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Discovery of Gene Functions in Crops by Genome Editing and Genomics

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 (25 April 2024) | Viewed by 5504

Special Issue Editor

Prof. Dr. Dénes Dudits

E-Mail Website
Guest Editor
Biological Research Center at Hungarian Academy of Sciences, H-6726 Szeged, Hungary
Interests: plant genetics and breeding

Special Issue Information

Dear Colleagues,

Crop plants are in a central position in ensuring the food supply under increasing demands. The future of our living environment is largely dependent on plant functions. Increases in plant productivity requires a deep understanding and specific alterations of gene functions. The development of high-throughput sequencing technologies, along with a wide range of gene isolation and transformation protocols, have opened efficient ways for determining the function of specific genes and their targeted mutant forms. Recently, the extensive use of genome editing technologies, preferentially CRISPR-Cas9 technology, has triggered a new area in linking genes with phenotypic traits. The present Special Issue will be focused on the improvement of genome editing tools in order to gain better a understanding of the genetic regulation of plant productivity. Transformation via CRISPR vectors is frequently carried out in in vitro cultures; therefore, plant regeneration of mutant plants is a basic requirement. Identification of targeted cells using fluorescence microscopy and selection of mutated cells is a key issue. We might expect more studies on in planta editing. There is a need for genome editing tools that result in transgene-free plants. In this case, the uptake of DNS or protein molecules into morphogenic plant cells is a key research topic. Synthetic oligonucleotide directed mutagenesis (ODM) is expected to gain more attention in the plant field. We welcome the submission of original research and methodological articles that contribute to progress in gene discovery projects or in the actual breeding of crop species.

Prof. Dr. Dénes Dudits
Guest Editor

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 vectors
  • transgenic
  • recombination
  • chromatin structure
  • directed mutagenesis for stress tolerance
  • oligonucleotide mutagenesis
  • in planta

Published Papers (5 papers)

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Research

16 pages, 8498 KiB  
Article
Combining Transcriptome and Whole Genome Re-Sequencing to Screen Disease Resistance Genes for Wheat Dwarf Bunt
by Yufeng Jia, Tong Shen, Zhiwei Wen, Jing Chen and Qi Liu
Int. J. Mol. Sci. 2023, 24(24), 17356; https://doi.org/10.3390/ijms242417356 - 11 Dec 2023
Viewed by 901
Abstract
Wheat dwarf bunt is a damaging disease caused by Tilletia controversa Kühn (TCK). Once the disease infects wheat, it is difficult to control and will significantly reduce wheat output and quality. RNA sequencing and whole genome re-sequencing were used to search for potential [...] Read more.
Wheat dwarf bunt is a damaging disease caused by Tilletia controversa Kühn (TCK). Once the disease infects wheat, it is difficult to control and will significantly reduce wheat output and quality. RNA sequencing and whole genome re-sequencing were used to search for potential TCK resistance genes in Yili 053 (sensitive variety) and Zhongmai 175 (moderately resistant variety) in the mid-filling, late-filling, and maturity stages. The transcriptomic analysis revealed 11 potential disease resistance genes. An association analysis of the findings from re-sequencing found nine genes with single nucleotide polymorphism mutations. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that three up-regulated genes were involved in the synthesis of benzoxazinone and tryptophan metabolism. Additionally, quantitative real-time polymerase chain reaction confirmed the RNA sequencing results. The results revealed novel TCK resistance genes and provide a theoretical basis for researching the function of resistance genes and molecular breeding. Full article
(This article belongs to the Special Issue Discovery of Gene Functions in Crops by Genome Editing and Genomics)
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19 pages, 5988 KiB  
Article
Kernel Transcriptome Profiles of Susceptible Wheat Genotypes in Response to Wheat Dwarf Bunt
by Shenqiang Su, Zihao Zhang, Tong Shen, Jing Chen and Qi Liu
Int. J. Mol. Sci. 2023, 24(24), 17281; https://doi.org/10.3390/ijms242417281 - 08 Dec 2023
Cited by 1 | Viewed by 750
Abstract
Wheat dwarf bunt is caused by Tilletia controversa J. G. Kühn (TCK), which is a serious fungal diseases affecting kernels of wheat. In order to identify candidate genes involved in the abnormal development of kernels in wheat, we used RNA sequencing technology to [...] Read more.
Wheat dwarf bunt is caused by Tilletia controversa J. G. Kühn (TCK), which is a serious fungal diseases affecting kernels of wheat. In order to identify candidate genes involved in the abnormal development of kernels in wheat, we used RNA sequencing technology to analyze the transcriptome of the abnormal and healthy kernels of a susceptible variety (Yili053) at the mid-filling stage, late-filling stage, and maturity stage, respectively. The differentially expressed genes (DEGs) were analyzed, and there were 3930 DEGs, 28,422 DEGs, and 20,874 DEGs found at the mid-filling stage, late-filling stage, and maturity stage in Yili053, respectively. A total of 1592 DEGs (506 DEGs up-regulated) showed continuously differential expression in the three stages. Gene ontology analysis showed that these DEGs were related to biological regulation, metabolic processes, and the response to stimulus. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that these DEGs play major roles in pathways including photosynthesis, carbon metabolism, carbon fixation in photosynthetic organisms, and glyoxylate and dicarboxylate metabolism. Moreover, we predicted that 13 MADS-MIKC transcription factors, which were continuously up-regulated, were crucial for regulating the maturation and senescence of eukaryotes. Some 21 genes related to the plant hormone signaling transduction pathway and 61 genes related to the response to stimulus were analyzed. A total of 26 of them were successful validated with a qPCR analysis. These genes were thought to be involved in the abnormal development of kernels infected by TCK. A transcriptomics analysis of wheat kernels in response to TCK will contribute to understanding the interaction of TCK and wheat, and may provide a basis for knowledge of molecular events in the abnormal development of kernels, which will be helpful for more efficient TCK management. Full article
(This article belongs to the Special Issue Discovery of Gene Functions in Crops by Genome Editing and Genomics)
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12 pages, 4496 KiB  
Article
CRISPR/Cas9 Mutagenesis through Introducing a Nanoparticle Complex Made of a Cationic Polymer and Nucleic Acids into Maize Protoplasts
by Bettina Nagy, Ayşegül Öktem, Györgyi Ferenc, Ditta Ungor, Aladina Kalac, Ildikó Kelemen-Valkony, Elfrieda Fodor, István Nagy, Dénes Dudits and Ferhan Ayaydin
Int. J. Mol. Sci. 2023, 24(22), 16137; https://doi.org/10.3390/ijms242216137 - 09 Nov 2023
Cited by 1 | Viewed by 982
Abstract
Presently, targeted gene mutagenesis attracts increasing attention both in plant research and crop improvement. In these approaches, successes are largely dependent on the efficiency of the delivery of gene editing components into plant cells. Here, we report the optimization of the cationic polymer [...] Read more.
Presently, targeted gene mutagenesis attracts increasing attention both in plant research and crop improvement. In these approaches, successes are largely dependent on the efficiency of the delivery of gene editing components into plant cells. Here, we report the optimization of the cationic polymer poly(2-hydroxypropylene imine) (PHPI)-mediated delivery of plasmid DNAs, or single-stranded oligonucleotides labelled with Cyanine3 (Cy3) or 6-Carboxyfluorescein (6-FAM)-fluorescent dyes into maize protoplasts. Co-delivery of the GFP-expressing plasmid and the Cy3-conjugated oligonucleotides has resulted in the cytoplasmic and nuclear accumulation of the green fluorescent protein and a preferential nuclear localization of oligonucleotides. We show the application of nanoparticle complexes, i.e., “polyplexes” that comprise cationic polymers and nucleic acids, for CRISPR/Cas9 editing of maize cells. Knocking out the functional EGFP gene in transgenic maize protoplasts was achieved through the co-delivery of plasmids encoding components of the editing factors Cas9 (pFGC-pcoCas9) and gRNA (pZmU3-gRNA) after complexing with a cationic polymer (PHPI). Several edited microcalli were identified based on the lack of a GFP fluorescence signal. Multi-base and single-base deletions in the EGFP gene were confirmed using Sanger sequencing. The presented results support the use of the PHPI cationic polymer in plant protoplast-mediated genome editing approaches. Full article
(This article belongs to the Special Issue Discovery of Gene Functions in Crops by Genome Editing and Genomics)
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11 pages, 977 KiB  
Article
The Detection of Yr Genes in Xinjiang Wheat Cultivars Using Different Molecular Markers
by Minghao Zhang, Ainisai Saimi, Qi Liu, Zeyu Ma and Jing Chen
Int. J. Mol. Sci. 2023, 24(17), 13372; https://doi.org/10.3390/ijms241713372 - 29 Aug 2023
Cited by 1 | Viewed by 1011
Abstract
Wheat stripe rust is a fungal disease caused by Puccinia striiformis f. sp. Tritici (Pst). It significantly impacts wheat yields in Xinjiang, China. Breeding and promoting disease-resistant cultivars carrying disease-resistance genes remains the most cost-effective strategy with which to control the [...] Read more.
Wheat stripe rust is a fungal disease caused by Puccinia striiformis f. sp. Tritici (Pst). It significantly impacts wheat yields in Xinjiang, China. Breeding and promoting disease-resistant cultivars carrying disease-resistance genes remains the most cost-effective strategy with which to control the disease. In this study, 17 molecular markers were used to identify Yr5, Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, Yr41, Yr44, and Yr50 in 82 wheat cultivars from Xinjiang. According to the differences in SNP loci, the KASP markers for Yr30, Yr52, Yr78, Yr80, and Yr81 were designed and detected in the same set of 82 wheat cultivars. The results showed that there was a diverse distribution of Yr genes across all wheat cultivars in Xinjiang, and the detection rates of Yr5, Yr15, Yr17, Yr26, Yr41, and Yr50 were the highest, ranging from 74.39% to 98.78%. In addition, Yr5 and Yr15 were prevalent in spring wheat cultivars, with detection rates of 100% and 97.56%, respectively. A substantial 85.37% of wheat cultivars carried at least six or more different combinations of Yr genes. The cultivar Xindong No.15 exhibited the remarkable presence of 11 targeted Yr genes. The pedigree analysis results showed that 33.33% of Xinjiang wheat cultivars shared similar parentage, potentially leading to a loss of resistance against Pst. The results clarified the Yr gene distribution of the Xinjiang wheat cultivars and screened out varieties with a high resistance against Pst. Full article
(This article belongs to the Special Issue Discovery of Gene Functions in Crops by Genome Editing and Genomics)
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14 pages, 2863 KiB  
Article
RNA-Seq Transcriptome Analysis and Evolution of OsEBS, a Gene Involved in Enhanced Spikelet Number per Panicle in Rice
by Fuan Niu, Mingyu Liu, Shiqing Dong, Xianxin Dong, Ying Wang, Can Cheng, Huangwei Chu, Zejun Hu, Fuying Ma, Peiwen Yan, Dengyong Lan, Jianming Zhang, Jihua Zhou, Bin Sun, Anpeng Zhang, Jian Hu, Xinwei Zhang, Shicong He, Jinhao Cui, Xinyu Yuan, Jinshui Yang, Liming Cao and Xiaojin Luoadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2023, 24(12), 10303; https://doi.org/10.3390/ijms241210303 - 18 Jun 2023
Viewed by 1208
Abstract
Spikelet number per panicle (SNP) is one of the most important yield components in rice. Rice ENHANCING BIOMASS AND SPIKELET NUMBER (OsEBS), a gene involved in improved SNP and yield, has been cloned from an accession of Dongxiang wild rice. However, [...] Read more.
Spikelet number per panicle (SNP) is one of the most important yield components in rice. Rice ENHANCING BIOMASS AND SPIKELET NUMBER (OsEBS), a gene involved in improved SNP and yield, has been cloned from an accession of Dongxiang wild rice. However, the mechanism of OsEBS increasing rice SNP is poorly understood. In this study, the RNA-Seq technology was used to analyze the transcriptome of wildtype Guichao 2 and OsEBS over-expression line B102 at the heading stage, and analysis of the evolution of OsEBS was also conducted. A total of 5369 differentially expressed genes (DEGs) were identified between Guichao2 and B102, most of which were down-regulated in B102. Analysis of the expression of endogenous hormone-related genes revealed that 63 auxin-related genes were significantly down-regulated in B102. Gene Ontogeny (GO) enrichment analysis showed that the 63 DEGs were mainly enriched in eight GO terms, including auxin-activated signaling pathway, auxin polar transport, auxin transport, basipetal auxin transport, and amino acid transmembrane transport, most of which were directly or indirectly related to polar auxin transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis further verified that the down-regulated genes related to polar auxin transport had important effects on increased SNP. Analysis of the evolution of OsEBS found that OsEBS was involved in the differentiation of indica and japonica, and the differentiation of OsEBS supported the multi-origin model of rice domestication. Indica (XI) subspecies harbored higher nucleotide diversity than japonica (GJ) subspecies in the OsEBS region, and XI experienced strong balancing selection during evolution, while selection in GJ was neutral. The degree of genetic differentiation between GJ and Bas subspecies was the smallest, while it was the highest between GJ and Aus. Phylogenetic analysis of the Hsp70 family in O. sativa, Brachypodium distachyon, and Arabidopsis thaliana indicated that changes in the sequences of OsEBS were accelerated during evolution. Accelerated evolution and domain loss in OsEBS resulted in neofunctionalization. The results obtained from this study provide an important theoretical basis for high-yield rice breeding. Full article
(This article belongs to the Special Issue Discovery of Gene Functions in Crops by Genome Editing and Genomics)
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