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Molecular Breeding of Plants: From CRISPR/Cas9 to Transcriptomics and MABc

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (20 April 2026) | Viewed by 5923

Editor


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Guest Editor
Division of Horticultural Biotechnology, Hankyung National University, Anseong 17579, Republic of Korea
Interests: functional analysis of genes via CRISPR/Cas9; functional genomics; MABc (marker-assisted backcross); transcriptomics; plant biotechnology; molecular breeding in plants
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Special Issue Information

Dear Colleagues,

The study of cellular processes using novel genome-reading strategies, especially CRISPR/Cas9, is becoming increasingly feasible and powerful. Clustered regular interspersed short palindromic repeat (CRISPR) RNA (crRNA) is commonly used with the CRISPR-associated 9 (Cas9) nuclease to disrupt genes for loss-of-function assays. These mechanisms are approaches to introduce or reverse DNA fragments exhibiting polymorphisms in the genome using the error-prone nonhomologous end-joining (NHEJ) DNA repair pathway or the much less efficient homology directed repair (HDR) pathway. This report is interesting to see how gene editing, such as NHEJ and HDR, affects the expression of many other genes in the genome, as well as breeding mutations. Therefore, as a means to secure various genetic resources, we plan to accept papers presented on the development of new breeding programs using gene editing technology and various analysis methods. This Special Issue of the International Journal of Molecular Sciences (IJMS) welcomes articles on reviews and findings.

Prof. Dr. Kwon-Kyoo Kang
Guest Editor

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Keywords

  • CRISPR/Cas9
  • transcriptomics
  • marker-assisted breeding
  • genome editing
  • plant genetics
  • gene expression
  • plant genomics
  • quantitative trait loci (QTL)
  • crop improvement

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Published Papers (2 papers)

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Research

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12 pages, 3044 KB  
Article
Physicochemical Properties and Antioxidant Activity of CRISPR/Cas9-Edited Tomato SGR1 Knockout (KO) Line
by Jin Young Kim, Dong Hyun Kim, Me-Sun Kim, Yu Jin Jung and Kwon Kyoo Kang
Int. J. Mol. Sci. 2024, 25(10), 5111; https://doi.org/10.3390/ijms25105111 - 8 May 2024
Cited by 16 | Viewed by 3204
Abstract
Tomatoes contain many secondary metabolites such as β-carotene, lycopene, phenols, flavonoids, and vitamin C, which are responsible for antioxidant activity. SlSGR1 encodes a STAY-GREEN protein that plays a critical role in the regulation of chlorophyll degradation in tomato leaves and fruits. Therefore, [...] Read more.
Tomatoes contain many secondary metabolites such as β-carotene, lycopene, phenols, flavonoids, and vitamin C, which are responsible for antioxidant activity. SlSGR1 encodes a STAY-GREEN protein that plays a critical role in the regulation of chlorophyll degradation in tomato leaves and fruits. Therefore, the present study was conducted to evaluate the sgr1 null lines based on their physicochemical characteristics, the content of secondary metabolites, and the γ-Aminobutyric acid (GABA) content. The total soluble solids (TSS), titrated acidity (TA), and brix acid ratio (BAR) of the sgr1 null lines were higher than those of the wild type(WT). Additionally, the sgr1 null lines accumulated higher levels of flavor-inducing ascorbic acid and total carotenoids compared to WT. Also, the total phenolic content, total flavonoids, GABA content, and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical content of the sgr1 null lines were higher than those of the WT. Therefore, these studies suggest that the knockout of the SGR1 gene by the CRISPR/Cas9 system can improve various functional compounds in tomato fruit, thereby satisfying the antioxidant properties required by consumers. Full article
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Review

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24 pages, 1604 KB  
Review
Advances in CRISPR Plant Applications
by Leo Jing, Devjyoti Roy and Melanie Kalischuk
Int. J. Mol. Sci. 2026, 27(9), 4095; https://doi.org/10.3390/ijms27094095 - 3 May 2026
Viewed by 1499
Abstract
The ability to precisely edit genetic characteristics with a CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) immunity complex is a revolutionary advance in science. Originally discovered in bacteria as part of a natural defense mechanism against viruses, CRISPR/Cas provides a precise, efficient, [...] Read more.
The ability to precisely edit genetic characteristics with a CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) immunity complex is a revolutionary advance in science. Originally discovered in bacteria as part of a natural defense mechanism against viruses, CRISPR/Cas provides a precise, efficient, and relatively simple method for editing genes in microbes, plants, animals, and humans. The process relies on the Cas protein, an enzyme that cleaves and unwinds DNA at targeted locations. This process is guided by RNA sequences complementary to the DNA or RNA sequence of interest, allowing for changes to the genome through innate non-homologous end joining (NHEJ) and homology-directed repair (HDR). The potential applications of CRISPR/Cas are immense and, in agriculture, is facilitating crop development with resistance to abiotic, biotic, and agronomic characteristics that improve yield, quality, and food security. Gene editing also facilitates the relatively rapid modification of regulatory and complex pathways that enable studies to advance our understanding of gene function. This review provides an update of the fast-evolving CRISPR/Cas modification of important crops to address emerging global population, as well as environmental and climate challenges. Full article
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