Zhaohui Zhong

University of Electronic Science and Technology of China

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Yong Zhang

Sichuan University

Xuelian Zheng

Sichuan University

Yiping Qi

University of Maryland, College Park

Qiurong Ren

University of Electronic Science and Technology of China

Xu Tang

Institute of Geology and Geophysics

Jianping Zhou

BGI Research

Tao Zhang

Yangzhou University

Shishi Liu

Xiamen University

Binglin Liu

Nanning Normal University

Yao He

Yibin University

Cooperative Institutions

University of Electronic Science and Technology of China

Chinese Academy of Sciences

Sichuan Agricultural University

Rice Research Institute

Southwest University

University of Maryland, College Park

University of Chinese Academy of Sciences

Zhejiang University

Yangzhou University

Wuhan University

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Multiplex QTL editing of grain-related genes improves yield in elite rice varieties

Plant Cell Reports (2018)

Jianping Zhou Xuhui Xin Yao He Hongqiao Chen Qian Li

Multiplex

Panicle

Trait

Marker-Assisted Selection

10.1007/s00299-018-2340-3

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Citations (159)

Hypercompact CRISPR–Cas12j2 (CasΦ) enables genome editing, gene activation, and epigenome editing in plants

Plant Communications (2022)

Shishi Liu Simon Sretenovic Tingting Fan Yanhao Cheng Gen Li

Epigenome

10.1016/j.xplc.2022.100453

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Citations (42)

Knockout of the OsNAC006 Transcription Factor Causes Drought and Heat Sensitivity in Rice

International Journal of Molecular Sciences (2020)

Bo Wang Zhaohui Zhong Xia Wang Han Xiangyan Deshui Yu

Rice (Oryza sativa) responds to various abiotic stresses during growth. Plant-specific NAM, ATAF1/2, and CUC2 (NAC) transcription factors (TFs) play an important role in controlling numerous vital growth and developmental processes. To date, 170 NAC TFs have been reported in rice, but their roles remain largely unknown. Herein, we discovered that the TF OsNAC006 is constitutively expressed in rice, and regulated by H2O2, cold, heat, abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin (GA), NaCl, and polyethylene glycol (PEG) 6000 treatments. Furthermore, knockout of OsNAC006 using the CRISPR-Cas9 system resulted in drought and heat sensitivity. RNA sequencing (RNA-seq) transcriptome analysis revealed that OsNAC006 regulates the expression of genes mainly involved in response to stimuli, oxidoreductase activity, cofactor binding, and membrane-related pathways. Our findings elucidate the important role of OsNAC006 in drought responses, and provide valuable information for genetic manipulation to enhance stress tolerance in future plant breeding programs.

Drought Tolerance

Oryza

10.3390/ijms21072288

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Citations (97)

Targeted Mutagenesis of NAC Transcription Factor Gene, OsNAC041, Leading to Salt Sensitivity in Rice

Rice Science (2019)

Bo Wang Zhaohui Zhong Huan‐Huan Zhang Xia Wang Binglin Liu

Salinity is a major abiotic stress factor that seriously affects plant growth. Many genes are involved in the response to salt stress with various metabolism pathways. A number of plant transcription factor family genes have been found to be involved in the salt stress response, and NAM, ATAF and CUC (NAC) transcription factors are thought to act as active regulators during abiotic stress, especially salt stress. In this study, we detected a rice NAC transcription factor coding gene, OsNAC041, and confirmed that it influenced the germination of seeds under salt stress and salt tolerance of plants. OsNAC041 was primarily expressed in the leaves and located in the nucleus. Furthermore, the CRISPR/Cas9 method was used to obtain a targeted osnac041 mutant, of which the plant height was higher than that of the wild-type, showing increased salt sensitivity. Moreover, RNA-seq analysis revealed a number of differentially expressed genes (DEGs) involved in several important signaling pathways in the osnac041 mutant. Subsequently, Kyoto Encyclopedia of Genes and Genomes annotation also revealed differential expression of DEGs associated with mitogen-activated protein kinase signaling, peroxisome, eukaryotic- type ABC transporters, photosynthesis and plant hormones, which are involved in stress-related signaling pathways. Overall, our study suggested that OsNAC041 was involved in the salt stress response in rice. These findings not only provide empirical evidence of OsNAC041 function, but also provide new insight into its potential application in rice resistance breeding.

10.1016/j.rsci.2018.12.005

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Citations (111)

A Single Transcript CRISPR-Cas9 System for Multiplex Genome Editing in Plants

Methods in molecular biology (2019)

Xu Tang Zhaohui Zhong Qiurong Ren Binglin Liu Yong Zhang

Multiplex

Subgenomic mRNA

10.1007/978-1-4939-8991-1_6

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Citations (2)

Additional file 3 of Intron-Based Single Transcript Unit CRISPR Systems for Plant Genome Editing

Figshare (2020)

Zhaohui Zhong Shishi Liu Xiaopei Liu Binglin Liu Xu Tang

Additional file 3:Â Table S2. T-DNA constructs used in this study.

10.6084/m9.figshare.11797464

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Citations (0)

Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system

Nature Communications (2023)

Zhaohui Zhong Guanqing Liu Zhongjie Tang Shuyue Xiang Liang Yang

Abstract Among CRISPR-Cas genome editing systems, Streptococcus pyogenes Cas9 (SpCas9), sourced from a human pathogen, is the most widely used. Here, through in silico data mining, we have established an efficient plant genome engineering system using CRISPR-Cas9 from probiotic Lactobacillus rhamnosus . We have confirmed the predicted 5’-NGAAA-3’ PAM via a bacterial PAM depletion assay and showcased its exceptional editing efficiency in rice, wheat, tomato, and Larix cells, surpassing LbCas12a, SpCas9-NG, and SpRY when targeting the identical sequences. In stable rice lines, LrCas9 facilitates multiplexed gene knockout through coding sequence editing and achieves gene knockdown via targeted promoter deletion, demonstrating high specificity. We have also developed LrCas9-derived cytosine and adenine base editors, expanding base editing capabilities. Finally, by harnessing LrCas9’s A/T-rich PAM targeting preference, we have created efficient CRISPR interference and activation systems in plants. Together, our work establishes CRISPR-LrCas9 as an efficient and user-friendly genome engineering tool for diverse applications in crops and beyond.

Genome Engineering

10.1038/s41467-023-41802-9

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Citations (16)

Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice

bioRxiv (Cold Spring Harbor Laboratory) (2022)

Yuechao Wu Qiurong Ren Zhaohui Zhong Guanqing Liu Yangshuo Han

PAM-relaxed Cas9 nucleases, cytosine base editors and adenine base editors are promising tools for precise genome editing in plants. However, their genome-wide off-target effects are largely undetermined. Here, we conduct whole-genome sequencing (WGS) analyses of transgenic plants edited by xCas9, Cas9-NGv1, Cas9-NG, SpRY, nCas9-NG-PmCDA1, nSpRY-PmCDA1 and nSpRY-ABE8e in rice. Our results reveal different guide RNA (gRNA)-dependent off-target effects with different editors. De novo generated new gRNAs by SpRY editors lead to additional but not substantial off-target mutations. Strikingly, ABE8e results in ~500 genome-wide A-to-G off-target mutations at TA motif sites per transgenic plant. The preference of the TA motif by ABE8e is also observed at the target sites. Finally, we investigate the timeline and mechanism of somaclonal variation due to tissue culture, which chiefly contributes to the background mutations. This study provides a comprehensive understanding on the scales and mechanisms of off-target and background mutations during PAM-relaxed genome editing in plants.

Guide RNA

10.1101/2022.02.09.479813

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A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice

Genome biology (2018)

Xu Tang Guanqing Liu Jianping Zhou Qiurong Ren Qi You

Targeting specificity has been a barrier to applying genome editing systems in functional genomics, precise medicine and plant breeding. In plants, only limited studies have used whole-genome sequencing (WGS) to test off-target effects of Cas9. The cause of numerous discovered mutations is still controversial. Furthermore, WGS-based off-target analysis of Cpf1 (Cas12a) has not been reported in any higher organism to date.

Human genetics

Personal genomics

10.1186/s13059-018-1458-5

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Citations (255)

CRISPR–Cas12b enables efficient plant genome engineering

Nature Plants (2020)

Meiling Ming Qiurong Ren Changtian Pan Yao He Yingxiao Zhang

Genome Engineering

10.1038/s41477-020-0614-6

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Citations (148)