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Applications of CRISPR/Cas System in Plants

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The CRISPR/Cas Tool Kit for Genome Editing

Abstract

Over decades, success of genetic engineering has been proved by provision of several solutions to the problems related to biotic or abiotic stress, growth, yield, nutrition, and quality of the plants. Value addition and aesthetic improvement have also been addressed by genetic engineering techniques. Last decades witness a steeply development and progress in genetic engineering of plants using genome editing tools with more precision and accuracy. CRISPR/Cas, being an advanced genome editing tool, has been used more frequently for this purpose owing to its simplicity, designing, ease in cloning, and high modularity with low cost and high adaptability. Several plant parameters have been modified and improved using CRISPR technology. CRISPR toolbox has a variety of tools for gene editing/modification such as Cas9, Cas12, Cas13, base editors, prime editors, etc. Along with gene modifications, CRISPR/Cas has also been successfully deployed for gene regulation using CRISPRi and CRISPRa and epigenetic modifications using epigenetic modifiers such as LSD, TET1, etc. Moreover, multiplexing feature of CRISPR/Cas9 has given this technology an advantage over all other contemporary gene editing technologies to effectively target genomes. This chapter encompasses applications of CRISPR technology in several plant species for genetic improvement of multiple traits. We describe potential applications of CRISPR system in model as well as horticultural, legumes, and tree species. Finally, we discussed biosafety rules, regulations, and prospects of CRISPR technology in plant genome engineering.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

AGPase:

ADP-glucose pyrophosphorylase

BAC:

Bacterial artificial chromosome

cDNA:

Complementary DNA

CL:

Coumarate ligase

Cpf1:

CRISPR from Prevotella and Francisella

cr RNA:

CRISPR RNA

CRISPR:

Clustered regularly interspaced short palindromic repeats

CRISPRa:

CRISPR activation

CRISPRi:

CRISPR interference

dCas9:

Deactivated nuclease

DNA:

Deoxyribonucleic acid

DREB:

Dehydration-responsive element-binding protein

ERF:

Ethylene response factor

GBSS:

Granule-bound starch synthase

GenEd:

Genome editing

GEOs:

Genome edited organisms

GFP:

Green fluorescent protein

GM:

Genetically modified

GMOs:

Genetically modified organisms

gRNA:

Guided RNA

HDR:

Homology directed repair

KO:

Knockout

KRAB:

Kruppel-associated box

LSD:

Lysergic acid diethylamide

MDH:

Malate dehydrogenase

nGM:

Novel genetic modification techniques

NHEJ:

Non-homologous end joining

PAM:

Protospacer adjacent motif

PDS:

Phytoene desaturase

PEPC:

Phosphoenolpyruvate carboxylase

RGEN:

RNA-guided endonuclease

RNA:

Ribonucleic acid

RNAi:

RNA interference

RNP:

Ribonucleoprotein

SgRNA:

Single guided RNA

SSNs:

Sequence-specific nucleases

TALEN:

Transcription activator-like effector nucleases

TCA:

Tricarboxylic acid cycle

TILLING:

Targeting induced local lesions in genomes

tracrRNA:

Trans-activating CRISPR RNA

USDA:

United States Department of Agriculture

WDV:

Wheat dwarf virus

ZFN:

Zinc finger nucleases

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Authors and Affiliations

  1. Center of Agricultural Biochemistry and Biotechnology (CABB)/US-Pakistan Center for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan

    Sultan Habibullah Khan

  2. Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan

    Muhammad Zubair Ghouri & Muhammad Salman Mubarik

  3. Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan

    Muhammad Zubair Ghouri & Muhammad Salman Mubarik

  4. Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Sharif University of Agriculture, Multan, Pakistan

    Hooran Tariq, Iqra Farooq, Hira Tasleeem & Zulqurnain Khan

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  1. Sultan Habibullah Khan
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  2. Hooran Tariq
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  3. Iqra Farooq
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  5. Muhammad Zubair Ghouri
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  7. Zulqurnain Khan
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Editors and Affiliations

  1. Department of Biochemistry/US-Pakistan Center for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan

    Aftab Ahmad

  2. Center of Agricultural Biochemistry and Biotechnology (CABB)/US-Pakistan Center for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan

    Sultan Habibullah Khan

  3. Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Sharif University of Agriculture, Multan, Pakistan

    Zulqurnain Khan

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Khan, S.H. et al. (2022). Applications of CRISPR/Cas System in Plants. In: Ahmad, A., Khan, S.H., Khan, Z. (eds) The CRISPR/Cas Tool Kit for Genome Editing. Springer, Singapore. https://doi.org/10.1007/978-981-16-6305-5_9

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