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Genetic and Biological Diversity of Plants
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Genetic and Biological Diversity of Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 March 2025 | Viewed by 6044

Special Issue Editors

Dr. Zhonglong Guo

E-Mail Website
Guest Editor
Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
Interests: bioinformatics; evolution; microRNA; Databases; non-coding miRNA
Prof. Dr. Lei Li

E-Mail Website
Guest Editor
State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
Interests: retrograde signaling; plant development; miRNA; organelles; cell biology; genomics; stress tolerance

Special Issue Information

Dear Colleagues,

Genetic diversity is a fundamental source of biological diversity and it encompasses the variety of genes within species and the diversity of species within ecosystems. This diversity is crucial for the survival of plants, enabling them to adapt to changing environmental conditions, resist diseases, and interact with other organisms in complex ecological networks. Understanding genetic and biological diversity is essential for the conservation of plant species and the sustainable use of plant resources. It provides insights into mechanisms of evolution and adaptation, and informs breeding programs for crops, forests, and forages. In this Special Issue, we invite researchers to submit original research articles and reviews that enhance our understanding of plant genetic and biological diversity, and research focused on omics analysis, multi-species database, plant–insect–microbe interactions is also welcome.

Dr. Zhonglong Guo
Prof. Dr. Lei Li
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. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • multi-omics
  • plant diversity
  • plant–insect–microbe interactions
  • databases
  • non-coding RNA

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Published Papers (6 papers)

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Research

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21 pages, 4948 KiB  
Article
Evaluation of the Spike Diversity of Seven Hexaploid Wheat Species and an Artificial Amphidiploid Using a Quadrangle Model Obtained from 2D Images
by Evgenii G. Komyshev, Mikhail A. Genaev, Yuliya V. Kruchinina, Vasily S. Koval, Nikolay P. Goncharov and Dmitry A. Afonnikov
Plants 2024, 13(19), 2736; https://doi.org/10.3390/plants13192736 - 30 Sep 2024
Viewed by 472
Abstract
The spike shape and morphometric characteristics are among the key characteristics of cultivated cereals, being associated with their productivity. These traits are often used for the plant taxonomy and authenticity of hexaploid wheat species. Manual measurement of spike characteristics is tedious and not [...] Read more.
The spike shape and morphometric characteristics are among the key characteristics of cultivated cereals, being associated with their productivity. These traits are often used for the plant taxonomy and authenticity of hexaploid wheat species. Manual measurement of spike characteristics is tedious and not precise. Recently, the authors of this study developed a method for wheat spike morphometry utilizing 2D image analysis. Here, this method is applied to study variations in spike size and shape for 190 plants of seven hexaploid (2n = 6x = 42) species and one artificial amphidiploid of wheat. Five manually estimated spike traits and 26 traits obtained from digital image analysis were analyzed. Image-based traits describe the characteristics of the base, center and apex of the spike and common parameters (circularity, roundness, perimeter, etc.). Estimates of similar traits by manual measurement and image analysis were shown to be highly correlated, suggesting the practical importance of digital spike phenotyping. The utility of spike traits for classification into types (spelt, normal and compact) and species or amphidiploid is shown. It is also demonstrated that the estimates obtained made it possible to identify the spike characteristics differing significantly between species or between accessions within the same species. The present work suggests the usefulness of wheat spike shape analysis using an approach based on characteristics obtained by digital image analysis. Full article
(This article belongs to the Special Issue Genetic and Biological Diversity of Plants)
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19 pages, 4364 KiB  
Article
Impact of Chromosomal Fusion and Transposable Elements on the Genomic Evolution and Genetic Diversity of Ilex Species
by Zhenxiu Xu, Haikun Wei, Mingyue Li, Yingjie Qiu, Lei Li, Ke-Wang Xu and Zhonglong Guo
Plants 2024, 13(18), 2649; https://doi.org/10.3390/plants13182649 - 21 Sep 2024
Viewed by 854
Abstract
The genus Ilex belongs to the sole family and is the single genus within the order Aquifoliales, exhibiting significant phenotypic diversity. However, the genetic differences underlying these phenotypic variations have rarely been studied. In this study, collinearity analyses of three Ilex genomes, Ilex [...] Read more.
The genus Ilex belongs to the sole family and is the single genus within the order Aquifoliales, exhibiting significant phenotypic diversity. However, the genetic differences underlying these phenotypic variations have rarely been studied. In this study, collinearity analyses of three Ilex genomes, Ilex latifolia Thunb., Ilex polyneura (Hand.-Mazz.) S. Y. Hu, and Ilex asprella Champ. ex Benth., indicated a recent fusion event contributing to the reduction of chromosomes in I. asprella. Comparative genome analyses showed slight differences in gene annotation among the three species, implying a minimal disruption of genes following chromosomal fusion in I. asprella. Comprehensive annotation of transposable elements (TEs) revealed that TEs constitute a significant portion of the Ilex genomes, with LTR transposons being predominant. TEs exhibited an inverse relationship with gene density, potentially influencing gene regulation and chromosomal architecture. TE insertions were shown to affect the conformation and binding sites of key genes such as 7-deoxyloganetin glucosyltransferase and transmembrane kinase (TMK) genes, highlighting potential functional impacts. The structural variations caused by TE insertions suggest significant roles in the evolutionary dynamics, leading to either loss or gain of gene function. This study underscores the importance of TEs in shaping the genomic landscape and evolutionary trajectories of Ilex species. Full article
(This article belongs to the Special Issue Genetic and Biological Diversity of Plants)
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29 pages, 4376 KiB  
Article
Cryopreservation of Medicinal Plant Seeds: Strategies for Genetic Diversity Conservation and Sustainability
by Lin Zeng, Zheng Sun, Li Fu, Yakun Gu, Rongtao Li, Mingjun He and Jianhe Wei
Plants 2024, 13(18), 2577; https://doi.org/10.3390/plants13182577 - 13 Sep 2024
Viewed by 939
Abstract
The depletion of medicinal plant resources leads to the irreversible loss of their genetic diversity. The preservation of medicinal plant germplasm using cryobanks is crucial for maintaining the sustainability of these resources. This study examined the efficacy of cryopreservation on 164 medicinal plant [...] Read more.
The depletion of medicinal plant resources leads to the irreversible loss of their genetic diversity. The preservation of medicinal plant germplasm using cryobanks is crucial for maintaining the sustainability of these resources. This study examined the efficacy of cryopreservation on 164 medicinal plant seeds, identified general principles for preserving medicinal plant seeds at ultra-low temperatures, and established a cryobank for dry-sensitive medicinal plant seeds. Over 90% of orthodox seeds were unaffected by freezing, with optimal conditions being a 5–10% moisture content and direct freezing. Intermediate seeds were best frozen with a 7–15% moisture content, and those with a lower initial moisture content were best suited to direct freezing. While recalcitrant seeds’ freezing was most influenced by moisture content, there was no specific range. Direct freezing is appropriate for recalcitrant seeds possessing a hard seed coat and a firm seed kernel, whereas seeds with a brittle or soft seed coat are better suited for vitrification or stepwise freezing methods. There was no significant correlation between alterations in physiological and biochemical indicators and microscopic structures of seeds before and following liquid nitrogen freezing, as well as their storage characteristics. The findings of this research offer evidence in favor of the extended conservation of plant seeds and the extensive utilization of ultra-low temperature technology and provides an example of protecting the genetic diversity of plant resources. Full article
(This article belongs to the Special Issue Genetic and Biological Diversity of Plants)
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19 pages, 5239 KiB  
Article
Effects of Grazing and Leaf Spot Disease on the Structure and Diversity of Phyllosphere Microbiome Communities in Leymus chinensis
by Yani Qian, Yuanyuan Jin, Xinyao Han, Kamran Malik, Chunjie Li and Binhua Yu
Plants 2024, 13(15), 2128; https://doi.org/10.3390/plants13152128 - 1 Aug 2024
Viewed by 918
Abstract
Leymus chinensis is a high-quality forage with wide distribution. Disease is an important factor affecting the yield and quality of L. chinensis. To investigate the effect of grazing on the phyllosphere microbiome community and leaf spot disease in L. chinensis, high-throughput [...] Read more.
Leymus chinensis is a high-quality forage with wide distribution. Disease is an important factor affecting the yield and quality of L. chinensis. To investigate the effect of grazing on the phyllosphere microbiome community and leaf spot disease in L. chinensis, high-throughput sequencing technology was used to study the differences in the composition and structure of the phyllosphere fungal and bacterial communities of healthy and diseased leaves under different grazing intensities. The results showed that grazing significantly reduced leaf spot disease incidence and severity. There were significant differences in the phyllosphere microbiome composition between healthy and diseased leaves, and interestingly, diseased leaves showed more complex microbial activity. Grazing altered the relative abundance of micro-organisms and affected microbial dispersal and colonization either directly through behavior or indirectly by altering plant community structure. In this study, we found that the phyllosphere microbiome responded strongly to pathogen infection, and that plants recruited beneficial microbes to protect themselves after disease development. Grazing could regulate microbial community composition and structure, either directly or indirectly, and plays a crucial role in maintaining the health of L. chinensis. Full article
(This article belongs to the Special Issue Genetic and Biological Diversity of Plants)
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16 pages, 5383 KiB  
Article
TkJAZs-TkMYC2-TkSRPP/REF Regulates the Biosynthesis of Natural Rubber in Taraxacum kok-saghyz
by Yulin Wu, Gaoquan Dong, Fengqi Luo, Hao Xie, Xiaodong Li and Jie Yan
Plants 2024, 13(15), 2034; https://doi.org/10.3390/plants13152034 - 24 Jul 2024
Viewed by 837
Abstract
Taraxacum kok-saghyz (TKS) is a natural rubber (NR)-producing plant and a model plant for studying the biosynthesis of NR. Analyzing and studying the biosynthetic mechanism of NR is an important way to cultivate high-yield rubber TKS varieties. JAZ proteins, which belong to the [...] Read more.
Taraxacum kok-saghyz (TKS) is a natural rubber (NR)-producing plant and a model plant for studying the biosynthesis of NR. Analyzing and studying the biosynthetic mechanism of NR is an important way to cultivate high-yield rubber TKS varieties. JAZ proteins, which belong to the Jasmonate ZIM domain family, function as negative regulators in the jasmonic acid (JA) signal transduction pathway. MYC2 is typically regarded as a regulatory factor for the target genes of JAZ proteins; JAZ proteins indirectly influence the gene expression regulated by MYC2 by modulating its activity. Theoretically, JAZ is expected to participate in growth, development, and responses to environmental cues related to rubber and biomass accumulation in TKS, all of which rely on the interaction between JAZ and MYC2. In this study, we identified 11 TkJAZs through homology searching of the TKS genomes and bioinformatics analyses. Subcellular localization, Y2H, and BiFC analysis demonstrate that TkJAZs and TkMYC2 are localized in the nucleus, with all TkJAZs and TkMYC2 showing nuclear colocalization interactions. Overexpression of TkMYC2 in TKS inhibited leaf development, promoted root growth, and simultaneously increased NR production. RNA-seq and qRT-PCR analysis revealed that the TkSRPP/REF genes exhibit varying degrees of upregulation compared to the wild type, upregulating the TkREF1 gene by 3.7-fold, suggesting that TkMYC2 regulates the synthesis of NR by modulating the TkSRPP/REF genes. Full article
(This article belongs to the Special Issue Genetic and Biological Diversity of Plants)
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Review

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14 pages, 2596 KiB  
Review
bZIP Transcription Factors: Structure, Modification, Abiotic Stress Responses and Application in Plant Improvement
by Zhonglong Guo, Raphael Dzinyela, Liming Yang and Delight Hwarari
Plants 2024, 13(15), 2058; https://doi.org/10.3390/plants13152058 - 25 Jul 2024
Cited by 3 | Viewed by 1591
Abstract
Plant growth, yield, and distribution are significantly impacted by abiotic stresses, affecting global ecosystems and forestry practices. However, plants have evolved complex adaptation mechanisms governed by numerous genes and transcription factors (TFs) to manage these stresses. Among these, bZIP (basic leucine zipper) is [...] Read more.
Plant growth, yield, and distribution are significantly impacted by abiotic stresses, affecting global ecosystems and forestry practices. However, plants have evolved complex adaptation mechanisms governed by numerous genes and transcription factors (TFs) to manage these stresses. Among these, bZIP (basic leucine zipper) is a crucial regulator orchestrating morphological adaptations. This review aims to elucidate the multifaceted roles of bZIP TFs in plant species. We discuss the morphological changes induced by stress stimuli and the pivotal functions of bZIP TFs in mediating these responses. While several publications have explored the mechanisms of bZIP TFs in response to abiotic stresses, this review delves into the intricate regulatory networks, summarizing alternative splicing and post-translational modifications, signaling networks interacting with bZIP TFs, and genetic engineering of bZIP TFs. By synthesizing current research, this review provides an updated discussion on bZIP interactions with other proteins to regulate stresses such as cold, heat, drought, and salt. Additionally, it offers avenues for future research and applications of bZIP TFs to improve abiotic stress resilience in plants through genetic engineering. Full article
(This article belongs to the Special Issue Genetic and Biological Diversity of Plants)
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