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Structural and Functional Genomics for Plant Development and Stress Tolerance
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Structural and Functional Genomics for Plant Development and Stress Tolerance

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 16532

Special Issue Editors

Dr. Manoj Kumar

E-Mail Website
Guest Editor
Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
Interests: plant molecular biology; genetic engineering; genome editing; abiotic stress tolerance in plants
Special Issues, Collections and Topics in MDPI journals
Dr. Baozhu Guo

E-Mail Website
Guest Editor
ARS, USDA, Crop Protect & Management Res Unit, Tifton, GA 31793, USA
Interests: evaluate corn germplasm for reduced aflatoxin contamination and to identify genes responding to Aspergillus colonization and drought stress; develop peanut genetic and genomic resources for improvement of peanut resistance to diseases and aflatoxin contamination
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Various abiotic and biotic stresses can affect plant growth and development at physiological, biochemical, and molecular levels, including alterations in gene expression, accumulation of organic solutes, imbalance in phytohormones excretion, and inhibition of plant growth. A better understanding of structural and functional genomics in plants would help to design and create new plant varieties more efficiently and quickly, which can sustain their performance under different stress and climate change scenarios. Gene discovery and functional genomics have disclosed diverse mechanisms and gene families, which confer enhanced productivity and adaptation to environmental stresses. Next-generation genomics and functional validation approaches have provided further opportunities to deep dive into the molecular mechanisms and guide genetic improvement strategies to breed next-generation plant species. In this Special Issue of the International Journal of Molecular Sciences, we aim to publish high-quality research articles and reviews on the understanding of gene expression in plants for their growth development and stress responses.

Dr. Manoj Kumar
Dr. Baozhu Guo
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

  • structural genomics
  • gene expression
  • functional validation
  • plant development
  • stress tolerance
  • genetic engineering and gene editing
  • crop productivity

Published Papers (6 papers)

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Research

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15 pages, 70196 KiB  
Article
Genome-Wide Identification of LBD Genes in Foxtail Millet (Setaria italica) and Functional Characterization of SiLBD21
by Kunjie Li, Yaning Wei, Yimin Wang, Bin Tan, Shoukun Chen and Haifeng Li
Int. J. Mol. Sci. 2023, 24(8), 7110; https://doi.org/10.3390/ijms24087110 - 12 Apr 2023
Cited by 3 | Viewed by 1350
Abstract
Plant-specific lateral organ boundaries domain (LBD) proteins play important roles in plant growth and development. Foxtail millet (Setaria italica) is one new C4 model crop. However, the functions of foxtail millet LBD genes are unknown. In this study, a genome-wide [...] Read more.
Plant-specific lateral organ boundaries domain (LBD) proteins play important roles in plant growth and development. Foxtail millet (Setaria italica) is one new C4 model crop. However, the functions of foxtail millet LBD genes are unknown. In this study, a genome-wide identification of foxtail millet LBD genes and a systematical analysis were conducted. A total of 33 SiLBD genes were identified. They are unevenly distributed on nine chromosomes. Among these SiLBD genes, six segmental duplication pairs were detected. The thirty-three encoded SiLBD proteins could be classified into two classes and seven clades. Members in the same clade have similar gene structure and motif composition. Forty-seven kinds of cis-elements were found in the putative promoters, and they are related to development/growth, hormone, and abiotic stress response, respectively. Meanwhile, the expression pattern was investigated. Most SiLBD genes are expressed in different tissues, while several genes are mainly expressed in one or two kinds of tissues. In addition, most SiLBD genes respond to different abiotic stresses. Furthermore, the function of SiLBD21, which is mainly expressed in roots, was characterized by ectopic expression in Arabidopsis and rice. Compared to controls, transgenic plants generated shorter primary roots and more lateral roots, indicating the function of SiLBD21 in root development. Overall, our study laid the foundation for further functional elucidation of SiLBD genes. Full article
(This article belongs to the Special Issue Structural and Functional Genomics for Plant Development and Stress Tolerance)
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14 pages, 3844 KiB  
Article
Prolonged Exposure to High Temperature Inhibits Shoot Primary and Root Secondary Growth in Panax ginseng
by Jeongeui Hong, Kyoung Rok Geem, Jaewook Kim, Ick-Hyun Jo, Tae-Jin Yang, Donghwan Shim and Hojin Ryu
Int. J. Mol. Sci. 2022, 23(19), 11647; https://doi.org/10.3390/ijms231911647 - 1 Oct 2022
Cited by 4 | Viewed by 1807
Abstract
High temperature is one of the most significant abiotic stresses reducing crop yield and quality by inhibiting plant growth and development. Global warming has recently increased the frequency of heat waves, which negatively impacts agricultural fields. Despite numerous studies on heat stress responses [...] Read more.
High temperature is one of the most significant abiotic stresses reducing crop yield and quality by inhibiting plant growth and development. Global warming has recently increased the frequency of heat waves, which negatively impacts agricultural fields. Despite numerous studies on heat stress responses and signal transduction in model plant species, the molecular mechanism underlying thermomorphogenesis in Panax ginseng remains largely unknown. Here, we investigated the high temperature response of ginseng at the phenotypic and molecular levels. Both the primary shoot growth and secondary root growth of ginseng plants were significantly reduced at high temperature. Histological analysis revealed that these decreases in shoot and root growth were caused by decreases in cell elongation and cambium stem cell activity, respectively. Analysis of P. ginseng RNA-seq data revealed that heat-stress-repressed stem and root growth is closely related to changes in photosynthesis, cell wall organization, cell wall loosening, and abscisic acid (ABA) and jasmonic acid (JA) signaling. Reduction in both the light and dark reactions of photosynthesis resulted in defects in starch granule development in the storage parenchymal cells of the main tap root. Thus, by combining bioinformatics and histological analyses, we show that high temperature signaling pathways are integrated with crucial biological processes that repress stem and root growth in ginseng, providing novel insight into the heat stress response mechanism of P. ginseng. Full article
(This article belongs to the Special Issue Structural and Functional Genomics for Plant Development and Stress Tolerance)
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21 pages, 5327 KiB  
Article
Identification and Characterization of Abiotic Stress–Responsive NF-YB Family Genes in Medicago
by Wenxuan Du, Junfeng Yang, Qian Li, Chunfeng He and Yongzhen Pang
Int. J. Mol. Sci. 2022, 23(13), 6906; https://doi.org/10.3390/ijms23136906 - 21 Jun 2022
Cited by 4 | Viewed by 1791
Abstract
Nuclear factor YB (NF-YB) are plant-specific transcription factors that play a critical regulatory role in plant growth and development as well as in plant resistance against various stresses. In this study, a total of 49 NF-YB genes were identified from the genomes of [...] Read more.
Nuclear factor YB (NF-YB) are plant-specific transcription factors that play a critical regulatory role in plant growth and development as well as in plant resistance against various stresses. In this study, a total of 49 NF-YB genes were identified from the genomes of Medicago truncatula and Medicago sativa. Multiple sequence alignment analysis showed that all of these NF-YB members contain DNA binding domain, NF-YA interaction domain and NF-YC interaction domain. Phylogenetic analysis suggested that these NF-YB proteins could be classified into five distinct clusters. We also analyzed the exon–intron organizations and conserved motifs of these NF-YB genes and their deduced proteins. We also found many stress-related cis-acting elements in their promoter region. In addition, analyses on genechip for M. truncatula and transcriptome data for M. sativa indicated that these NF-YB genes exhibited a distinct expression pattern in various tissues; many of these could be induced by drought and/or salt treatments. In particular, RT-qPCR analysis revealed that the expression levels of gene pairs MsNF-YB27/MtNF-YB15 and MsNF-YB28/MtNF-YB16 were significantly up-regulated under NaCl and mannitol treatments, indicating that they are most likely involved in salt and drought stress response. Taken together, our study on NF-YB family genes in Medicago is valuable for their functional characterization, as well as for the application of NF-YB genes in genetic breeding for high-yield and high-resistance alfalfa. Full article
(This article belongs to the Special Issue Structural and Functional Genomics for Plant Development and Stress Tolerance)
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18 pages, 2602 KiB  
Article
GWAS Reveals a Novel Candidate Gene CmoAP2/ERF in Pumpkin (Cucurbita moschata) Involved in Resistance to Powdery Mildew
by Hemasundar Alavilli, Jeong-Jin Lee, Chae-Rin You, Yugandhar Poli, Hyeon-Jai Kim, Ajay Jain and Kihwan Song
Int. J. Mol. Sci. 2022, 23(12), 6524; https://doi.org/10.3390/ijms23126524 - 10 Jun 2022
Cited by 6 | Viewed by 2808
Abstract
Pumpkin (Cucurbita moschata Duchesne ex Poir.) is a multipurpose cash crop rich in antioxidants, minerals, and vitamins; the seeds are also a good source of quality oils. However, pumpkin is susceptible to the fungus Podosphaera xanthii, an obligate biotrophic pathogen, which [...] Read more.
Pumpkin (Cucurbita moschata Duchesne ex Poir.) is a multipurpose cash crop rich in antioxidants, minerals, and vitamins; the seeds are also a good source of quality oils. However, pumpkin is susceptible to the fungus Podosphaera xanthii, an obligate biotrophic pathogen, which usually causes powdery mildew (PM) on both sides of the leaves and reduces photosynthesis. The fruits of infected plants are often smaller than usual and unpalatable. This study identified a novel gene that involves PM resistance in pumpkins through a genome-wide association study (GWAS). The allelic variation identified in the CmoCh3G009850 gene encoding for AP2-like ethylene-responsive transcription factor (CmoAP2/ERF) was proven to be involved in PM resistance. Validation of the GWAS data revealed six single nucleotide polymorphism (SNP) variations in the CmoAP2/ERF coding sequence between the resistant (IT 274039 [PMR]) and the susceptible (IT 278592 [PMS]). A polymorphic marker (dCAPS) was developed based on the allelic diversity to differentiate these two haplotypes. Genetic analysis in the segregating population derived from PMS and PMR parents provided evidence for an incomplete dominant gene-mediated PM resistance. Further, the qRT-PCR assay validated the elevated expression of CmoAP2/ERF during PM infection in the PMR compared with PMS. These results highlighted the pivotal role of CmoAP2/ERF in conferring resistance to PM and identifies it as a valuable molecular entity for breeding resistant pumpkin cultivars. Full article
(This article belongs to the Special Issue Structural and Functional Genomics for Plant Development and Stress Tolerance)
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Review

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17 pages, 803 KiB  
Review
Function of Nuclear Pore Complexes in Regulation of Plant Defense Signaling
by Xi Wu, Junyou Han and Changkui Guo
Int. J. Mol. Sci. 2022, 23(6), 3031; https://doi.org/10.3390/ijms23063031 - 11 Mar 2022
Cited by 4 | Viewed by 4982
Abstract
In eukaryotes, the nucleus is the regulatory center of cytogenetics and metabolism, and it is critical for fundamental biological processes, including DNA replication and transcription, protein synthesis, and biological macromolecule transportation. The eukaryotic nucleus is surrounded by a lipid bilayer called the nuclear [...] Read more.
In eukaryotes, the nucleus is the regulatory center of cytogenetics and metabolism, and it is critical for fundamental biological processes, including DNA replication and transcription, protein synthesis, and biological macromolecule transportation. The eukaryotic nucleus is surrounded by a lipid bilayer called the nuclear envelope (NE), which creates a microenvironment for sophisticated cellular processes. The NE is perforated by the nuclear pore complex (NPC), which is the channel for biological macromolecule bi-directional transport between the nucleus and cytoplasm. It is well known that NPC is the spatial designer of the genome and the manager of genomic function. Moreover, the NPC is considered to be a platform for the continual adaptation and evolution of eukaryotes. So far, a number of nucleoporins required for plant-defense processes have been identified. Here, we first provide an overview of NPC organization in plants, and then discuss recent findings in the plant NPC to elaborate on and dissect the distinct defensive functions of different NPC subcomponents in plant immune defense, growth and development, hormone signaling, and temperature response. Nucleoporins located in different components of NPC have their unique functions, and the link between the NPC and nucleocytoplasmic trafficking promotes crosstalk of different defense signals in plants. It is necessary to explore appropriate components of the NPC as potential targets for the breeding of high-quality and broad spectrum resistance crop varieties. Full article
(This article belongs to the Special Issue Structural and Functional Genomics for Plant Development and Stress Tolerance)
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29 pages, 7853 KiB  
Review
Breeding and Genomics Interventions for Developing Ascochyta Blight Resistant Grain Legumes
by Uday C. Jha, Kamal Dev Sharma, Harsh Nayyar, Swarup K. Parida and Kadambot H. M. Siddique
Int. J. Mol. Sci. 2022, 23(4), 2217; https://doi.org/10.3390/ijms23042217 - 17 Feb 2022
Cited by 6 | Viewed by 2904
Abstract
Grain legumes are a key food source for ensuring global food security and sustaining agriculture. However, grain legume production is challenged by growing disease incidence due to global climate change. Ascochyta blight (AB) is a major disease, causing substantial yield losses in grain [...] Read more.
Grain legumes are a key food source for ensuring global food security and sustaining agriculture. However, grain legume production is challenged by growing disease incidence due to global climate change. Ascochyta blight (AB) is a major disease, causing substantial yield losses in grain legumes worldwide. Harnessing the untapped reserve of global grain legume germplasm, landraces, and crop wild relatives (CWRs) could help minimize yield losses caused by AB infection in grain legumes. Several genetic determinants controlling AB resistance in various grain legumes have been identified following classical genetic and conventional breeding approaches. However, the advent of molecular markers, biparental quantitative trait loci (QTL) mapping, genome-wide association studies, genomic resources developed from various genome sequence assemblies, and whole-genome resequencing of global germplasm has revealed AB-resistant gene(s)/QTL/genomic regions/haplotypes on various linkage groups. These genomics resources allow plant breeders to embrace genomics-assisted selection for developing/transferring AB-resistant genomic regions to elite cultivars with great precision. Likewise, advances in functional genomics, especially transcriptomics and proteomics, have assisted in discovering possible candidate gene(s) and proteins and the underlying molecular mechanisms of AB resistance in various grain legumes. We discuss how emerging cutting-edge next-generation breeding tools, such as rapid generation advancement, field-based high-throughput phenotyping tools, genomic selection, and CRISPR/Cas9, could be used for fast-tracking AB-resistant grain legumes to meet the increasing demand for grain legume-based protein diets and thus ensuring global food security. Full article
(This article belongs to the Special Issue Structural and Functional Genomics for Plant Development and Stress Tolerance)
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