An update on precision genome editing by homology-directed repair in plants

CRISPR/Cas9 Induced Somatic Recombination at the CRTISO Locus in Tomato

(2021) Ilan Ben Shlush et al.   Genes

A route to de novo domestication of wild allotetraploid rice

(2021) Hong Yu et al.   CELL

Efficient gene targeting in Nicotiana tabacum using CRISPR/SaCas9 and temperature tolerant LbCas12a

(2021) Teng‐Kuei Huang et al.   PLANT BIOTECHNOLOGY JOURNAL

Single-strand template repair: key insights to increase the efficiency of gene editing

(2021) Danielle N. Gallagher et al.   CURRENT GENETICS

High-throughput functional variant screens via in vivo production of single-stranded DNA

(2021) Max G. Schubert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome editing reagent delivery in plants

(2021) Rishikesh Ghogare et al.   TRANSGENIC RESEARCH

Efficient embryonic homozygous gene conversion via RAD51-enhanced interhomolog repair

(2021) Jonathan J. Wilde et al.   CELL

Highly efficient heritable genome editing in wheat using an RNA virus and bypassing tissue culture

(2021) Tingdong Li et al.   Molecular Plant

Precise genome editing without exogenous donor DNA via retron editing system in human cells

(2021) Xiangfeng Kong et al.   Protein & Cell

Improvement of the LbCas12a-crRNA System for Efficient Gene Targeting in Tomato

(2021) Tien Van Vu et al.   Frontiers in Plant Science

Targeted Inter-Homologs Recombination in Arabidopsis Euchromatin and Heterochromatin

(2021) Shdema Filler-Hayut et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Marker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9

(2020) Oliver Xiaoou Dong et al.   Nature Communications

Precise Modifications of Both Exogenous and Endogenous Genes in Rice by Prime Editing

(2020) Huiyuan Li et al.   Molecular Plant

Versatile Nucleotides Substitution in Plant Using an Improved Prime Editing System

(2020) Wen Xu et al.   Molecular Plant

Prime genome editing in rice and wheat

(2020) Qiupeng Lin et al.   NATURE BIOTECHNOLOGY

Highly efficient homology‐directed repair using CRISPR/Cpf1‐geminiviral replicon in tomato

(2020) Tien Van Vu et al.   PLANT BIOTECHNOLOGY JOURNAL

Enhancing in planta gene targeting efficiencies in Arabidopsis using temperature‐tolerant CRISPR/ Lb Cas12a

(2020) Laura Merker et al.   PLANT BIOTECHNOLOGY JOURNAL

Toward Precision Genome Editing in Crop Plants

(2020) Jingying Li et al.   Molecular Plant

Efficient Gene Targeting in Maize Using Inducible CRISPR-Cas9 and Marker-free Donor Template

(2020) Pierluigi Barone et al.   Molecular Plant

Targeted, efficient sequence insertion and replacement in rice

(2020) Yuming Lu et al.   NATURE BIOTECHNOLOGY

A GRF–GIF chimeric protein improves the regeneration efficiency of transgenic plants

(2020) Juan M. Debernardi et al.   NATURE BIOTECHNOLOGY

Changing local recombination patterns in Arabidopsis by CRISPR/Cas mediated chromosome engineering

(2020) Carla Schmidt et al.   Nature Communications

Overexpression of the Transcription Factor GROWTH-REGULATING FACTOR5 Improves Transformation of Dicot and Monocot Species

(2020) Jixiang Kong et al.   Frontiers in Plant Science

Bacterial Retrons Function In Anti-Phage Defense

(2020) Adi Millman et al.   CELL

Rice Protein Tagging Project: A Call for International Collaborations on Genome-wide In-Locus Tagging of Rice Proteins

(2020) Yuming Lu et al.   Molecular Plant

Some characteristics of crossing over in induced recombination between chromosomes of wheat and rye

(2020) Chaolan Fan et al.   PLANT JOURNAL

Transgene-Free Genome Editing in Tomato and Potato Plants Using Agrobacterium-Mediated Delivery of a CRISPR/Cas9 Cytidine Base Editor

(2019) Florian Veillet et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

POLQ plays a key role in repair of CRISPR/Cas9 induced double strand breaks in the moss Physcomitrella patens

(2019) Kostlend Mara et al.   NEW PHYTOLOGIST

CRISPR ‐LbCas12a‐mediated modification of citrus

(2019) Hongge Jia et al.   PLANT BIOTECHNOLOGY JOURNAL

Precise gene replacement in rice by RNA transcript-templated homologous recombination

(2019) Shaoya Li et al.   NATURE BIOTECHNOLOGY

One-step genome editing of elite crop germplasm during haploid induction

(2019) Timothy Kelliher et al.   NATURE BIOTECHNOLOGY

Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis

(2019) Aimee A. Malzahn et al.   BMC BIOLOGY

De Novo Domestication: An Alternative Route toward New Crops for the Future

(2019) Alisdair R. Fernie et al.   Molecular Plant

Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

(2019) Fei He et al.   NATURE GENETICS

Assessment of Cas12a‐mediated gene editing efficiency in plants

(2019) Joan Miquel Bernabé‐Orts et al.   PLANT BIOTECHNOLOGY JOURNAL

Robust CRISPR /Cpf1(Cas12a) mediated genome editing in allotetraploid cotton ( G. hirsutum )

(2019) Bo Li et al.   PLANT BIOTECHNOLOGY JOURNAL

Breeding crops to feed 10 billion

(2019) Lee T. Hickey et al.   NATURE BIOTECHNOLOGY

In planta gene targeting can be enhanced by the use of CRISPR/Cas12a

(2019) Felix Wolter et al.   PLANT JOURNAL

Revolutions in agriculture chart a course for targeted breeding of old and new crops

(2019) Yuval Eshed et al.   SCIENCE

ssODN-Mediated In-Frame Deletion with CRISPR/Cas9 Restores FVIII Function in Hemophilia A-Patient-Derived iPSCs and ECs

(2019) Zhiqing Hu et al.   Molecular Therapy-Nucleic Acids

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

Engineering CRISPR/ Lb Cas12a for highly efficient, temperature‐tolerant plant gene editing

(2019) Patrick Schindele et al.   PLANT BIOTECHNOLOGY JOURNAL

Gene targeting in Arabidopsis via an all‐in‐one strategy that uses a translational enhancer to aid Cas9 expression

(2019) Fangnan Peng et al.   PLANT BIOTECHNOLOGY JOURNAL

CRISPR‐Cas12a enables efficient biallelic gene targeting in rice

(2019) Shaoya Li et al.   PLANT BIOTECHNOLOGY JOURNAL

Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency

(2019) David N. Nguyen et al.   NATURE BIOTECHNOLOGY

Plant gene editing through de novo induction of meristems

(2019) Michael F. Maher et al.   NATURE BIOTECHNOLOGY

Rapid genotype “independent” Zea mays L. (maize) transformation via direct somatic embryogenesis

(2018) Keith Lowe et al.   IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-PLANT

Suppressing Ku70/Ku80 expression elevates homology-directed repair efficiency in primary fibroblasts

(2018) Guoling Li et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Synthesis-dependent repair of Cpf1-induced double strand DNA breaks enables targeted gene replacement in rice

(2018) Shaoya Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

Efficient allelic replacement in rice by gene editing: A case study of the NRT1.1B gene

(2018) Jingying Li et al.   Journal of Integrative Plant Biology

Activities and specificities of CRISPR-Cas9 and Cas12a nucleases for targeted mutagenesis in maize

(2018) Keunsub Lee et al.   PLANT BIOTECHNOLOGY JOURNAL

Efficient in planta gene targeting in Arabidopsis using egg cell-specific expression of the Cas9 nuclease of Staphylococcus aureus

(2018) Felix Wolter et al.   PLANT JOURNAL

Efficient in planta gene targeting in tomato using geminiviral replicons and the CRISPR/Cas9 system

(2018) Tal Dahan-Meir et al.   PLANT JOURNAL

CRISPR/Cas9-mediated gene targeting in Arabidopsis using sequential transformation

(2018) Daisuke Miki et al.   Nature Communications

True gene-targeting events by CRISPR/Cas-induced DSB repair of the PPO locus with an ectopically integrated repair template

(2018) Sylvia de Pater et al.   Scientific Reports

Homology-Directed Repair of a Defective Glabrous Gene in Arabidopsis With Cas9-Based Gene Targeting

(2018) Florian Hahn et al.   Frontiers in Plant Science

Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing

(2018) Eilon Sharon et al.   CELL

Genome sequence of the progenitor of wheat A subgenome Triticum urartu

(2018) Hong-Qing Ling et al.   NATURE

Modulating plant growth–metabolism coordination for sustainable agriculture

(2018) Shan Li et al.   NATURE

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

Highly efficient genome editing by CRISPR-Cpf1 using CRISPR RNA with a uridinylate-rich 3′-overhang

(2018) Su Bin Moon et al.   Nature Communications

Programmable DNA repair with CRISPRa/i enhanced homology-directed repair efficiency with a single Cas9

(2018) Lupeng Ye et al.   Cell Discovery

ZFN, TALEN and CRISPR-Cas9 mediated homology directed gene insertion in Arabidopsis: A disconnect between somatic and germinal cells

(2018) Qiwei Shan et al.   Journal of Genetics and Genomics

Domestication of wild tomato is accelerated by genome editing

(2018) Tingdong Li et al.   NATURE BIOTECHNOLOGY

De novo domestication of wild tomato using genome editing

(2018) Agustin Zsögön et al.   NATURE BIOTECHNOLOGY

Mechanisms of precise genome editing using oligonucleotide donors

(2017) Yinan Kan et al.   GENOME RESEARCH

Gene Targeting by Homology-Directed Repair in Rice Using a Geminivirus-Based CRISPR/Cas9 System

(2017) Mugui Wang et al.   Molecular Plant

Multiplex Gene Editing in Rice Using the CRISPR-Cpf1 System

(2017) Mugui Wang et al.   Molecular Plant

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

Generation of targeted mutant rice using a CRISPR-Cpf1 system

(2017) Rongfang Xu et al.   PLANT BIOTECHNOLOGY JOURNAL

High-efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9

(2017) Javier Gil-Humanes et al.   PLANT JOURNAL

Precision genome editing using synthesis-dependent repair of Cas9-induced DNA breaks

(2017) Alexandre Paix et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted recombination between homologous chromosomes for precise breeding in tomato

(2017) Shdema Filler Hayut et al.   Nature Communications

CRISPR/Cpf1-mediated DNA-free plant genome editing

(2017) Hyeran Kim et al.   Nature Communications

Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule

(2017) Haroon Butt et al.   Frontiers in Plant Science

Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases

(2017) Matthew B. Begemann et al.   Scientific Reports

CRISPR/Cas9-induced Targeted Mutagenesis and Gene Replacement to Generate Long-shelf Life Tomato Lines

(2017) Qing-hui Yu et al.   Scientific Reports

Engineering Herbicide-Resistant Rice Plants through CRISPR/Cas9-Mediated Homologous Recombination of Acetolactate Synthase

(2016) Yongwei Sun et al.   Molecular Plant

The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA

(2016) Ines Fonfara et al.   NATURE

Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9

(2016) Dominik Paquet et al.   NATURE

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA

(2016) Christopher D Richardson et al.   NATURE BIOTECHNOLOGY

Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array

(2016) Bernd Zetsche et al.   NATURE BIOTECHNOLOGY

ARGOS8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions

(2016) Jinrui Shi et al.   PLANT BIOTECHNOLOGY JOURNAL

Morphogenic Regulators Baby boom and Wuschel Improve Monocot Transformation

(2016) Keith Lowe et al.   PLANT CELL

Homology-based double-strand break-induced genome engineering in plants

(2016) Jeannette Steinert et al.   PLANT CELL REPORTS

Oligonucleotide-Mediated Genome Editing Provides Precision and Function to Engineered Nucleases and Antibiotics in Plants

(2016) Noel J. Sauer et al.   PLANT PHYSIOLOGY

Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes

(2016) Sergei Svitashev et al.   Nature Communications

Post-translational Regulation of Cas9 during G1 Enhances Homology-Directed Repair

(2016) Tony Gutschner et al.   Cell Reports

Geminivirus-Mediated Genome Editing in Potato (Solanum tuberosum L.) Using Sequence-Specific Nucleases

(2016) Nathaniel M. Butler et al.   Frontiers in Plant Science

Precise Genome Modification via Sequence-Specific Nucleases-Mediated Gene Targeting for Crop Improvement

(2016) Yongwei Sun et al.   Frontiers in Plant Science

Enrichment of G2/M cell cycle phase in human pluripotent stem cells enhances HDR-mediated gene repair with customizable endonucleases

(2016) Diane Yang et al.   Scientific Reports

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

A mechanism for the suppression of homologous recombination in G1 cells

(2015) Alexandre Orthwein et al.   NATURE

Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining

(2015) Takeshi Maruyama et al.   NATURE BIOTECHNOLOGY

Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells

(2015) Van Trung Chu et al.   NATURE BIOTECHNOLOGY

Biallelic Gene Targeting in Rice

(2015) Masaki Endo et al.   PLANT PHYSIOLOGY

Overexpression of ARGOS Genes Modifies Plant Sensitivity to Ethylene, Leading to Improved Drought Tolerance in Both Arabidopsis and Maize

(2015) Jinrui Shi et al.   PLANT PHYSIOLOGY

Cas9-Guide RNA Directed Genome Editing in Soybean

(2015) Zhongsen Li et al.   PLANT PHYSIOLOGY

Targeted Mutagenesis, Precise Gene Editing, and Site-Specific Gene Insertion in Maize Using Cas9 and Guide RNA

(2015) Sergei Svitashev et al.   PLANT PHYSIOLOGY

Enabling plant synthetic biology through genome engineering

(2015) Nicholas J. Baltes et al.   TRENDS IN BIOTECHNOLOGY

Transcript-RNA-templated DNA recombination and repair

(2014) Havva Keskin et al.   NATURE

Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells

(2014) Susan M. Byrne et al.   NUCLEIC ACIDS RESEARCH

DNA Replicons for Plant Genome Engineering

(2014) N. J. Baltes et al.   PLANT CELL

The CRISPR/Cas system can be used as nuclease forin plantagene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny

(2014) Simon Schiml et al.   PLANT JOURNAL

Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery

(2014) Steven Lin et al.   eLife

Genes offering the potential for designing yield-related traits in rice

(2013) Mayuko Ikeda et al.   CURRENT OPINION IN PLANT BIOLOGY

Gene targeting in plants: 25 years later

(2013) Holger Puchta et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

The transience of transient overexpression

(2013) Toby J Gibson et al.   NATURE METHODS

Synthetic nucleases for genome engineering in plants: prospects for a bright future

(2013) Holger Puchta et al.   PLANT JOURNAL

Overexpression of OsRecQl4 and/or OsExo1 Enhances DSB-Induced Homologous Recombination in Rice

(2012) Yong-Ik Kwon et al.   PLANT AND CELL PHYSIOLOGY

Double-Strand Break End Resection and Repair Pathway Choice

(2011) Lorraine S. Symington et al.   Annual Review of Genetics

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Pathways to meiotic recombination in Arabidopsis thaliana

(2011) Kim Osman et al.   NEW PHYTOLOGIST

Localized egg-cell expression of effector proteins for targeted modification of the Arabidopsis genome

(2011) Liron Even-Faitelson et al.   PLANT JOURNAL

OsPHF1 Regulates the Plasma Membrane Localization of Low- and High-Affinity Inorganic Phosphate Transporters and Determines Inorganic Phosphate Uptake and Translocation in Rice

(2011) Jieyu Chen et al.   PLANT PHYSIOLOGY

Coping with DNA double strand breaks

(2010) Kevin Hiom   DNA REPAIR

Precise genome modification in the crop species Zea mays using zinc-finger nucleases

(2009) Vipula K. Shukla et al.   NATURE