Yiping Qi

Yiping Qi

Title: Assistant Professor
Area of Study: Plant disease resistance and precise genome editing
Phone: 252-328-9764
Fax: 252-328-4178
E-mail: qiy@ecu.edu
Office: 508 Science & Technology Building
Address: Department of Biology
East Carolina University
Greenville, NC 27858

Education

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

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

B.S., Microbiology,Nankai University, 2000

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Research Interests:

My first research interest is plant disease resistance. Plant disease resistance is critical for sustainable crop production. Despite relatively successful disease control (mainly through chemicals which are not environmentally friendly), plant disease still causes a significant yield loss in crops (10% to 20%) globally. The mechanisms for plant disease resistance can be generally divided into two types. The first type is constitutive resistance which is based on pre-formed structures and compounds (such as cuticles, trichomes, cell walls, antimicrobial chemicals, proteins, etc.). The second type is inducible resistance, which often involves strengthening the first type of resistance as well as producing other effective chemicals and proteins upon pathogen attack. The inducible disease resistance relies on two types of plant immune receptors: resistance (R) proteins (often encoded by NB-LRR genes) and pattern-recognition receptors (PRRs) (often encoded by receptor-like kinase (RLK) genes). I am interested in studying how these immune receptors function in plant cells through both genetic and biochemical approaches. We employ a model system where Arabidopsis thaliana is the plant host and Pseudomonas syringae is the bacterial pathogen. In the long run, I hope to transform knowledge gained from basic research to engineering disease resistance crops, which will be facilitated by the technology related to my second interest (see below).

My second research interest is precise genome editing in plants. In plant cells (as well as in cells of other higher organisms), the broken DNA is typically repaired by one of the two repair pathways: non-homologous end-joining (NHEJ) and homologous recombination (HR). The NHEJ pathway is error-prone and can thus leads to mutations. The HR pathway utilizes a homologous DNA template for repair and allows precise DNA modifications such as gene replacement. With "DNA scissors" that can induce DNA double strand breaks (DSBs) in a site-specific manner, targeted mutagenesis (through NHEJ) or gene replacement (through HR) can be achieved. In the past, it was very difficult to engineer such customizable "DNA scissors" which are site-specific nucleases. However, recent rapid technology advancement has made three different types of site-specific nucleases available. They are Zinc Finger Nuclease (ZFN), Transcription Activator-like Effector Nuclease (TALEN) and the CRISPR/CAS9 nuclease system. I will use these site-specific nucleases as reverse genetics tools in my study on plant disease resistance. In addition, I would like to further develop efficient genome modification means in crop species. Precise genome modification will greatly change how genetically modified (GM) crops are made and probably how they are perceived by the public.

Targeted genome modification (by meganuclease, ZFN and TALEN) was named "Methods of the Year 2011" by Nature methods. The TALEN technology was named one of the top 10 scientific breakthroughs of the Year 2012 by Science magazine.These technologies are expected to revolutionize many things, such as reverse genetics in model organisms and cell lines, GM crop making and gene therapy.Multiple projects involving these site-specific nucleases are current available at my lab. I encourage motivated graduate and undergraduate students contact me for these exciting opportunities.

Publications:

16. Yadong Huang*, Chun Yao Li*, Yiping Qi, Sungjin Park and Susan I. Gibson. SIS8, a putative mitogen-activated protein kinase kinase kinase, regulates suger resistant seedling development in Arabidopsis. The Plant Journal, 2014 (doi: 10.1111/tpj.12404. [Epub ahead of print])

15. Yiping Qi, Colby Starker, Feng Zhang, Nicholas Baltes and Daniel Voytas. Tailor-made mutations in Arabidopsis using zinc finger nucleases. In: Methods in Molecular Biology, 2014, 1062: 193-209

14. Michelle L. Christian*, Yiping Qi*, Yong Zhang and Daniel F. Voytas. Targeted mutagenesis in Arabidopsis thaliana using Engineered TAL effector nucleases (TALENs). G3 (Bethesda).  2013 Oct 3; 3(10):1697-705. 

13. 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 (Bethesda).  2013 Oct 3; 3(10):1707-15.

12. Hua Shi, Qiujing Shen, Yiping Qi, Haozhen Nie, Yongfang Chen, Ting Zhao, Fumiaki Katagiri, Dingzhong Tang. Arabidopsis BR-SIGNALING KINASE1 physically associates with the PAMP receptor FLAGELLIN SENSING2 and regulates plant innate immunity. Plant Cell, 2013 Mar;25(3):1143-57

11. 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 Mar;23(3):547-54

10. Yong Zhang*, Feng Zhang*, Xiaohong Li, Joshua Baller, Yiping Qi, Colby G. Starker, and Daniel F. Voytas. High efficiency plant genome engineering using TALENs. Plant Physiology, 2013, 161(1):20-7

9. Yiping Qi and Fumiaki Katagiri. A membrane microdomain may be a platform for immune signaling. Plant Signaling & Behavior, 2012, 7 (4): 454-456

8. 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

7. 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

6. Yiping Qi, Kenichi Tsuda, Jane Glazebrook and Fumiaki Katagiri. Physical association of PTI and ETI immune receptors in Arabidopsis. Molecular Plant Pathology 2011, 12 (7): 702-708

5. Yiping Qi, Fumiaki Katagiri. Purification of resistance protein complexes using a biotinylated affinity tag. In: Methods in Molecular Biology, Humana Press, 2011, 712: 21-30

4. 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, 2010,8: 67-69

3. 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

2. 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

1. 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

Courses Taught:

BIOL 4890 (Biochemistry II)

Laboratory Personnel

Charles-Brooks-Class-of-2016_1

 

Charles Brooks

Courtney-Frost-Class-of-2016_1

 

Courtney Frost

Elida-Kirkland-Class-of-2015

 

Elida Kirkland

Joseph-Paul-Class-of-2016_1

 

Joseph Paul

Kishan-Darji-Class-of-2016_2

 

Kishan Darji

Melissa-Jones-Class-of-2014_1

 

Melissa Jones

Meriam-Hawng-Class-of-2015_1

 

Meriam Hawng

Tany-Lee-Class-of-2014

 

Tany Lee