Genome Editing for Resistance to Insect Pests: An Emerging Tool for Crop Improvement

A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from Prevotella and Francisella1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.

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Genetic and signalling pathways of dry fruit size: targets for genome editing‐based crop improvement

Plant Biotechnology Journal ◽

10.1111/pbi.13318 ◽

2020 ◽

Vol 18 (5) ◽

pp. 1124-1140

Author(s):

Quaid Hussain ◽

Jiaqin Shi ◽

Armin Scheben ◽

Jiepeng Zhan ◽

Xinfa Wang ◽

...

Keyword(s):

Genome Editing ◽

Crop Improvement ◽

Fruit Size ◽

Signalling Pathways ◽

Dry Fruit

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Concepts of Molecular Plant Breeding and Genome Editing

Advances in Environmental Engineering and Green Technologies - Molecular Plant Breeding and Genome Editing Tools for Crop Improvement ◽

10.4018/978-1-7998-4312-2.ch001 ◽

2021 ◽

pp. 1-15

Keyword(s):

Plant Breeding ◽

Genome Editing ◽

Genetic Linkage ◽

Selection Process ◽

Crop Improvement ◽

Zinc Finger Nucleases ◽

Induced Mutations ◽

Transcription Activator ◽

Targeted Gene Editing ◽

Breeding Techniques

Traditional plant breeding depends on spontaneous and induced mutations available in the crop plants. Such mutations are rare and occur randomly. By contrast, molecular breeding and genome editing are advanced breeding techniques that can enhance the selection process and produce precisely targeted modifications in any crop. Identification of molecular markers, based on SSRs and SNPs, and the availability of high-throughput (HTP) genotyping platforms have accelerated the process of generating dense genetic linkage maps and thereby enhanced application of marker-assisted breeding for crop improvement. Advanced molecular biology techniques that facilitate precise, efficient, and targeted modifications at genomic loci are termed as “genome editing.” The genome editing tools include “zinc-finger nucleases (ZNFs),” “transcription activator-like effector nucleases (TALENs),” oligonucleotide-directed mutagenesis (ODM), and “clustered regularly interspersed short palindromic repeats (CRISPER/Cas) system,” which can be used for targeted gene editing. Concepts of molecular plant breeding and genome editing systems are presented in this chapter.

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Molecular Plant Breeding and Genome Editing Tools for Crop Improvement

10.4018/978-1-7998-4312-2 ◽

2021 ◽

Author(s):

Pradip Chandra Deka

Keyword(s):

Plant Breeding ◽

Genome Editing ◽

Crop Improvement

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Mutation Breeding in Tomato: Advances, Applicability and Challenges

Plants ◽

10.3390/plants8050128 ◽

2019 ◽

Vol 8 (5) ◽

pp. 128 ◽

Cited By ~ 12

Author(s):

Juhi Chaudhary ◽

Alisha Alisha ◽

Vacha Bhatt ◽

Sonali Chandanshive ◽

Nirbhay Kumar ◽

...

Keyword(s):

Genome Editing ◽

Large Scale ◽

Insertional Mutagenesis ◽

Crop Improvement ◽

Mutation Breeding ◽

Tomato Crop ◽

Technological Advances ◽

Trait Improvement ◽

Induced Mutagenesis ◽

Efficient Exploration

Induced mutagenesis is one of the most effective strategies for trait improvement without altering the well-optimized genetic background of the cultivars. In this review, several currently accessible methods such as physical, chemical and insertional mutagenesis have been discussed concerning their efficient exploration for the tomato crop improvement. Similarly, challenges for the adaptation of genome-editing, a newly developed technique providing an opportunity to induce precise mutation, have been addressed. Several efforts of genome-editing have been demonstrated in tomato and other crops, exploring its effectiveness and convenience for crop improvement. Descriptive data compiled here from such efforts will be helpful for the efficient exploration of technological advances. However, uncertainty about the regulation of genome-edited crops is still a significant concern, particularly when timely trait improvement in tomato cultivars is needed. In this regard, random approaches of induced mutagenesis are still promising if efficiently explored in breeding applications. Precise identification of casual mutation is a prerequisite for the molecular understanding of the trait development as well as its utilization for the breeding program. Recent advances in sequencing techniques provide an opportunity for the precise detection of mutagenesis-induced sequence variations at a large scale in the genome. Here, we reviewed several novel next-generation sequencing based mutation mapping approaches including Mutmap, MutChromeSeq, and whole-genome sequencing-based mapping which has enormous potential to accelerate the mutation breeding in tomato. The proper utilization of the existing well-characterized tomato mutant resources combined with novel mapping approaches would inevitably lead to rapid enhancement of tomato quality and yield. This article provides an overview of the principles and applications of mutagenesis approaches in tomato and discusses the current progress and challenges involved in tomato mutagenesis research.

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230 Genome editing applications in plants: high-throughput CRISPR/Cas editing for crop improvement

Journal of Animal Science ◽

10.1093/jas/skz258.115 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 56-56

Author(s):

Michael Thomson

Keyword(s):

Genome Editing ◽

High Throughput ◽

Positional Cloning ◽

Gene Editing ◽

Crop Improvement ◽

Cost Effective ◽

Gene Families ◽

Ease Of Use ◽

Plant Genome ◽

Wide Range

Abstract The precision and ease of use of CRISPR nucleases, such as Cas9 and Cpf1, for plant genome editing has the potential to accelerate a wide range of applications for crop improvement. For upstream research on gene discovery and validation, rapid gene knock-outs can enable testing of single genes and multi-gene families for functional effects. Large chromosomal deletions can test the function of tandem gene arrays and assist with positional cloning of QTLs by helping to narrow down the target region. Nuclease-deactivated Cas9 fusion proteins with transcriptional activators and repressors can be used to up and down-regulate gene expression. Even more promising, gene insertions and allele replacements can provide the opportunity to rapidly test the effects of different alleles at key loci in the same genetic background, providing a more precise alternative to marker-assisted backcrossing. Recently, Texas A&M AgriLife Research has supported the development of a Crop Genome Editing Lab at Texas A&M working towards optimizing a high-throughput gene editing pipeline and providing an efficient and cost-effective gene editing service for research and breeding groups. The lab is using rice as a model to test and optimize new approaches aimed towards overcoming current bottlenecks. For example, a wealth of genomics data from the rice community enables the development of novel approaches to predict which genes and target modifications may be most beneficial for crop improvement, taking advantage of known major genes, high-resolution GWAS data, multiple high-quality reference genomes, transcriptomics data, and resequencing data from the 3,000 Rice Genomes Project. Current projects have now expanded to work across multiple crops to provide breeding and research groups with a rapid gene editing pipeline to test candidate genes in their programs, with the ultimate goal of developing nutritious, high-yielding, stress-tolerant crops for the future.

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Genome Editing in Cereals: Approaches, Applications and Challenges

International Journal of Molecular Sciences ◽

10.3390/ijms21114040 ◽

2020 ◽

Vol 21 (11) ◽

pp. 4040 ◽

Cited By ~ 4

Author(s):

Waquar A. Ansari ◽

Sonali U. Chandanshive ◽

Vacha Bhatt ◽

Altafhusain B. Nadaf ◽

Sanskriti Vats ◽

...

Keyword(s):

Genome Editing ◽

Target Genes ◽

Crop Improvement ◽

Whole Genome Sequence ◽

Cereal Crops ◽

Sequence Information ◽

World Population ◽

Base Editing ◽

Crop Varieties ◽

Current Scenario

Over the past decades, numerous efforts were made towards the improvement of cereal crops mostly employing traditional or molecular breeding approaches. The current scenario made it possible to efficiently explore molecular understanding by targeting different genes to achieve desirable plants. To provide guaranteed food security for the rising world population particularly under vulnerable climatic condition, development of high yielding stress tolerant crops is needed. In this regard, technologies upgradation in the field of genome editing looks promising. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 is a rapidly growing genome editing technique being effectively applied in different organisms, that includes both model and crop plants. In recent times CRISPR/Cas9 is being considered as a technology which revolutionized fundamental as well as applied research in plant breeding. Genome editing using CRISPR/Cas9 system has been successfully demonstrated in many cereal crops including rice, wheat, maize, and barley. Availability of whole genome sequence information for number of crops along with the advancement in genome-editing techniques provides several possibilities to achieve desirable traits. In this review, the options available for crop improvement by implementing CRISPR/Cas9 based genome-editing techniques with special emphasis on cereal crops have been summarized. Recent advances providing opportunities to simultaneously edit many target genes were also discussed. The review also addressed recent advancements enabling precise base editing and gene expression modifications. In addition, the article also highlighted limitations such as transformation efficiency, specific promoters and most importantly the ethical and regulatory issues related to commercial release of novel crop varieties developed through genome editing.

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Enhancement of the use and impact of germplasm in crop improvement

Plant Genetic Resources ◽

10.1017/s1479262114000458 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S155-S159 ◽

Cited By ~ 5

Author(s):

H. D. Upadhyaya ◽

S. L. Dwivedi ◽

S. Sharma ◽

N. Lalitha ◽

S. Singh ◽

...

Keyword(s):

Insect Pests ◽

Raw Materials ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Breeding Programs ◽

Genome Wide ◽

Pod Borer ◽

Genetic Stocks ◽

Beneficial Traits ◽

Allelic Variations

Plant genetic resources are raw materials and their use in breeding is one of the most sustainable ways to conserve biodiversity. The ICRISAT has over 120,000 accessions of its five mandate crops and six small millets. The management and utilization of such large diversity are greatest challenges to germplasm curators and crop breeders. New sources of variations have been discovered using core and minicore collections developed at the ICRISAT. About 1.4 million seed samples have been distributed; some accessions with specific attributes have been requested more frequently. The advances in genomics have led researchers to dissect population structure and diversity and mine allelic variations associated with agronomically beneficial traits. Genome-wide association mapping in sorghum has revealed significant marker–trait associations for many agronomically beneficial traits. Wild relatives harbour genes for resistance to diseases and insect pests. Resistance to pod borer in chickpea and pigeonpea and resistance to rust and late leaf spot in groundnut have been successfully introgressed into a cultivated genetic background. Synthetics in groundnut are available to broaden the cultigen's gene pool. ICRISAT has notified the release of 266 varieties/cultivars, germplasm, and elite genetic stocks with unique traits, with some having a significant impact on breeding programs. Seventy-five germplasm lines have been directly released for cultivation in 39 countries.

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