Diverse Systems for Efficient Sequence Insertion and Replacement in Precise Plant Genome Editing

BioDesign Research ◽

10.34133/2020/8659064 ◽

2020 ◽

Vol 2020 ◽

pp. 1-4

Author(s):

Yingxiao Zhang ◽

Yiping Qi

Keyword(s):

Genome Editing ◽

Genetic Variants ◽

Agronomic Traits ◽

Gene Knockout ◽

Plant Genome ◽

Chemically Modified ◽

Limited Success ◽

Efficient Sequence

CRISPR-mediated genome editing has been widely applied in plants to make uncomplicated genomic modifications including gene knockout and base changes. However, the introduction of many genetic variants related to valuable agronomic traits requires complex and precise DNA changes. Different CRISPR systems have been developed to achieve efficient sequence insertion and replacement but with limited success. A recent study has significantly improved NHEJ- and HDR-mediated sequence insertion and replacement using chemically modified donor templates. Together with other newly developed precise editing systems, such as prime editing and CRISPR-associated transposases, these technologies will provide new avenues to further the plant genome editing field.

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Prospects for Knockout of MYB60, a Transcriptional Repressor of Anthocyanin Biosynthesis, in Brassicaceae Plants by Genome Editing

KnE Life Sciences ◽

10.18502/kls.v7i1.10157 ◽

2022 ◽

Author(s):

Elena Mikhaylova ◽

Alexander Artyukhin ◽

Michael Shein ◽

Khalit Musin ◽

Anna Sukhareva ◽

...

Keyword(s):

Transcription Factors ◽

Genome Editing ◽

Agronomic Traits ◽

Anthocyanin Biosynthesis ◽

Gene Knockout ◽

Transcriptional Repressor ◽

Academic Community ◽

Plant Responses ◽

Individual Plant ◽

Brassica Napus L

The Brassicaceae plant family contains many economically important crops such as Brassica napus L., Brassica rapa L., Brassica oleracea L., Brassica juncea L., Eruca sativa Mill., Camelina sativa L. and Raphanus sativus L. Insufficient data on the genetic regulation of agronomic traits in these species complicates the editing of their genomes. In recent years, the attention of the academic community has been drawn to anthocyanin hyperaccumulation. This trait is not only beneficial for human health, but can also increase plant resistance to stress. MYB transcription factors are the main regulators of flavonoid biosynthesis in plants. Some of them are well studied in Arabidopsis thaliana. The AtMYB60 gene is a transcriptional repressor of anthocyanin biosynthesis, and it also negatively impacts plant responses to drought stress. Myb60 is one of the least studied transcription factors with similar functions in Brassicaceae. There is a high degree of homology between predicted MYB60 genes of A. thaliana and related plant species. However, functions of these homologous genes have never been studied. Gene knockout by CRISPR/Cas technology remains the easiest way to perform genome editing in order to discover the role of individual plant genes. Disruption of genes acting as negative regulators of anthocyanin biosynthesis could result in color staining of plant tissues and an increase in stress tolerance. In the present study, we investigated the AtMYB60 gene and its homologs in Brassicaceae plants and suggested universal gRNAs to knockout these genes. Keywords: CRISPR, Brassicaceae, MYB60, knockout, anthocyanin

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Plant Genome Editing – Policies and Governance

10.3389/978-2-88963-670-9 ◽

2020 ◽

Keyword(s):

Genome Editing ◽

Plant Genome

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An Era of CRISPR/ Cas9 Mediated Plant Genome Editing

Current Issues in Molecular Biology ◽

10.21775/cimb.026.047 ◽

2018 ◽

pp. 47-54 ◽

Cited By ~ 1

Author(s):

Haris Khurshid ◽

Sohail Ahmad Jan ◽

Zabta Khan Shinwari ◽

Muhammad Jamal ◽

Sabir Hussain Shah

Keyword(s):

Genome Editing ◽

Plant Genome

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Exosome/Liposome-like Nanoparticles: New Carriers for CRISPR Genome Editing in Plants

International Journal of Molecular Sciences ◽

10.3390/ijms22147456 ◽

2021 ◽

Vol 22 (14) ◽

pp. 7456

Author(s):

Mousa A. Alghuthaymi ◽

Aftab Ahmad ◽

Zulqurnain Khan ◽

Sultan Habibullah Khan ◽

Farah K. Ahmed ◽

...

Keyword(s):

Genome Editing ◽

Viral Vectors ◽

Polymeric Materials ◽

Inorganic Nanoparticles ◽

Plant Genome ◽

Delivery Methods ◽

Detailed Consideration ◽

Crispr System ◽

Efficient Delivery ◽

Low Cytotoxicity

Rapid developments in the field of plant genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems necessitate more detailed consideration of the delivery of the CRISPR system into plants. Successful and safe editing of plant genomes is partly based on efficient delivery of the CRISPR system. Along with the use of plasmids and viral vectors as cargo material for genome editing, non-viral vectors have also been considered for delivery purposes. These non-viral vectors can be made of a variety of materials, including inorganic nanoparticles, carbon nanotubes, liposomes, and protein- and peptide-based nanoparticles, as well as nanoscale polymeric materials. They have a decreased immune response, an advantage over viral vectors, and offer additional flexibility in their design, allowing them to be functionalized and targeted to specific sites in a biological system with low cytotoxicity. This review is dedicated to describing the delivery methods of CRISPR system into plants with emphasis on the use of non-viral vectors.

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Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation

Genome Medicine ◽

10.1186/s13073-021-00857-3 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Shuquan Rao ◽

Yao Yao ◽

Daniel E. Bauer

Keyword(s):

Genome Editing ◽

Genetic Variants ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Functional Studies ◽

Functional Genetics ◽

Genome Wide ◽

Causal Variants ◽

Experimental Approaches

AbstractGenome-wide association studies (GWAS) have uncovered thousands of genetic variants that influence risk for human diseases and traits. Yet understanding the mechanisms by which these genetic variants, mainly noncoding, have an impact on associated diseases and traits remains a significant hurdle. In this review, we discuss emerging experimental approaches that are being applied for functional studies of causal variants and translational advances from GWAS findings to disease prevention and treatment. We highlight the use of genome editing technologies in GWAS functional studies to modify genomic sequences, with proof-of-principle examples. We discuss the challenges in interrogating causal variants, points for consideration in experimental design and interpretation of GWAS locus mechanisms, and the potential for novel therapeutic opportunities. With the accumulation of knowledge of functional genetics, therapeutic genome editing based on GWAS discoveries will become increasingly feasible.

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Knowing when to talk? Plant genome editing as a site for pre-engagement institutional reflexivity

Public Understanding of Science ◽

10.1177/0963662521999796 ◽

2021 ◽

pp. 096366252199979

Author(s):

Robert D.J. Smith ◽

Sarah Hartley ◽

Patrick Middleton ◽

Tracey Jewitt

Keyword(s):

Genome Editing ◽

Theory And Practice ◽

Plant Genome ◽

Limited Attention ◽

Full Potential ◽

Policy Makers ◽

Institutional Dynamics ◽

Social Studies Of Science ◽

High Profile ◽

A Site

Citizen and stakeholder engagement is frequently portrayed as vital for socially accountable science policy but there is a growing understanding of how institutional dynamics shape engagement exercises in ways that prevent them from realising their full potential. Limited attention has been devoted to developing the means to expose institutional features, allow policy-makers to reflect on how they will shape engagement and respond appropriately. Here, therefore, we develop and test a methodological framework to facilitate pre-engagement institutional reflexivity with one of the United Kingdom’s eminent science organisations as it grappled with a new, high-profile and politicised technology, genome editing. We show how this approach allowed policy-makers to reflect on their institutional position and enrich decision-making at a time when they faced pressure to legitimate decisions with engagement. Further descriptions of such pre-engagement institutional reflexivity are needed to better bridge theory and practice in the social studies of science.

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Recent advances in CRISPR/Cas9 and applications for wheat functional genomics and breeding

aBIOTECH ◽

10.1007/s42994-021-00042-5 ◽

2021 ◽

Author(s):

Jun Li ◽

Yan Li ◽

Ligeng Ma

Keyword(s):

Functional Genomics ◽

Genome Editing ◽

Functional Annotation ◽

Genome Engineering ◽

Agronomic Traits ◽

Wheat Breeding ◽

Breeding Programs ◽

Base Editing ◽

The World ◽

World Food Security

AbstractCommon wheat (Triticum aestivum L.) is one of the three major food crops in the world; thus, wheat breeding programs are important for world food security. Characterizing the genes that control important agronomic traits and finding new ways to alter them are necessary to improve wheat breeding. Functional genomics and breeding in polyploid wheat has been greatly accelerated by the advent of several powerful tools, especially CRISPR/Cas9 genome editing technology, which allows multiplex genome engineering. Here, we describe the development of CRISPR/Cas9, which has revolutionized the field of genome editing. In addition, we emphasize technological breakthroughs (e.g., base editing and prime editing) based on CRISPR/Cas9. We also summarize recent applications and advances in the functional annotation and breeding of wheat, and we introduce the production of CRISPR-edited DNA-free wheat. Combined with other achievements, CRISPR and CRISPR-based genome editing will speed progress in wheat biology and promote sustainable agriculture.

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Virus-induced plant genome editing

Current Opinion in Plant Biology ◽

10.1016/j.pbi.2020.101992 ◽

2021 ◽

Vol 60 ◽

pp. 101992

Author(s):

Youngbin Oh ◽

Hyeonjin Kim ◽

Sang-Gyu Kim

Keyword(s):

Genome Editing ◽

Plant Genome

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An Efficient, Rapid, and Recyclable System for CRISPR-Mediated Genome Editing in Candida albicans

mSphere ◽

10.1128/mspheredirect.00149-17 ◽

2017 ◽

Vol 2 (2) ◽

Cited By ~ 33

Author(s):

Namkha Nguyen ◽

Morgan M. F. Quail ◽

Aaron D. Hernday

Keyword(s):

Candida Albicans ◽

Genome Editing ◽

Fungal Pathogen ◽

Gene Knockout ◽

Strain Engineering ◽

Molecular Genetic Analysis ◽

Content Type ◽

Highly Efficient ◽

Discovery Research ◽

Gene Knockouts

ABSTRACT Candida albicans is the most common fungal pathogen of humans. Historically, molecular genetic analysis of this important pathogen has been hampered by the lack of stable plasmids or meiotic cell division, limited selectable markers, and inefficient methods for generating gene knockouts. The recent development of clustered regularly interspaced short palindromic repeat(s) (CRISPR)-based tools for use with C. albicans has opened the door to more efficient genome editing; however, previously reported systems have specific limitations. We report the development of an optimized CRISPR-based genome editing system for use with C. albicans. Our system is highly efficient, does not require molecular cloning, does not leave permanent markers in the genome, and supports rapid, precise genome editing in C. albicans. We also demonstrate the utility of our system for generating two independent homozygous gene knockouts in a single transformation and present a method for generating homozygous wild-type gene addbacks at the native locus. Furthermore, each step of our protocol is compatible with high-throughput strain engineering approaches, thus opening the door to the generation of a complete C. albicans gene knockout library. IMPORTANCE Candida albicans is the major fungal pathogen of humans and is the subject of intense biomedical and discovery research. Until recently, the pace of research in this field has been hampered by the lack of efficient methods for genome editing. We report the development of a highly efficient and flexible genome editing system for use with C. albicans. This system improves upon previously published C. albicans CRISPR systems and enables rapid, precise genome editing without the use of permanent markers. This new tool kit promises to expedite the pace of research on this important fungal pathogen.

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