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Special Issue "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: 30 September 2023 | Viewed by 1425

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 (2 papers)

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Research

Article
The Detection of Yr Genes in Xinjiang Wheat Cultivars Using Different Molecular Markers
Int. J. Mol. Sci. 2023, 24(17), 13372; https://doi.org/10.3390/ijms241713372 - 29 Aug 2023
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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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Article
RNA-Seq Transcriptome Analysis and Evolution of OsEBS, a Gene Involved in Enhanced Spikelet Number per Panicle in Rice
Int. J. Mol. Sci. 2023, 24(12), 10303; https://doi.org/10.3390/ijms241210303 - 18 Jun 2023
Viewed by 610
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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