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Plant Genetic and Epigenetic Engineering: New Advances and Molecular Tools

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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 2023) | Viewed by 7453

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Dr. Konstantin V. Kiselev

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Guest Editor

Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
Interests: plant secondary metabolism; stilbenes; plant gene expression; plant cell cultures; calcium signaling
Special Issues, Collections and Topics in MDPI journals

Dr. Alexandra S. Dubrovina

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Guest Editor

Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
Interests: plant secondary metabolism; RNA interference; plant gene regulation; abiotic stress; transgenic plants; calcium sensor proteins
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant biotechnology is considered a collection of breakthrough technologies that can help meet challenges in agriculture, horticulture, and forestry to obain plants with improved production properties and resilience to environmental cues. Plant biotechnology is an intensively developing field aimed at modifying plant properties with the assistance of modern molecular and physiolgical techniques in order to reach new or improved desirable plant characteristics. This Special Issue welcomes original research papers, reviews, communications, and opinion papers presenting new advances in the field of plant biotechnology and genetic engineering.

We welcome papers including, but not limited to, the following specific topics:

New advances in plant genetic engineering;
New advances using CRISPR–Cas technology;
Plant cell culture-based biotechnological approaches;
Creation, conservation, and utilization of genetic crop variability;
RNAi-based plant gene regulation techniques;
Host-induced gene silencing (HIGS);
Virus-induced gene silencing (VIGS);
Spray-induced gene silencing (SIGS);
Plant endophytes and their biotechnological applications;
Modern breeding methods;
Social, environmental, and global aspects of plant biotechnology.

Dr. Konstantin V. Kiselev
Dr. Alexandra S. Dubrovina
Guest Editors

Manuscript Submission Information

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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.

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Keywords

plant biotechnolgoy
genetic engineering
plant cell cultures
transgenic plants
CRISPR–Cas
plant gene regulation
RNA interference
gene silencing
crop variability
stress resistance

Published Papers (7 papers)

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Research

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14 pages, 3028 KiB

Open AccessArticle

pOsHAK1:OsSUT1 Promotes Sugar Transport and Enhances Drought Tolerance in Rice

by Guang Chen, Wenli Lian, Anjing Geng, Yihan Wang, Minghao Liu, Yue Zhang and Xu Wang

Int. J. Mol. Sci. 2024, 25(4), 2158; https://doi.org/10.3390/ijms25042158 - 10 Feb 2024

Viewed by 551

Abstract

Plant cells accumulate osmotic substances (e.g., sugar) to protect cell components and maintain osmotic balance under drought stress conditions. Previous studies found that pOsHAK1:OsFLN2 promotes sugar metabolism and improves the drought tolerance of rice plants under drought stress. This study further evaluated the effect of the ectopic expression of the OsSUT1 gene driven by the OsHAK1 promoter on the sugar transport and drought tolerance of rice. The results showed that the net photosynthetic rate and sucrose phosphate synthase activity of plants expressing the OsSUT1 gene were not significantly different from those of wild-type (WT) rice plants under drought conditions. However, the sucrose transport rate in the phloem increased in the transgenic plants, and the sucrose contents were significantly lower in the leaves but significantly higher in the roots of transgenic plants than those in WT plants. The pOsHAK1:OsSUT1 and pOsHAK1:OsFLN2 transgenic lines had similar rates of long-distance sucrose transport and drought tolerance, which were higher than those of the WT plants. The relative water content of the transgenic plants was higher, while their water loss rate, hydrogen peroxide (H₂O₂), and malondialdehyde (MDA) contents were lower than those of the WT plants. The stress-responsive gene OsbZIP23 and the antioxidant-related gene OsCATB were significantly upregulated in the drought-treated transgenic lines, while the senescence indicator gene SGR and the stress-responsive gene OsNAC2 were down-regulated compared to WT plants. These results showed that promoting the long-distance sugar transport through the expression of pOsHAK1:OsSUT1 could produce an improved drought tolerance effect similar to that of pOsHAK1:OsFLN2, providing an effective way to improve the drought tolerance of cereal crops at the seedling stage. Full article

(This article belongs to the Special Issue Plant Genetic and Epigenetic Engineering: New Advances and Molecular Tools)

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18 pages, 10135 KiB

Open AccessArticle

Picea wilsonii NAC31 and DREB2A Cooperatively Activate ERD1 to Modulate Drought Resistance in Transgenic Arabidopsis

by Yiming Huang, Bingshuai Du, Mingxin Yu, Yibo Cao, Kehao Liang and Lingyun Zhang

Int. J. Mol. Sci. 2024, 25(4), 2037; https://doi.org/10.3390/ijms25042037 - 07 Feb 2024

Viewed by 597

Abstract

The NAC family of transcription factors (TFs) regulate plant development and abiotic stress. However, the specific function and response mechanism of NAC TFs that increase drought resistance in Picea wilsonii remain largely unknown. In this study, we functionally characterized a member of the PwNAC family known as PwNAC31. PwNAC31 is a nuclear-localized protein with transcriptional activation activity and contains an NAC domain that shows extensive homology with ANAC072 in Arabidopsis. The expression level of PwNAC31 is significantly upregulated under drought and ABA treatments. The heterologous expression of PwNAC31 in atnac072 Arabidopsis mutants enhances the seed vigor and germination rates and restores the hypersensitive phenotype of atnac072 under drought stress, accompanied by the up-regulated expression of drought-responsive genes such as DREB2A (DEHYDRATION-RESPONSIVE ELEMENT BINDING PROTEIN 2A) and ERD1 (EARLY RESPONSIVE TO DEHYDRATION STRESS 1). Yeast two-hybrid and bimolecular fluorescence complementation assays confirmed that PwNAC31 interacts with DREB2A and ABF3 (ABSCISIC ACID-RESPONSIVE ELEMENT-BINDING FACTOR 3). Yeast one-hybrid and dual-luciferase assays showed that PwNAC31, together with its interaction protein DREB2A, directly regulated the expression of ERD1 by binding to the DRE element of the ERD1 promoter. Collectively, our study provides evidence that PwNAC31 activates ERD1 by interacting with DREB2A to enhance drought tolerance in transgenic Arabidopsis. Full article

(This article belongs to the Special Issue Plant Genetic and Epigenetic Engineering: New Advances and Molecular Tools)

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16 pages, 4528 KiB

Open AccessArticle

Genetic Model Identification and Major QTL Mapping for Petiole Thickness in Non-Heading Chinese Cabbage

by Guangyuan Liu, Yongkuan Li, Jia Si, Rong Lu and Maixia Hui

Int. J. Mol. Sci. 2024, 25(2), 802; https://doi.org/10.3390/ijms25020802 - 09 Jan 2024

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Abstract

Petioles of non-heading Chinese cabbage are not only an important edible part but also a conduit for nutrient transport, holding significant agricultural and research value. In this study, we conducted a comprehensive genetic analysis of petiole-related traits using a segregating population. Modern quantitative genetic approaches were applied to investigate the genetic regulation of petiole thickness. The results indicated that petiole thickness is a quantitative trait, and the identified genetic model was consistent with two pairs of additive-dominant main genes and additive-dominant polygenes (2MG-AD). BSA-seq analysis identified a major effect of QTL controlling petiole thickness on chromosome A09: 42.08–45.09 Mb, spanning 3.01 Mb, designated as QTL-BrLH9. Utilizing InDel markers, the interval was narrowed down to 51 kb, encompassing 14 genes with annotations for 10 of them. Within the interval, four mutated genes were detected. Combined with gene annotation, protein sequence analysis, and homology alignment, it was found that BraA09g063520.3C’s homologous gene SMXL6 in Arabidopsis (Arabidopsis thaliana (L.) Heynh) is an inhibitor of the coding and synthesis of the strigolactone pathway. Strigolactone (SLs) plays an important role in plant growth and development. The cloning results showed that multiple frameshift mutations and non-synonymous mutations occurred on the exon. The qPCR results showed that the expression of the gene was significantly different between the two parents at the adult stage, so it was speculated that it would lead to changes in petiole thickness. BraA09g063520.3C was predicted as the final candidate gene. Full article

(This article belongs to the Special Issue Plant Genetic and Epigenetic Engineering: New Advances and Molecular Tools)

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20 pages, 14197 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of MYB Gene Family and Analysis of Its Sex-Biased Expression Pattern in Spinacia oleracea L.

by Zhilong Zhang, Zhiyuan Liu, Hao Wu, Zhaosheng Xu, Helong Zhang, Wei Qian, Wujun Gao and Hongbing She

Int. J. Mol. Sci. 2024, 25(2), 795; https://doi.org/10.3390/ijms25020795 - 08 Jan 2024

Cited by 1 | Viewed by 919

Abstract

The members of the myeloblastosis (MYB) family of transcription factors (TFs) participate in a variety of biological regulatory processes in plants, such as circadian rhythm, metabolism, and flower development. However, the characterization of MYB genes across the genomes of spinach Spinacia oleracea L. has not been reported. Here, we identified 140 MYB genes in spinach and described their characteristics using bioinformatics approaches. Among the MYB genes, 54 were 1R-MYB, 80 were 2R-MYB, 5 were 3R-MYB, and 1 was 4R-MYB. Almost all MYB genes were located in the 0–30 Mb region of autosomes; however, the 20 MYB genes were enriched at both ends of the sex chromosome (chromosome 4). Based on phylogeny, conserved motifs, and the structure of genes, 2R-MYB exhibited higher conservation relative to 1R-MYB genes. Tandem duplication and collinearity of spinach MYB genes drive their evolution, enabling the functional diversification of spinach genes. Subcellular localization prediction indicated that spinach MYB genes were mainly located in the nucleus. Cis-acting element analysis confirmed that MYB genes were involved in various processes of spinach growth and development, such as circadian rhythm, cell differentiation, and reproduction through hormone synthesis. Furthermore, through the transcriptome data analysis of male and female flower organs at five different periods, ten candidate genes showed biased expression in spinach males, suggesting that these genes might be related to the development of spinach anthers. Collectively, this study provides useful information for further investigating the function of MYB TFs and novel insights into the regulation of sex determination in spinach. Full article

(This article belongs to the Special Issue Plant Genetic and Epigenetic Engineering: New Advances and Molecular Tools)

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17 pages, 4607 KiB

Open AccessArticle

Impact of Intron and Retransformation on Transgene Expression in Leaf and Fruit Tissues of Field-Grown Pear Trees

by Vadim Lebedev

Int. J. Mol. Sci. 2023, 24(16), 12883; https://doi.org/10.3390/ijms241612883 - 17 Aug 2023

Viewed by 789

Abstract

Stable and high expression of introduced genes is a prerequisite for using transgenic trees. Transgene stacking enables combining several valuable traits, but repeated transformation increases the risk of unintended effects. This work studied the stability and intron-mediated enhancement of uidA gene expression in leaves and different anatomical parts of pear fruits during field trials over 14 years. The stability of reporter and herbicide resistance transgenes in retransformed pear plants, as well as possible unintended effects using high-throughput phenotyping tools, were also investigated. The activity of β-glucuronidase (GUS) varied depending on the year, but silencing did not occur. The uidA gene was expressed to a maximum in seeds, slightly less in the peel and peduncles, and much less in the pulp of pear fruits. The intron in the uidA gene stably increased expression in leaves and fruits by approximately twofold. Retransformants with the bar gene showed long-term herbicide resistance and exhibited no consistent changes in leaf size and shape. The transgenic pear was used as rootstock and scion, but grafted plants showed no transport of the GUS protein through the graft in the greenhouse and field. This longest field trial of transgenic fruit trees demonstrates stable expression under varying environmental conditions, the expression-enhancing effect of intron and the absence of unintended effects in single- and double-transformed woody plants. Full article

(This article belongs to the Special Issue Plant Genetic and Epigenetic Engineering: New Advances and Molecular Tools)

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Review

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18 pages, 1590 KiB

Open AccessReview

Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding

by Ilya Kirov

Int. J. Mol. Sci. 2023, 24(23), 17054; https://doi.org/10.3390/ijms242317054 - 02 Dec 2023

Viewed by 1538

Abstract

Genetic diversity is a key factor for plant breeding. The birth of novel genic and genomic variants is also crucial for plant adaptation in nature. Therefore, the genomes of almost all living organisms possess natural mutagenic mechanisms. Transposable elements (TEs) are a major mutagenic force driving genetic diversity in wild plants and modern crops. The relatively rare TE transposition activity during the thousand-year crop domestication process has led to the phenotypic diversity of many cultivated species. The utilization of TE mutagenesis by artificial and transient acceleration of their activity in a controlled mode is an attractive foundation for a novel type of mutagenesis called TE-mediated biological mutagenesis. Here, I focus on TEs as mutagenic sources for plant breeding and discuss existing and emerging transgene-free approaches for TE activation in plants. Furthermore, I also review the non-randomness of TE insertions in a plant genome and the molecular and epigenetic factors involved in shaping TE insertion preferences. Additionally, I discuss the molecular mechanisms that prevent TE transpositions in germline plant cells (e.g., meiocytes, pollen, egg and embryo cells, and shoot apical meristem), thereby reducing the chances of TE insertion inheritance. Knowledge of these mechanisms can expand the TE activation toolbox using novel gene targeting approaches. Finally, the challenges and future perspectives of plant populations with induced novel TE insertions (iTE plant collections) are discussed. Full article

(This article belongs to the Special Issue Plant Genetic and Epigenetic Engineering: New Advances and Molecular Tools)

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28 pages, 1219 KiB

Open AccessReview

Nanoplatforms for the Delivery of Nucleic Acids into Plant Cells

by Tatiana Komarova, Irina Ilina, Michael Taliansky and Natalia Ershova

Int. J. Mol. Sci. 2023, 24(23), 16665; https://doi.org/10.3390/ijms242316665 - 23 Nov 2023

Viewed by 1308

Abstract

Nanocarriers are widely used for efficient delivery of different cargo into mammalian cells; however, delivery into plant cells remains a challenging issue due to physical and mechanical barriers such as the cuticle and cell wall. Here, we discuss recent progress on biodegradable and biosafe nanomaterials that were demonstrated to be applicable to the delivery of nucleic acids into plant cells. This review covers studies the object of which is the plant cell and the cargo for the nanocarrier is either DNA or RNA. The following nanoplatforms that could be potentially used for nucleic acid foliar delivery via spraying are discussed: mesoporous silica nanoparticles, layered double hydroxides (nanoclay), carbon-based materials (carbon dots and single-walled nanotubes), chitosan and, finally, cell-penetrating peptides (CPPs). Hybrid nanomaterials, for example, chitosan- or CPP-functionalized carbon nanotubes, are taken into account. The selected nanocarriers are analyzed according to the following aspects: biosafety, adjustability for the particular cargo and task (e.g., organelle targeting), penetration efficiency and ability to protect nucleic acid from environmental and cellular factors (pH, UV, nucleases, etc.) and to mediate the gradual and timely release of cargo. In addition, we discuss the method of application, experimental system and approaches that are used to assess the efficiency of the tested formulation in the overviewed studies. This review presents recent progress in developing the most promising nanoparticle-based materials that are applicable to both laboratory experiments and field applications. Full article

(This article belongs to the Special Issue Plant Genetic and Epigenetic Engineering: New Advances and Molecular Tools)

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