award
2018NSF Plant Genome Early Career Award
2009Philip C. Hamm Memorial Scholarship, University of Minnesota
2009PBS Doctoral Dissertation Fellowship, University of Minnesota
1996-2000TOLEDO Scholarship, Nankai University
2000Excellent Student Leader, Nankai University
1999Merit Student, Nankai University
1998Merit Student, Nankai University
1997Special Scholarship, Nankai University
1996Merit Student of Jiangsu Province, China

 

Professional Work

Professional Positions Held: 

2023-presentProfessor, University of Maryland, College Park
2020-2023Associate Professor, University of Maryland, College Park
2017-2020Assistant Professor, University of Maryland, College Park
2013-2016Assistant Professor, East Carolina University, Greenville, NC
2011-2013Research Associate, University of Minnesota- Twin Cities, MN
2009-2011Post Doctoral Researcher, University of Minnesota- Twin Cities, MN

Professional Service: 

Leadership roles:

Co-Chair, DOE BER Workshop-Plant Design for a Developing Bioeconomy, Oct 2024-May 2025

Chair, Plant Biotechnology Section, Society of In Vitro Biology (SIVB), 2024-2026; 2026-2028

Chair, The 21st IUFRO Tree Biotech Conference Organizing Committee, 2024

Panel Manager, USDA-NIFA BRAG Program, 2023

Chair, Mid-Atlantic Section of American Society of Plant Biologists (MAS-ASPB), 2021-2023

Membership:

American Society of Plant Biologists (ASPB)

Advancing Science Serving Society (AAAS)

American Phytopathological Society (APS)

The Society for In Vitro Biology (SIVB)

Editorship:

Section Editor, Plant Cell Reports, 2025-

Associate Editor, Plant Biotechnology Journal, 2020-

Associate Editor,  aBiotech, 2019-

Associate Editor,  BioDesign Research, 2021-

Associate Editor,  Frontier in Genome Editing, 2019-

Editorial board, Plant Communications, 2019-

Associate Editor, Plant Cell Reports, 2019-2025

Editorial board, Journal of Genetics and Genomics, 2020-2023

Editor, MiMB book "Plant Genome Editing with CRISPR Systems: Methods and Protocols", 2019

Research

Current Research: 

Please refer to my personal website: 

https://qilab.weebly.com/research.html

Presentations

Presentations

Keynote and Plenary

1.    Oct 20, 2025. 8th Brazilian Biotechnology Congress. Natal-RN, Brazil. TITLE: Boosting Plant Regeneration and Genome Editing by CRISPR-Combo
2.    August 5, 2025. The 3rd Forest Tree Molecular Biology and Biotechnology Conference. Harbin, China. TITLE: Promoting Plant Regeneration and Genome Editing in Multiple Crops by CRISPR-Combo
3.    Nov 14, 2024. ARPA-E program meeting, San Antonio, Texas. TITLE: Progress and outlook of plant genome engineering
4.    August 2, 2023. New Frontiers-Cell To Seed: Revolutions in Breeding Technologies, Corteva Agriscience, Johnston, IA. TITLE: Development of CRISPR-Cas12a systems for genome editing in plants
5.    June 27, 2022. National Workshop-CUM-Webinar on Genome Editing, Indian National Young Academy of Sciences. TITLE: Boosting plant genome engineering: from CRISPR-Act3.0 to CRISPR-Combo 
6.    12th International Scientific Agriculture Symposium "AGROSYM 2021", Oct 7-10, 2021. Bosnia and Herzegovina. Virtual. TITLE: Cutting-Edge Crop Breeding with CRISPR-Cas genome editing technologies
7.    The 2021 Joint MAS-ASPB and UMD Plant Symposium, May 27-28, 2021. Virtual. TITLE: Development of CRISPR tools for multiplexed and large-scale plant genome engineering
8.    The 50th Brazilian Congress of Plant Pathology (BCPP), Aug 21-23, 2017, Uberlandia, Minas Gerais, Brazil. TITLE: Boosting Basic and Translational Science in Plants with Genome Editing Tools 
9.    The 14th International Symposium on Rice Functional Genomics, Sep 25-29, 2016, Montpellier, France. TITLE: Boosting basic and translational science in plants with genome editing tools

 

Research talks other than the keynote/Plenary

  1. January 13, 2026, Plant and Animal Genome Conference. San Diego, CA.  Non-Editing Applications of CRISPR-Cas Systems. TITLE: Efficient gene activation in plants by CRISPR-Act3.0 and CRISPR-Combo

  2. January 13, 2026, Plant and Animal Genome Conference. San Diego, CA.  Scaling Up: New Frontiers in Large-scale Plant Genome Engineering. TITLE: Genotype-independent genome editing in wheat via shoot apical meristem delivery

  3. January 11, 2026, Plant and Animal Genome Conference. San Diego, CA.  Development and Application of Genome Engineering and Transgenic Technology to the Agriculture. TITLE: From Single Base Pairs to Kilobases: Developing CRISPR Platforms for Tunable Targeted Deletions in Plants

  4. Nov 12, 2025. Plant Biotechnology Journal Editors’ Symposium 2025. London, UK. TITLE: Plant Genome Engineering with CRISPR-Combo Systems

  5. Nov 6, 2025. Annual Arab Asian Biotechnology Conference (AABC 2025): Desert Biotechnology and Sustaining Life in Arid regions. Bibliotheca Alexandra, Egypt. TITLE: Versatile Plant Genome Engineering by CRISPR-Combo

  6. Oct 21, 2025. 8th Brazilian Biotechnology Congress. Natal-RN, Brazil. TITLE: CRISPR-Cas12a genome editing tools for plant research and crop improvement.

  7. September 23, 2025. The Nitroplast workshop. The Gates Foundation. Seattle, WA. TITLE: Tools for plant transformation -current state of art

  8. September 15, 2025. The M. S. Swaminathan Centenary Lecture Series. India. TITLE: Genome engineering for a sustainable planet: from cereals to trees

  9. August 15, 2025. Plant Biotech Academy Seminar, Bayer. TITLE: Boosting Plant Regeneration and Genome Editing by CRISPR-Combo

  10. June 25, 2025. ASHS Plant Biotech Interest Group Webinar. TITLE: Enhancing Plant Transformation and Genome Editing with CRISPR-Combo

  11. June 9, 2025. SIVB 2025: In Vitro Biology Meeting. Norfolk, VA. TITLE: Boosting Plant Regeneration Via CRISPR Activation-based Reprogramming 

  12. June 8, 2025. SIVB 2025: In Vitro Biology Meeting. Norfolk, VA. TITLE: Investigating Off-targeting Effects of Genome Editing Technologies in Crops

  13. May 9, 2025. Department of Plant and Microbial biology, University of Minnesota, Twin Cities. TITLE: A Novel Type I-F CRISPR System Confers Kilobase-scale Deletions in Plants

  14. April 30, 2025. Department of Plant Biology. University of Illinois Urbana-Champaign, IL. TITLE: Developing Genome Engineering Tools to Advance Crop Improvement

  15. April 2, 2025. The International Plant Communications Symposium. TITLE: CRISPR-Cas12a genome editing tools for plant research and crop improvement

  16. March 31, 2025. Department of Biology, Washington University, St. Louis, MO. TITLE: Developing Genome Engineering Tools to Advance Crop Improvement

  17. February 13, 2025. College of Agriculture and Life Science, North Carolina State University. TITLE: Innovating Genome Editing:  Tools and Applications for Transforming Plant Research and Crop Improvement

  18. February 4-6, 2025. The 7th CRISPR AgBio congress. Raleigh, NC. TITLE: Boosting plant tissue culture and genome editing in diverse crops by CRISPR-Combo

  19. January 14, 2025, Plant and Animal Genome Conference. San Diego, CA.  Scaling Up: New Frontiers in Large-scale Plant Genome Engineering. TITLE: All-in-one CRISPR vectors for large-scale screens in plants

  20. January 12, 2025, Plant and Animal Genome Conference. San Diego, CA.  Development and Application of Genome Engineering and Transgenic Technology to the Agriculture. TITLE: Boosting plant tissue culture and genome editing in a variety of dicot plants by CRISPR-Combo 

  21. January 12, 2025, Plant and Animal Genome Conference. San Diego, CA.  Forest Tree workshop. TITLE: Genome-edited trees for high-performance engineered wood

  22. January 12, 2025, Plant and Animal Genome Conference. San Diego, CA.  Plant Organellar Genome Engineering workshop. TITLE: Simultaneous organellar gene editing and nuclear gene activation in plants

  23. January 5-10, 2025. Carotenoids Gordon Research Conference: Metabolism and Function of Carotenoids and Their Derivatives Across Kingdoms. Ventura, CA. TITLE: Engineering next-generation Golden Rice

  24. October 23, 2024. Overcoming the crop transformation bottleneck with CRISPR-Combo. UIC Fall Conference, Cleveland, Mississippi.

  25. August 22, 2024. Developing Genome Engineering Tools to Advance Crop Improvement. IITA, CGIAR. Nairobi, Kenya. 

  26. June 18, 2024. Plant Genome Stability and Change-EMBO Workshop. Olomouc, Czech Republic. TITLE: Overcoming the crop transformation bottleneck with CRISPR-Combo

  27. May 23, 2024. Plant Center Spring Symposium, University of Georgia. TITLE: Developing Genome Engineering Tools to Advance Crop Improvement

  28. April 16, 2024. Innovative Genomics Institute, UC-Berkeley. TITLE: Developing Genome Engineering Tools to Advance Crop Improvement

  29. March 7, 2024. aBiotech Journal Webinar. TITLE: Continuous improvement of CRISPR-Cas12a systems for genome editing in plants

  30. March 5, 2024. Recombination and Genome Editing in Plants. Federation of American Societies for Experimental Biology (FASEB). TITLE: Versatile plant genome engineering with CRISPR-Combo systems.

  31. February 22, 2024. 6th CRISPR AgBio Congress. Theme: Engineer the Next Generation of Agriculture, Raleigh, NC. TITLE: Advancing CRISPR-Cas12a Technologies for Genome Editing in Plants.

  32. February 20, 2024. Enhancing the Global Food System’s Resilience to Biological Threats. Scowcroft Institute of International Affairs, The BUSH School, TAMU. TITLE: Genome Engineering for Disease Resistance and Pathogen Detection in Crops. 

  33. January 30, 2024, Maximizing Agriculture to Enhance Nutrient Composition to Better Fulfill Dietary Recommendations. Workshop by National Academies of Sciences, Engineering, and Medicine. TITLE: Genome-Edited Foods.

  34. January 14, 2024, Plant and Animal Genome Conference. Organellar Genome Engineering Workshop. San Diego, CA. TITLE: Targeted base editing in the plastid genome with monomeric TALE-based deaminases

  35. January 14, 2024, Plant and Animal Genome Conference. Development and Application of Genome Engineering and Transgenic Technology to the Agriculture Workshop. San Diego, CA. TITLE: Rapid Evolution of CRISPR-Cas12a Technologies for Genome Engineering in Crops

  36. October 13, 2023. Department of Plant Biology, Rutgers University, NJ. TITLE: Developing Genome Engineering Tools to Advance Crop Improvement

  37. September 29, 2023. School of Life Sciences, University of Nevada, Las Vegas, NV. TITLE: Developing Genome Engineering Tools to Advance Crop Improvement

  38. July 13, 2023. Gates Masterclass on construct design for crop engineering, gene regulation and genome editing. Online. TITLE: CRISPR-Combo enabled simultaneous genome editing and gene activation

  39. March 17, 2023. Department of Genetics and Biochemistry. Clemson University, Clemson, SC. TITLE: Developing Genome Engineering Tools to Advance Crop Improvement

  40. February 14,2023. The 5th Annual CRISPR AgBio Congress, San Diego, CA. TITLE: Off-target Effects of Multiplexed Genome Editing & Base Editing in Plants

  41. February 7, 2023. Center for Computational & Integrative Biology, Rutgers-Camden, New Jersey. TITLE: Developing Genome Engineering Tools to Advance Crop Improvement

  42. January 19, 2023. International Seminar and Workshop on CRISPR/Cas-based Plant Functional Genomics and Computational Modeling, Jan 18-21, 2023. Jorhat, Assam, India. TITLE: Boosting plant genome editing with a versatile CRISPR-Combo system

  43. January 15, 2023. Plant and Animal Genome Conference, Jan 13-18, 2023. San Diego, CA. TITLE: Boosting plant genome editing with a versatile CRISPR-Combo system

  44. January 13, 2023. Plant and Animal Genome Conference, Jan 13-18, 2023. San Diego, CA. TITLE: Development and Assessment of Highly Efficient Cytosine and Adenine Base Editors in Plants

  45. November 18, 2022. The 2nd International Symposium for Horticultural Plant Biology and Biotechnology. Beijing, China. TITLE: A CRISPR-Combo System for Accelerating Genome Editing-Based Breeding in Plants. 

  46. October 31, 2022. The 5th International Conference on CRISPR Technologies. Berkeley, CA. TITLE: CRISPR-Combo Enables Speed Breeding and Improved Tissue Culture in Plants

  47. October 24, 2022. The 9th Plant Genomics and Gene Editing Congress (USA). Raleigh, NC. TITLE: A Versatile CRISPR-Combo System to Boost Plant Genome Editing

  48. September 14, 2022. The Center of Soybean Research of the Chinese University of Hong Kong & USDA’s Agricultural Trade Office (ATO) in Hong Kong. TITLE: Cutting-Edge Crop Breeding with CRISPR-Cas genome editing technologies

  49. August 30, 2022. Rubber Research Institute, Chinese Academy of Tropical Agricultural Science. TITLE: Progress and application of plant gene editing

  50. August 10, 2022. The 3rd International Symposium of Horticulture and Plant Biology, Huazhong Agriculture University, Wuhan. TITLE: Boosting Plant Genome Editing With a Versatile CRISPR-Combo System

  51. July 29, 2022. 2022 International Symposium on Plant Biotic Interactions and Plant Health, Wuhan, China. TITLE: Boosting plant genome editing with a versatile CRISPR-Combo system

  52. July 10, 2022. Plant Biology 2022. ASPB and CSPB/SCBV. Portland, USA. TITLE: A versatile CRISPR-Combo system for boosting plant genome editing

  53. July 7, 2022. The 20th IUFRO Tree Biotech Meeting, Harbin, China. TITLE: A CRISPR-combo Approach for Boosting Tissue Culture and Regeneration of Genome-edited Poplar Trees

  54. June 29, 2022. PlantEd COST Action - plant genome editing. European Cooperation in Science and Technology. TITLE: Boosting plant genome editing with a versatile CRISPR-Combo system

  55. June 7, 2022. 2022 In Vitro Biology Meeting, San Diego, CA. TITLE: A CRISPR-combo Approach for Speed Breeding and Regeneration of Genome-edited Plants

  56. June 5, 2022. 2022 In Vitro Biology Meeting, San Diego, CA. TITLE: Developing Highly Efficient Base Editing and Prime Editing Tools in Plants

  57. May 29, 2022. The 23rd Penn State Symposium in Plant Biology -- RNA Biology. State College, PA. TITLE: Boosting plant genome editing with a versatile CRISPR-Combo system

  58. May 25, 2022. Novel Crop Breeding Techniques: Towards more sustainable agriculture (http://plantepigenetics.ch/NBT2022/), ERC Consolidator Project BUNGEE 725701. TITLE: Boosting plant genome editing with a versatile CRISPR-Combo system

  59. February 10, 2022. Dale Bumpers National Rice Research Center-USDA-ARS. Stuttgart, AR. TITLE: Development of CRISPR tools for multiplexed and large-scale genome engineering in Plants 

  60. January 10, 2022. Plant and Animal Genome XXIX Conference, Jan 8-12, 2022. San Diego, CA. TITLE: Developing and Improving Precise Base Editing Tools in Crops

  61. 2021 ASA, CSSA,SSSAINTERNATIONALANNUAL MEETING NOVEMBER 7-10 | SALTLAKE CITY, UT. Symposium--Frontiers in Plant Genome Editing for Crop Improvement: TITLE: Improving Precise Base Editing Tools in Crops

  62. September 15, 2021. 2nd Congress of Geneticists in Bosnia and Herzegovina with International Participation. TITLE: Cutting-Edge Crop Breeding with CRISPR-Cas Technologies

  63. September 14, 2021. Virtual Workshop on Advanced Biotechnology in Bosnia and Herzegovina. TITLE: Cutting-Edge Crop Breeding with CRISPR-Cas Technologies- a comprehensive overview of CRISPR technologies and their applications in agriculture [Virtual presentation]

  64. September 2, 2021. National Center for Genome Editing in Agriculture, Israel. TITLE: Development of CRISPR tools for multiplexed and large-scale genome engineering in Plants [Virtual presentation]

  65. August 17, 2021. CTC Genomics, St. Louis, Missouri. TITLE: Development of CRISPR tools for multiplexed and large-scale genome engineering in Plants

  66. July 28, 2021. Genome Writers Guild (GWG) Virtual Conference. University of Minnesota. TITLE: Development of tools for multiplexed plant genome engineering

  67. July 21, 2021. Reliance Industries Limited (RIL) R&D Community Webinar Series. TITLE: Development of CRISPR tools for multiplexed and large-scale genome engineering in Plants [Virtual presentation]

  68. June 6, 2021. SIVB 2021: In Vitro OnLine. Session: Variables Controlling Successful Gene Editing in Plants/New Tools. TITLE: Optimizing CRISPR-Cas Systems for Efficient Multiplexed Genome Engineering in Plants

  69. March 31, 2021. Genome Editing Webinar series organized by BioDesign Research and Nanjing Agriculture University in China. TITLE: Improved CRISPR tools for multiplex plant genome engineering 

  70. March 25, 2021. Hands-on Laboratory Course on CRISPR-Cas Gene Editing. SGT University, Gurgaon & Alliance of Bioversity International and CIAT, Asia-India, New Delhi, India. TITLE: Multiplex editing with CRISPR-Cas12a [Virtual presentation]

  71. March 9, 2021. Keystone eSymposia- Plant Genome Engineering: From Lab to Field. TITLE: Expanding the Targeting Range of CRISPR in Plants

  72. March 3, 2021. 8th Plant Genomes & Gene Editing Congress: USA. Virtual Conference. TITLE: Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems

  73. February 25, 2021. Department of Biology, East Carolina University, Greenville, NC. TITLE: Improved CRISPR tools for multiplex plant genome engineering

  74. January 19, 2021. Cellfies Symposium, Hosted by Bayer AgConnect. TITLE: Developing Efficient CRISPR Systems for Multiplexed Genome Engineering in Plants [Virtual presentation]

  75. October 20, 2020. 2nd International Plant Genetics and Genomics Symposium-IPGG, Assiut University, Egypt. TITLE: Improved CRISPR tools for multiplex plant genome engineering [Virtual presentation]

  76. September 17, 2020. Department of Biology, University of Pennsylvania, PA. TITLE: Improved CRISPR tools for multiplex plant genome engineering [Virtual presentation]

  77. September 14, 2020. International workshop on plant genome editing, Paris, France. TITLE: Development of Precise Base Editing Systems in Plants [Virtual presentation]

  78. June 11, 2020. Center for Desert Agriculture, KAUST, Saudi Arabia. TITLE: Plant Genome Editing with CRISPR Systems [Virtual presentation]

  79. June 8, 2020. 2020 World Congress on In Vitro Biology, San Diego. TITLE: CRISPR-Cas12b Genome Engineering Systems in Plants [Virtual presentation]

  80. May 11, 2020. Inari Agriculture, Cambridge, MA. TITLE: Precise Plant Genome Editing [Virtual presentation]

  81. February 5, 2020. FFAR Foster Our Future. Washington DC. TITLE: Rapid Evolution of CRISPR Systems for Plant Genome Editing

  82. January 13, 2020. PAG XXVIII - Plant & Animal Genome Conference, Jan 11-15, 2020. San Diego, CA. TITLE: CRISPR-Cas12 Genome Engineering Systems in Plants

  83. November 6, 2019. Syngenta, Research Triangle Park, NC. TITLE: Plant genome engineering with CRISPR systems

  84. November 6, 2019. Pairwise Plants, Durham, NC. TITLE: Plant genome engineering with CRISPR systems

  85. November 4, 2019. 7th Plant Genomes & Gene Editing Congress: USA. Raleigh, NC. TITLE: Rapid evolution of CRISPR systems for plant genome editing 

  86. October 18, 2019. Department of Plant science and Landscape Architecture, University of Connecticut, Storrs, CT. TITLE: Plant genome editing with CRISPR-Cas9 and Cas12 systems

  87. October 14, 2019. Department of Plant Science, Penn State University, State College, PA. TITLE: Plant genome editing with CRISPR-Cas9 and Cas12 systems 

  88. September 6, 2019. NSF PGRP’s 22nd Annual Awardee Meeting, Alexandra, VA. TITLE: Improving CRISPR activation systems for plant genome reprogramming

  89. August 5, 2019. Plant Biology Annual Meeting |2019. San Jose, CA. TITLE: CRISPR-Cas12a Systems for Plant Genome Engineering

  90. June 25, 2019. CRISPR&NBT, AgroBio Congress 2019. San Diego, CA. TITLE: CRISPR-Cas Systems for Plant Genome Editing & Transcriptional Regulation

  91. June 14, 2019. Inaugural New Tech Talk at USDA-FAS, Washington, DC. TITLE: Cutting-edge Crop Breeding with CRISPR-Cas technologies

  92. June12, 2019. UF/IFAS Citrus Research and Education Center, University of Florida, Lake Alfred, FL. TITLE: Developing CRISPR-Cas Systems for Plant Genome Engineering

  93. June11, 2019. The 2019 Society for In Vitro Biology (SIVB) Meeting, Tampa, FL. TITLE: Activity and Specificity of CRISPR-Cas9 and Cas12a Systems in Plant Genome Editing

  94. April 8, 2019. Department of Plant, Soil and Microbial Sciences and Plant Resilience Institute, Michigan State University, MI. TITLE: Making productive and resilient crops by genome editing

  95. February 14, 2019. Department of Plant & Microbial Biology, University of California-Berkeley, CA. TITLE: Making productive and climate-resilient crops by genome engineering

  96. January 13, 2019. PAG XXVII - Plant & Animal Genome Conference, Jan 12-16, 2019. San Diego, CA. TITLE: Plant genome engineering with Cas9 and Cas12a: Exploring expression systems

  97. November 14, 2018. UCSD-Food & Fuel for the 21st Century-CRISPR in Plant Biology workshop. University of California-San Diego, La Jolla, CA. TITLE: Promise and challenges of CRISPR-Cas9 and Cas12a systems in plant genome editing

  98. November 5, 2018. Genome Editing for Crop Improvement Symposium, 2018 The American Society of Agronomy & the Crop Science Society of America (ASA&CSSA) International Meeting: "Enhancing Productivity in a Changing Climate". Baltimore, MD. TITLE: Activity and specificity of CRISPR-Cas9 and Cpf1 (Cas12a) systems in plant genome editing

  99. October 8, 2018. Botany seminar series, Yale University, New Haven, CT. TITLE: Plant genome editing with CRISPR-Cas9 and Cas12a

  100. October 4, 2018. Global Challenges: Building Healthy Food Systems Symposium. Session: Innovation Solutions for Food Systems. UMD, College Park, MD. TITILE: Precision breeding for crop improvement by genome editing

  101. October 1, 2018. Inari Agriculture, Cambridge, MA. TITLE: Plant genome editing with CRISPR-Cas systems

  102. September 3. CRISPRing-A New Beginning of Genetic Improvement of Plants and Microbes. Budapest, Hungary. TITLE: Revolutionizing plant breeding with CRISPR-Cas genome editing tools

  103. August 14, 2018. Mid-Atlantic Plant Molecular Biology Society (MAPMBS) 35th Annual Meeting. Laurel, MD. TITLE: Plant genome editing with CRISPR-Cpf1 systems

  104. July 25, 2018. International Symposium on Forest Tree Molecular Biology and Biotechnology (FTMB2018), Harbin, China. TITLE: The promise and challenges of plant genome editing

  105. May 10, 2018. The 2018 Loomis/CBC Symposium, Iowa State University, Ames, Iowa. TITLE: CRISPR-Cpf1 based plant genome editing

  106. May 2, 2018, The Hoover family invited seminar speaker, Department of Horticultural Science, University of Minnesota, Twin Cities. TITLE: Revolutionizing Plant Basic and Translational Science with Genome Editing Tools

  107. April 10, 2018. Plant Breeding & Genetics Section, Cornell University, Ithaca, NY. TITLE: The promise and challenges of plant genome editing

  108. Mar 26, 2018. GARNet Gene Editing Workshop, University of Bristol, Bristol, UK. TITLE: Use of CRISPR-Cpf1 for plant genome editing

  109. Mar 21, 2018. KWS Gateway Research Center, St. Louis, Missouri. TITILE: Plant genome editing using CRISPR-Cpf1

  110. Mar 20, 2018. Donald Danforth Plant Science Center, Creve Coeur, Missouri. TITLE: Rapid evolution of tools for plant genome editing and transcriptional regulation

  111. PAG XXVI - Plant & Animal Genome Conference, Jan 13-17, 2018. San Diego, CA. TITLE: Efficient Cas9 and Cpf1 systems for plant genome editing and transcriptional regulation

  112. Jan 10, 2018. Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel. TITLE: Current progress of plant genome editing

  113. TAU-UMD Virology Workshop, Jan 8-9, 2018. Tel Aviv University, Israel. TITLE: Boosting basic and translational science in plants with genome editing tools

  114. Agricultural Genomics 2017: Functional Genomics toward Green Crops for Sustainable Agriculture, Oct 25-27, 2017, Wuhan, China. TITLE: Developing plant epigenome editing tools for advancing basic and translational research

  115. 2017 Mid Atlantic Plant Molecular Biology Society (MAPMBS) 34th Annual Meeting, Aug 14-15, Laurel, MD. TITLE: Robust Transcriptional Activation in Plants Using Multiplexed CRISPR-ACT2.0 and mTALE-ACT Systems

  116. Aug 1, 2017, International Rice Research Institute (IRRI), Los Banos, Philippines. TITLE: The promise and challenges of plant genome editing 

  117. XIX International Botanical Congress (IBC 2017), July 23-29, Shenzhen, China. TITLE: A CRISPR-Cpf1 System for Efficient Genome Editing and Transcriptional Repression in Plants

  118. April 21, 2017, Center for Plant Cell Biology, University of California-Riverside, CA. TITLE: Revolutionizing Plant Basic and Translational Science with Genome Editing Tools 

  119. CRISPR-AgBio, Precision Genome Editing Congress, April 18-20, San Diego, CA. TITLE: Improving Multiplex CRISPR Systems for Plant Epigenome Editing

  120. Mar 23, 2017, Syngenta Biotechnology, Research triangle park, NC. TITLE: Plant genome editing with CRISPR systems

  121. Mar 22, 2017, Student invited speaker, Department of Biology, UNC-Greensboro, NC. TITLE: Boosting Basic and Translational Science in Plants with Genome Editing Tools

  122. Genome-Enabled Accelerated Crop Breeding Workshop, Oct 16-19,2016, The Banbury Center, Cold Spring Harbor Laboratory. TITLE: Multiplexing Systems for Plant Genome Editing and Transcriptional Regulation

  123. July 21, 2016, Brody School of Medicine, East Carolina University. TITLE: Discovering Hidden Value in the Laboratory

  124. Oct 16, 2015, BASF Plant Science, Research Triangle Park, NC. TITLE: Developing tools for plant genome editing 

  125. June 22, 2015, Shandong Academy of Agricultural Sciences (SAAS), Jinan, Shandong, China. TITLE: Precise genome editing using sequence-specific nucleases

  126. June 15, 2015, Shanghai Jiao Tong University, Shanghai, China. TITLE: Developing tools for plant genome editing and transcriptional regulation

  127. June 11, 2015, Yangzhou University, Yangzhou, China. TITLE: Developing tools for plant genome editing and transcriptional regulation

  128. May 31, 2015, In Vitro Biology Meeting 2015, Tucson, Arizona. TITLE: Developing toolkits for plant genome editing and transcriptional regulation

  129. May 7, 2015, Gene REG Seminar Series at DHMRI, Kannapolis, NC. TITLE: Developing tools for plant genome editing and transcriptional regulation

  130. Mar 17, 2015, Malopolska Center of Biotechnology, Krakow, Poland. TITLE: Developing tools for plant genome editing and gene regulation with engineered DNA binding proteins 

  131. Mar 16, 2015, GIN (global-innovative-networked) by USDA and Klaster LifeScience, Krakow, Poland. TITLE: Precise genome editing using sequence-specific nucleases

  132. Sep 2, 2014, Department of Plant & Microbial Biology, North Carolina State University, Raleigh, North Carolina. TITLE: Developing Protein Complex Purification and Genome Engineering Tools for Studying Plant Disease Resistance 

  133. July 29, 2014, Syngenta Biotechnology, Research Triangle Park, North Carolina. TITLE: Genome engineering for better crops

  134. 21st International Conference on Plant Growth Substances, June 18-22, 2013, Shanghai, China. TITLE:  Zinc Finger Nuclease (ZFN) and TAL Effector Nuclease (TALEN)-mediated Genome Modifications in Arabidopsis

  135. June 2013, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China, June 18th. TITLE: Developing Protein Purification and Genome Engineering Tools for Studying Plant Disease Resistance

  136. The 27th Annual Retreat of Plant Molecular Biology Consortium, Sept 13-15, 2013. Asheville, North Carolina. TITLE: Zinc Finger Nuclease (ZFN) and TAL Effector Nuclease (TALEN)-mediated Genome Modifications in Arabidopsis

  137. Annual Meeting of the American Society of Plant Biologists, July 20-24, 2012, Austin, Texas. TITLE: Enhancing Zinc Finger Nuclease-Mediated Genome Modification in Arabidopsis by Manipulating DNA Repair Pathways

  138. BIT’s 4th Annual Protein and Peptide Conference (PepCon-2011), March 23-25, 2011, Beijing, China. TITLE: Plant Genome Engineering Using Zinc Finger Nucleases (ZFNs)

Teaching

Plant Genetics (PLSC 411)

 

Plant and Fungal Metabolism (PLSC 404)

Publications

Selected Peer-Reviewed Journal Publications: 

* = corresponding/senior author; # = graduate student, post-doc or visiting scholar advised by Qi; ## = undergraduate or high school student advised by Qi; † = equal contribution. 

  1. Aytug Tuncel#,†, Changtian Pan†, Joshua Clem#, Degao Liu, Yiping Qi*. CRISPR–Cas applications in agriculture and plant research. Nature Reviews Molecular Cell Biology, 26, pages 419–441 (2025). https://www.nature.com/articles/s41580-025-00834-3 

  2. Sophia G Zebell, Carlos Martí-Gómez, Blaine Fitzgerald, Camila P Cunha, Michael Lach, Brooke M Seman, Anat Hendelman, Simon Sretenovic#, Yiping Qi, Madelaine Bartlett, Yuval Eshed, David M McCandlish, Zachary B Lippman. Cryptic variation fuels plant phenotypic change through hierarchical epistasis. Nature. September 2025. https://www.nature.com/articles/s41586-025-09243-0 

  3. Connor Thorpe, Weifeng Luo#, Qing Ji, Alan L Eggenberger, Aline S Chicowski, Weihui Xu, Ritinder Sandhu, Keunsub Lee, Steven A Whitham, Yiping Qi, Kan Wang, Shan Jiang. Enhancing biolistic plant transformation and genome editing with a flow guiding barrel. Nature Communications. July 2025. https://www.nature.com/articles/s41467-025-60761-x  

  4. Yanhao Cheng#, Gen Li#, Aileen Qi##, Changtian Pan#, Doris Wang##, Sophia Ge##, Yiping Qi*. A comprehensive all-in-one CRISPR toolbox for large-scale screens in plants.  Plant Cell. Volume 37, Issue 4, April 2025, koaf081, https://doi.org/10.1093/plcell/koaf081 

  5. Yu Liu, Gen Li, Yimin Mao, Yue Gao, Minhua Zhao, Alexandra Brozena, Derrick Wang, Samuel von Keitz, Taotao Meng, Hoon Kim, Xuejun Pan, Yiping Qi, Liangbing Hu. Genome-edited trees for high-performance engineered wood. Matter. 2024. https://www.cell.com/matter/abstract/S2590-2385(24)00396-5

  6. Tingting Fan, Yanhao Cheng, Yuechao Wu, Shishi Liu, Xu Tang, Yao He, Shanyue Liao, Xuelian Zheng, Tao Zhang*, Yiping Qi*, Yong Zhang*. High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants. Nature Communications.  2024. volume 15, Article number: 5103. https://www.nature.com/articles/s41467-024-49473-w 

  7. Zhaohui Zhong, Guanqing Liu, Zhongjie Tang, Shuyue Xiang, Liang Yang, Lan Huang, Yao He, Tingting Fan, Shishi Liu, Xuelian Zheng, Tao Zhang, Yiping Qi*, Jian Huang*, Yong Zhang*. Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system. Nature Communications. 2023 Sep 29;14(1):6102. https://www.nature.com/articles/s41467-023-41802-9 

  8. Changtian Pan#, Yiping Qi*. CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding. Nature Protocols. 2023. https://www.nature.com/articles/s41596-023-00823-w 

  9. Jianping Zhou, Guanqing Liu, Yuxin Zhao, Rui Zhang, Xu Tang, Ling Li, Xinyu Jia,Yachong Guo, YueChao Wu, Yangshuo Han, Yu Bao, Yao He, Han Yang, Xuelian Zheng, Tao Zhang*, Yiping Qi*, Yong Zhang*. An efficient promoter editing system for crop improvement. Nature Plants. 2023. 9: 588–604. https://www.nature.com/articles/s41477-023-01384-2

  10. Aytug Tuncel#, Changtian Pan, Thorben Sprink, Ralf Wilhelm, Rodolphe Barrangou, Li Li, Patrick M Shih, Rajeev K Varshney, Leena Tripathi, Joyce Van Eck, Kranthi Mandadi, Yiping Qi*. Genome-edited foods. Nature Reviews Bioengineering. Published: 04 October 2023. https://www.nature.com/articles/s44222-023-00115-8 

  11. Liyang Zhang, Gen Li#, Yingxiao Zhang#, Yanhao Cheng#, Steve Glenn, Michael Collingwood, Nicole Bode, Sarah Beaudoin, Christopher Vakulskas*, Yiping Qi*. Boosting genome editing efficiency in human cells and plants with novel Lbcas12a variants. Genome Biology. 2023. 24, Article number: 102. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02929-6 

  12. Changtian Pan#, Gen Li#, Aimee A. Malzahn#, Benjamin Leyson##, Simon Sretenovic#, Yanhao Cheng#, Filiz Gurel#, Gary D. Coleman, Yiping Qi*. Boosting plant genome editing with a versatile CRISPR-Combo system. Nature Plants, 2022. 8(5):513-525. https://www.nature.com/articles/s41477-022-01151-9 

  13. Changtian Pan#, Xincheng Wu##, Kasey Markel, Aimee A. Malzahn#, Neil Kundagrami##, Simon Sretenovic#, Yingxiao Zhang#, Yanhao Cheng#, Patrick M Shih, Yiping Qi*. CRISPR-Act3.0 for highly efficient multiplexed gene activation in plants. Nature Plants, 2021. https://www.nature.com/articles/s41477-021-00953-7 

  14. Yingxiao Zhang#, Ɨ, Qiurong RenƗ, Xu Tang,Ɨ, Shishi Liu, Aimee A. Malzahn#,Jiaheng Wang, Desuo Yin#, Changtian Pan#, Mingzhu Yuan, Lan Huang, Han Yang, Yuxin Zhao, Qing Fang, Xuelian Zheng, Li Tian, Yanhao Cheng, Ysa Le##, Bailey McCoy##, Lidiya Franklin##, Jeremy D. Selengut#, Stephen M. Mount, Qiudeng Que, Yong Zhang*, Yiping Qi*. Expanding the scope of plant genome engineering with novel Cas12a orthologs and highly multiplexable editing systems. Nature Communications, 2021. https://www.nature.com/articles/s41467-021-22330-w

  15. Kutubuddin Molla*, Simon Sretenovic#, Kailash C Bansal, Yiping Qi*. Precise plant genome editing with base editors and prime editors. Nature Plants, 2021, 7: 1166-1187. https://www.nature.com/articles/s41477-021-00991-1

  16. Qiurong Ren Ɨ, Simon Sretenovic#, Ɨ, Shishi LiuƗ, Xu Tang, Lan Huang, Yao He, Li Liu, Yachong Guo, Zhaohui Zhong, Guanqing Liu, Yanhao Cheng#, Xuelian Zheng, Changtian Pan#, Desuo Yin#, Yingxiao Zhang#, Wanfeng Li, Liwang Qi, Chenghao Li, Yiping Qi*, Yong Zhang*. PAM-less plant genome editing using a CRISPR–SpRY toolbox. Nature Plants, 2021, 7: 25-33. https://www.nature.com/articles/s41477-020-00827-4 

  17. Xu Tang Ɨ, Simon Sretenovic#, Ɨ, Qiurong Ren Ɨ, Xinyu Jia, Mengke Li, Tingting Fan Desuo Yin#, Shuyue Xiang, Yachong Guo, Li Liu, Xuelian Zheng, Yiping Qi*, Yong Zhang*. Plant Prime Editors Enable Precise Gene Editing in Rice Cells, Molecular Plant, 2020. https://doi.org/10.1016/j.molp.2020.03.010 

  18. Meiling Ming#,Ɨ, Qiurong RenƗ, Changtian Pan#,Ɨ, Yao He Ɨ, Yingxiao Zhang#, Ɨ, Shishi Liu, Zhaohui Zhong, Jiaheng Wang, Aimee A. Malzahn#, Jun Wu, Xuelian Zheng, Yong Zhang*, Yiping Qi*. CRISPR-Cas12b enables efficient plant genome engineering. Nature Plants, 2020, 6(3):202-208. https://www.nature.com/articles/s41477-020-0614-6

  19. Zhaohui Zhong Ɨ, Simon Sretenovic Ɨ,#, Qiurong RenƗ, Lijia Yang, Yu Bao, Caiyan Qi, Mingzhu Yuan, Yao He, Shishi Liu, Xiaopei Liu, Jiaheng Wang, Lan Huang,Yan Wang, Dibin Baby##, David Wang##, Tao Zhang, Yiping Qi*, Yong Zhang*. Improving plant genome editing with high-fidelity xCas9 and non-canonical PAM-targeting Cas9-NG. Molecular Plant. 2019, 12(7):1027-1036. https://doi.org/10.1016/j.molp.2019.03.011

  20. Yingxiao Zhang#, Aimee A Malzahn#, Simon Sretenovic# and Yiping Qi*. The emerging and uncultivated potential of CRISPR technology in plant science. Nature Plants, 2019, 5(8):778-794. https://www.nature.com/articles/s41477-019-0461-5

  21. Xu TangƗ, Guanqing LiuƗ, Jianping ZhouƗ, Qiurong Ren, Qi You, Li Tian, Xuhui Xin, Zhaohui Zhong, Binglin Liu, Xuelian Zheng, Dengwei Zhang, Aimee Malzahn#, Zhiyun Gong, Yiping Qi*, Tao Zhang*, Yong Zhang*. A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. Genome Biology. 2018, 19 (1) :84 https://doi.org/10.1186/s13059-018-1458-5

  22. Zhaohui Zhong†, Yingxiao Zhang†,#, Qi You†, Xu Tang, Qiurong Ren, Shishi Liu, Lijia Yang, Yan Wang, Xiaopei Liu, Binglin Liu, Tao Zhang, Xuelian Zheng, Ysa Le##, Yong Zhang*, Yiping Qi*. Plant genome editing using FnCpf1 and LbCpf1 nucleases at redefined and altered PAM sites. Molecular Plant. 2018, 11 (7): 999-1002. https://doi.org/10.1016/j.molp.2018.03.008 

  23. Levi G. Lowder#, Jianping Zhou, Yingxiao Zhang#, Aimee Malzahn#, Zhaohui Zhong, Tzung-Fu Hsieh, Daniel F. Voytas, Yong Zhang, Yiping Qi*.Robust transcriptional activation in plants using multiplexed CRISPR-Act2.0 and mTALE-Act systems. Molecular Plant. 2018, 11(2):245-256. https://doi.org/10.1016/j.molp.2017.11.010 

  24. Xu Tang†, Levi G. Lowder†,#, Tao Zhang, Aimee A. Malzahn#, Xuelian Zheng, Daniel F. Voytas, Zhaohui Zhong, Yiyi Chen, Qiurong Ren, Qian Li, Elida R. Kirkland, Yong Zhang*, Yiping Qi*. A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. Nature Plants, 2017. https://www.nature.com/articles/nplants201718

  25. Xu Tang, Xuelian Zheng, Yiping Qi, Dengwei Zhang, Yan Cheng, Aiting Tang, Daniel F Voytas, Yong Zhang. A single transcript CRISPR-Cas9 system for efficient genome editing in plants. Molecular Plant, 2016, 9 (7): 1088-1091. https://doi.org/10.1016/j.molp.2016.05.001

  26. Levi G. Lowder†#, Dengwei Zhang†, Nicholas J. Baltes, Joseph W. Paul, III##, Tang Xu, Xuelian Zheng, Daniel F. Voytas , Tzung-Fu Hsieh, Yong Zhang*, Yiping Qi*. A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation. Plant Physiology, 2015, 169(2):971-85. https://doi.org/10.1104/pp.15.00636

  27. Michelle L. Christian†, Yiping Qi†, Yong Zhang and Daniel F. Voytas. Targeted mutagenesis in Arabidopsis thaliana using Engineered TAL effector nucleases. G3, 2013, 3 (10) 1697-1705. https://doi.org/10.1534/g3.113.007104

  28. Yiping Qi, Xiaohong Li, Yong Zhang, Feng Zhang, Colby Starker, Nicholas J. Baltes, Jeffry D. Sander, Deepak Reyon, Drena Dobbs, J Keith Joung, Daniel F. Voytas. Targeted deletion and inversion of tandemly arrayed genes in Arabidopsis thaliana using zinc finger nucleases. G3, 2013, 3 (10) 1707-1715. https://doi.org/10.1534/g3.113.006270

  29. Yiping Qi†, Yong Zhang†, Feng Zhang, Joshua A. Baller, Spencer C. Cleland#, Yungil Ryu#, Colby G. Starker and Daniel F. Voytas. Increasing frequencies of site-specific mutagenesis and gene targeting in Arabidopsis by manipulating DNA repair pathways. Genome Research, 2013, 23 (3):547-54. https://genome.cshlp.org/content/23/3/547.short

  30. Yong Zhang, Feng Zhang, Xiaohong Li, Joshua Baller, Yiping Qi, Colby G. Starker, and Daniel F. Voytas. Transcription Activator-Like Effector Nucleases enable efficient plant genome engineering. Plant Physiology, 2013, 161(1):20-7. https://doi.org/10.1104/pp.112.205179 

  31. Kenichi Tsuda, Yiping Qi, Le V. Nguyen, Gerit Bethke, Yayoi Tsuda, Jane Glazebrook, and Fumiaki Katagiri. An efficient Agrobacterium-mediated transient transformation of Arabidopsis.The Plant Journal, 2012, 69 (4): 713-719. https://doi.org/10.1111/j.1365-313X.2011.04819.x

  32. Jeffry D Sander,Elizabeth J Dahlborg,Mathew J Goodwin,Lindsay Cade,Feng Zhang,Daniel Cifuentes,Shaun J Curtin,Jessica S Blackburn,Stacey Thibodeau-Beganny,Yiping Qi, Christopher J Pierick,Ellen Hoffman,Morgan L Maeder,Cyd Khayter,Deepak Reyon,Drena Dobbs,David M Langenau,Robert M Stupar,Antonio J Giraldez,Daniel F Voytas,Randall T Peterson,Jing-Ruey J Yeh& J Keith Joung. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nature Methods, 2011,8: 67-69. https://www.nature.com/articles/nmeth.1542

  33. Yiping Qi, Fumiaki Katagiri. Purification of low-abundance Arabidopsis plasma- membrane protein complexes and identification of candidate components. The Plant Journal, 2009, 57(5): 932-944. https://doi.org/10.1111/j.1365-313X.2008.03736.x 

  34. Yiping Qi, Kenichi Tsuda, Le V. Nguyen, Xia Wang, Jinshan Lin, Angus S. Murphy, Jane Glazebrook, Hans Thordal-Christensen and Fumiaki Katagiri. Physical association of Arabidopsis hypersensitive induced reaction proteins (HIRs) with the immune receptor RPS2. The Journal of Biological Chemistry, 2011, 286 (36): 31297-31307. https://doi.org/10.1074/jbc.M110.211615

  35. Yiping Qi, Kenichi Tsuda, Anna Joe, Masanao Sato, Le V. Nguyen, Jane Glazebrook , James R. Alfano, Jerry D. Cohen and Fumiaki Katagiri. A putative RNA-binding protein positively regulates salicylic acid-mediated immunity in Arabidopsis. Molecular Plant Microbe Interaction, 2010, 23(12): 1573-1583. https://doi.org/10.1094/MPMI-05-10-0106 

  36. Yiping Qi, Yue Sun, Lin Xu, Yuquan Xu, Hai Huang. ERECTA is required for protection against heat-stress in the AS1/AS2 pathway to regulate adaxial-abaxial leaf polarity in Arabidopsis. Planta. 2004, 219: 270-276. https://link.springer.com/article/10.1007/s00425-004-1248-z

Book chapters

  1. Gen Li#, Gary Coleman, Yiping Qi*. Highly Efficient Genome Editing in Plants with the LbCas12a-RRV Variant. Methods in Molecular Biology, CRISPR-Cas Methods, 2025,volume 3, pages 97-106. https://link.springer.com/protocol/10.1007/978-1-0716-4358-7_8 

  2. Yanhao Cheng#, Yiping Qi*. High-Efficiency Cas12a-Mediated A-to-G Base Editing in Rice. Methods in Molecular Biology, CRISPR-Cas Methods, 2025, volume 3, pages 117-129. https://link.springer.com/protocol/10.1007/978-1-0716-4358-7_10

  3. Shishi Liu, Xu Tang, Yiping Qi, Yong Zhang. Optimizing Rice Genomics: Employing the Hypercompact Cas12j2 System for Targeted Transcriptional Regulation and Epigenome Modification. Synthetic Promoters: Methods and Protocols. 2024. Methods in Molecular Biology, vol 2844. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-4063-0_9

  4. Changtian Pan#, Yiping Qi*. Targeted Activation of Arabidopsis Genes by a Potent CRISPR–Act3.0 System. Methods in Molecular Biology. 2023, 2698. https://link.springer.com/protocol/10.1007/978-1-0716-3354-0_3  

  5. Simon Sretenovic#, Xu Tang, Qiurong Ren, Yong Zhang, Yiping Qi*. PAM-Less CRISPR-SpRY Genome Editing in Plants. Methods in Molecular Biology. 2023, 2653. https://link.springer.com/protocol/10.1007/978-1-0716-3131-7_1 

  6. Gen Li#, Simon Sretenovic#, Gary Coleman, Yiping Qi*. Base Editing in Poplar Through an Agrobacterium-Mediated Transformation Method. Methods in Molecular Biology. 2023, 2653. https://link.springer.com/protocol/10.1007/978-1-0716-3131-7_4 

  7. Hong Fang#, James N Culver, Randall P Niedz, Yiping Qi*. Delivery of CRISPR-Cas12a Ribonucleoprotein Complex for Genome Editing in an Embryogenic Citrus Cell Line. Methods in Molecular Biology. 2023, 2653. https://link.springer.com/protocol/10.1007/978-1-0716-3131-7_10 

  8. Changtian Pan#, Yiping Qi*. CRISPR–Act3.0-based highly efficient multiplexed gene activation in plants. Current Protocols. 2022. https://doi.org/10.1002/cpz1.365 

  9. Yingxiao Zhang#, Yiping Qi*. Efficient multiplexed CRISPR-Cas12a genome editing in plants. Methods in Molecular Biology. 2021, Crop Breeding, 207-218. https://link.springer.com/protocol/10.1007/978-1-0716-1657-4_4 

  10. Simon Sretenovic#, Changtian Pan#, Yiping Qi*. Assembly and assessment of prime editing systems for precise genome editing in plants. Methods in Molecular Biology. 2021, CRISPR-Cas Methods, 83-101. https://link.springer.com/protocol/10.1007/978-1-0716-1657-4_7 

  11. Aimee Malzahn#, Yiping Qi*. Assembly of TALEN and mTALE-Act for Plant Genome Engineering. Methods in Molecular Biology. 2021, 2264: 207-218 https://link.springer.com/protocol/10.1007/978-1-0716-1201-9_15 

  12. Simon Sretenovic#, Changtian Pan#, Xu Tang, Yong Zhang, Yiping Qi*. Rapid vector construction and assessment of BE3 and Target-AID C to T base editing systems in rice protoplasts. Methods in Molecular Biology. 2021, 2238: 95-113 https://link.springer.com/protocol/10.1007/978-1-0716-1068-8_7 

  13. Guanqing Liu, Yiping Qi and Tao Zhang. Analysis of off-target mutations in CRISPR-edited rice plants using whole genome sequencing. Methods in Molecular Biology. 2021, 2238: 145-172 https://link.springer.com/protocol/10.1007/978-1-0716-1068-8_10 

  14. Yesuf Teslim Yimam, Jianping Zhou, Sayed Abdul Akher, Xuelian Zheng, Yiping Qi, Yong Zhang. Improving a quantitative trait in rice by multigene editing with CRISPR-Cas9. Methods in Molecular Biology. 2021, 2238: 205-219 https://link.springer.com/protocol/10.1007/978-1-0716-1068-8_13

  15. Xu Tang, Yiping Qi, Yong Zhang. Single transcript unit CRISPR 2.0 systems for genome editing in rice. Methods in Molecular Biology. 2021, 2238: 193-204 https://link.springer.com/protocol/10.1007/978-1-0716-1068-8_12 

  16. Aimee Malzahn#, Yong Zhang, Yiping Qi*. CRISPR-Act2.0: An Improved Multiplexed System for Plant Transcriptional Activation. Methods in Molecular Biology. 2019, 1917: 83-93. https://link.springer.com/protocol/10.1007/978-1-4939-8991-1_7 

  17. Weihang Gu, Dabing Zhang, Yiping Qi, Zheng Yuan. Generating Photoperiod-Sensitive Genic Male Sterile Rice Lines with CRISPR-Cas9. Methods in Molecular Biology. 2019, 1917: 97-107. https://link.springer.com/protocol/10.1007/978-1-4939-8991-1_8 

  18. Jianping Zhou, Zhaohui Zhong, Hongqiao Chen, Mengqiao Yang, Qian Li, Xuelian Zheng, Yiping Qi, Yong Zhang. Knocking out microRNA genes in rice with CRISPR-Cas9. Methods in Molecular Biology. 2019, 1917: 109-119. https://link.springer.com/protocol/10.1007/978-1-4939-8991-1_9

  19. Yingxiao Zhang#, Yong Zhang, Yiping Qi*. Plant Gene Knockout and Knockdown by CRISPR-Cpf1 (Cas12a) systems. Methods in Molecular Biology. 2019, 1917: 245-256. https://link.springer.com/protocol/10.1007/978-1-4939-8991-1_18 

  20. Levi G. Lowder#, Aimee A Malzahn#, Yiping Qi*. Plant Gene Regulation Using Multiplex CRISPR-dCas9 Artificial Transcription Factors. Methods in Molecular Biology. 2018; 1676:197-214. https://link.springer.com/protocol/10.1007/978-1-4939-7315-6_12 

  21. Levi G. Lowder#, Joseph W. Paull, III##, Yiping Qi*. Multiplexed Transcriptional Activation or Repression in Plants Using CRISPR-dCas9-Based Systems. Methods in Molecular Biology. 2017, 1629:167-184. https://link.springer.com/protocol/10.1007/978-1-4939-7125-1_12 

  22. Levi G. Lowder#, Aimee A. Malzahn#, Yiping Qi*. Rapid Construction of multiplexed CRISPR-Cas9 system for plant genome editing. Methods in Molecular Biology. 2017; 1578:291-307. https://link.springer.com/protocol/10.1007/978-1-4939-6859-6_25 

  23. Yiping Qi*. High efficient genome modification by designed Zinc Finger Nuclease. Advances in New Technology for Targeted Modifications of Plant Genomes, 2015, 39-53 https://link.springer.com/book/10.1007/978-1-4939-2556-8

  24. Yiping Qi, Colby Starker, Feng Zhang, Nicholas Baltes and Daniel Voytas. Tailor-made mutations in Arabidopsis using zinc finger nucleases.  Methods in Molecular Biology, 2014, https://link.springer.com/protocol/10.1007/978-1-62703-580-4_10

  25. Yiping Qi, Fumiaki Katagiri. Purification of resistance protein complexes using a biotinylated affinity tag. Methods in Molecular Biology, 2011, 712: 21-30. https://link.springer.com/protocol/10.1007/978-1-61737-998-7_3

Book 

Plant Genome Editing with CRISPR Systems