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Crop Genome Editing and Plant Breeding Innovation

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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 (30 December 2022) | Viewed by 13376

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Special Issue Editors

Prof. Dr. Ki-Hong Jung

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Guest Editor

Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
Interests: rice; root hair development; pollen genetics; ROS process; abiotic stress tolerance; transcirptome analysis; network analysis; genome editing; phylogenomics
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Jae-Yean Kim

E-Mail Website
Guest Editor

Division of Life Science, Gyeongsang National University, 27-306, 501 Jinju-Daero, Jinju, Gyeongnam 660-701, Republic of Korea
Interests: plasmodesmata; phloem; cell-to-cell communication; intercellular protein and RNA trafficking; genome editing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The introduction and commercialization of genetically modified organisms (GMOs) in the history of human agriculture was a landmark progress. GMO genomes contain foreign genes (foreign DNA fragments) as they are created by injecting recombinant foreign genes developed in a laboratory. Despite various obstacles, GMOs have succeeded in exceeding 50% of the global seed market within 18 years after launch. However, as the market power of GMOs grew, the anti-GMO movement also grew stronger. As with all technologies, the technology itself is not a perfect one, and it conceives new developments and sometimes becomes the mother of completely new innovative technologies. Here are new breeding techniques (NBT). NBT do not use recombinant DNA at all or even if NBT use the same recombinant genes developed in the laboratory, the final products produced by NBT do not contain the used recombinant foreign gene and contains only useful mutations in its own genome. Thus, these products are indistinguishable from traditionally bred products. This technology is innovative with more precision, efficiency, and safety. The techniques applied to crop improvement is called as new plant breeding techniques (NPBT) or plant breeding innovation (PBI) that now open a new era for crop breeding. Therefore, we would like to suggest a special issue on the R&D and application of crop gene editing technology related to PBI.

Papers submitted to this Special Issue must report novel results and/or plausible and testable new models or review. We also encourage authors to submit their manuscripts as extensions of our Special issue topic.

Prof. Dr. Ki-Hong Jung
Prof. Dr. Jae-Yean Kim
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

CRISPR/Cas

crop

crop genome editing

New Plant Breeding Techniques

New Genomic Techniques

Published Papers (5 papers)

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Research

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15 pages, 3956 KiB

Open AccessArticle

Identification and Functional Validation of Auxin-Responsive Tabzip Genes from Wheat Leaves in Arabidopsis

by Ziyao Jia, Mengjie Zhang, Can Ma, Zanqiang Wang, Zhonghua Wang, Yan Fang and Jun Wang

Int. J. Mol. Sci. 2023, 24(1), 756; https://doi.org/10.3390/ijms24010756 - 01 Jan 2023

Viewed by 1260

Abstract

Leaves are an essential and unique organ of plants, and many studies have proved that auxin has significant impacts on the architecture of leaves, thus the manipulation of the three-dimensional structure of a leaf could provide potential strategies for crop yields. In this study, 32 basic leucine zipper transcription factors (bZIP TFs) which responded to 50 μM of indole-acetic acid (IAA) were identified in wheat leaves by transcriptome analysis. Phylogenetic analysis indicated that the 32 auxin-responsive TabZIPs were classified into eight groups with possible different functions. Phenotypic analysis demonstrated that knocking out the homologous gene of the most down-regulated auxin-responsive TabZIP6D_20 in Arabidopsis (AtHY5) decreased its sensitivity to 1 and 50 μM IAA, while the TabZIP6D_20/hy5 complementary lines recovered its sensitivity to auxin as a wild type (Wassilewskija), suggesting that the down-regulated TabZIP6D_20 was a negative factor in the auxin-signaling pathway. These results demonstrated that the auxin-responsive TabZIP genes might have various and vital functions in the architecture of a wheat leaf under auxin response. Full article

(This article belongs to the Special Issue Crop Genome Editing and Plant Breeding Innovation)

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13 pages, 1499 KiB

Open AccessArticle

CRISPR/Cas9-Induced Mutagenesis of TMS5 Confers Thermosensitive Genic Male Sterility by Influencing Protein Expression in Rice (Oryza sativa L.)

by Yaoyu Fang, Jinlian Yang, Xinying Guo, Yufen Qin, Hai Zhou, Shanyue Liao, Fang Liu, Baoxiang Qin, Chuxiong Zhuang and Rongbai Li

Int. J. Mol. Sci. 2022, 23(15), 8354; https://doi.org/10.3390/ijms23158354 - 28 Jul 2022

Cited by 5 | Viewed by 1786

Abstract

The development of thermosensitive genic male sterile (TGMS) lines is the key to breeding two-line hybrid rice, which has been widely applied in China to increase grain yield. CRISPR/Cas9 has been widely used in genome editing to create novel mutants in rice. In the present study, a super grain quality line, GXU 47, was used to generate a new TGMS line with specific mutations in a major TGMS gene tms5 generated with CRISPR/Cas9-mediated genome editing in order to improve the rice quality of two-line hybrids. A mutagenesis efficiency level of 75% was achieved, and three homozygous T-DNA-free mutant lines were screened out. The mutants exhibited excellent thermosensitive male fertility transformation characteristics with complete male sterility at ≥24 °C and desirable male fertility at around 21 °C. Proteomic analysis based on isobaric tags for relative and absolute quantification (iTRAQ) was performed to unveil the subsequent proteomic changes. A total of 192 differentially expressed proteins (DEPs), including 35 upregulated and 157 downregulated, were found. Gene ontology (GO) analysis revealed that the DEPs were involved in a single-organism biosynthetic process, a single-organism metabolic process, oxidoreductase activity, and catalytic activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEPs were involved in ubiquinone and other terpenoid quinone biosynthesis, the biosynthesis of secondary metabolites, metabolic pathways, and phenylpropanoid biosynthesis. Our study shows that high mutation efficiency was achieved in both target sites, and T-DNA-free mutant lines were obtained in the T₁ generation. The present study results prove that it is feasible and efficient to generate an excellent mutant line with CRISPR/Cas9, which provides a novel molecular mechanism of male sterility caused by the mutation of tms5. Full article

(This article belongs to the Special Issue Crop Genome Editing and Plant Breeding Innovation)

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16 pages, 2069 KiB

Open AccessArticle

Identification of Differentially Expressed Genes in Resistant Tetraploid Wheat (Triticum turgidum) under Sitobion avenae (F.) Infestation

by Xinlun Liu, Xudan Kou, Shichao Bai, Yufeng Luo, Zhenyu Wang, Lincai Xie, Pingchuan Deng, Hong Zhang, Changyou Wang, Yajuan Wang, Jixin Zhao and Wanquan Ji

Int. J. Mol. Sci. 2022, 23(11), 6012; https://doi.org/10.3390/ijms23116012 - 27 May 2022

Cited by 1 | Viewed by 1469

Abstract

The grain aphid Sitobion avenae (Fabricius) is one of the most destructive pests of wheat (Triticum aestivum). Deployment of resistant wheat germplasm appears as an excellent solution for this problem. Elite bread wheat cultivars only have limited resistance to this pest. The present study was carried out to investigate the potential of the tetraploid wheat (Triticum turgidum) variety Lanmai, which showed high resistance to S. avenae at both seedling and adult plant stages, as a source of resistance genes. Based on apterous adult aphids’ fecundity tests and choice bioassays, Lanmai has been shown to display antixenosis and antibiosis. Suppression subtractive hybridization (SSH) was employed to identify and isolate the putative candidate defense genes in Lanmai against S. avenae infestation. A total of 134 expressed sequence tags (ESTs) were identified and categorized based on their putative functions. RT-qPCR analysis of 30 selected genes confirmed their differential expression over time between the resistant wheat variety Lanmai and susceptible wheat variety Polan305 during S. avenae infestation. There were 11 genes related to the photosynthesis process, and only 3 genes showed higher expression in Lanmai than in Polan305 after S. avenae infestation. Gene expression analysis also revealed that Lanmai played a critical role in salicylic acid and jasmonic acid pathways after S. avenae infestation. This study provided further insights into the role of defense signaling networks in wheat resistance to S. avenae and indicates that the resistant tetraploid wheat variety Lanmai may provide a valuable resource for aphid tolerance improvement in wheat. Full article

(This article belongs to the Special Issue Crop Genome Editing and Plant Breeding Innovation)

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18 pages, 3844 KiB

Open AccessArticle

Transcriptome Analysis of Triple Mutant for OsMADS62, OsMADS63, and OsMADS68 Reveals the Downstream Regulatory Mechanism for Pollen Germination in Rice (Oryza sativa)

by Eui-Jung Kim, Woo-Jong Hong, Yu-Jin Kim and Ki-Hong Jung

Int. J. Mol. Sci. 2022, 23(1), 239; https://doi.org/10.3390/ijms23010239 - 27 Dec 2021

Cited by 14 | Viewed by 3472

Abstract

The MADS (MCM1-AGAMOUS-DEFFICIENS-SRF) gene family has a preserved domain called MADS-box that regulates downstream gene expression as a transcriptional factor. Reports have revealed three MADS genes in rice, OsMADS62, OsMADS63, and OsMADS68, which exhibits preferential expression in mature rice pollen grains. To better understand the transcriptional regulation of pollen germination and tube growth in rice, we generated the loss-of-function homozygous mutant of these three OsMADS genes using the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9) system in wild-type backgrounds. Results showed that the triple knockout (KO) mutant showed a complete sterile phenotype without pollen germination. Next, to determine downstream candidate genes that are transcriptionally regulated by the three OsMADS genes during pollen development, we proceeded with RNA-seq analysis by sampling the mature anther of the mutant and wild-type. Two hundred and seventy-four upregulated and 658 downregulated genes with preferential expressions in the anthers were selected. Furthermore, downregulated genes possessed cell wall modification, clathrin coat assembly, and cellular cell wall organization features. We also selected downregulated genes predicted to be directly regulated by three OsMADS genes through the analyses for promoter sequences. Thus, this study provides a molecular background for understanding pollen germination and tube growth mediated by OsMADS62, OsMADS63, and OsMADS68 with mature pollen preferred expression. Full article

(This article belongs to the Special Issue Crop Genome Editing and Plant Breeding Innovation)

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Review

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17 pages, 1312 KiB

Open AccessReview

Recent Progress in Rice Broad-Spectrum Disease Resistance

by Zhiquan Liu, Yujun Zhu, Huanbin Shi, Jiehua Qiu, Xinhua Ding and Yanjun Kou

Int. J. Mol. Sci. 2021, 22(21), 11658; https://doi.org/10.3390/ijms222111658 - 28 Oct 2021

Cited by 21 | Viewed by 4330

Abstract

Rice is one of the most important food crops in the world. However, stable rice production is constrained by various diseases, in particular rice blast, sheath blight, bacterial blight, and virus diseases. Breeding and cultivation of resistant rice varieties is the most effective method to control the infection of pathogens. Exploitation and utilization of the genetic determinants of broad-spectrum resistance represent a desired way to improve the resistance of susceptible rice varieties. Recently, researchers have focused on the identification of rice broad-spectrum disease resistance genes, which include R genes, defense-regulator genes, and quantitative trait loci (QTL) against two or more pathogen species or many isolates of the same pathogen species. The cloning of broad-spectrum disease resistance genes and understanding their underlying mechanisms not only provide new genetic resources for breeding broad-spectrum rice varieties, but also promote the development of new disease resistance breeding strategies, such as editing susceptibility and executor R genes. In this review, the most recent advances in the identification of broad-spectrum disease resistance genes in rice and their application in crop improvement through biotechnology approaches during the past 10 years are summarized. Full article

(This article belongs to the Special Issue Crop Genome Editing and Plant Breeding Innovation)

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