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Functional Genomics of Energy Crops 2.0
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Functional Genomics of Energy Crops 2.0

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 (20 January 2025) | Viewed by 5127

Special Issue Editor

Prof. Dr. Gongke Zhou

E-Mail Website
Guest Editor
College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
Interests: regulation pathway of the secondary cell wall formation; regulation pathway utilization
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As is well known, biomass energy has always been crucial to human survival and will continue play an integral role in future sustainable energy systems. However, the bottleneck of biomass resources will seriously restrict the development of the biomass energy industry. Therefore, this Special Issue, entitled “Functional Genomics of Energy Crops”, aims to stimulate comprehensive research into energy crops.

We will consider any articles presenting the latest findings on biomass metabolism, high light efficiency, high biomass, functional genomics, breeding, biomass conversion, and stress resistance of energy crops for publication.

Overall, this Special Issue will present both basic science and applied research to construct a more cohesive comprehension of energy crop science, considering all the aspects of this complex puzzle.

Prof. Dr. Gongke Zhou
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

  • energy crops
  • high light efficiency
  • high biomass
  • lignocellulosic biomass
  • starch biomass
  • oil biomass
  • sugar biomass
  • biomass metabolism
  • transcriptional regulation
  • functional genomics
  • genetic engineering
  • breeding
  • biomass conversion
  • stress resistance
  • marginal land
  • bioenergy

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Related Special Issue

Published Papers (4 papers)

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Research

15 pages, 1031 KiB  
Article
Effect of the Aqueous Quercetin Solution on the Physiological Properties of Virginia Mallow (Ripariosida hermaphrodita) Grown Under Salt Stress Conditions
by Dagmara Migut, Michał Sobaszek, Marta Jańczak-Pieniążek and Karol Skrobacz
Int. J. Mol. Sci. 2025, 26(3), 1233; https://doi.org/10.3390/ijms26031233 - 30 Jan 2025
Viewed by 663
Abstract
The current increase in energy demand, along with the deepening climate crisis, has led to the need for alternative energy sources. One of these is the cultivation of energy crops. In turn, issues related to the deepening problem of soil salinization are an [...] Read more.
The current increase in energy demand, along with the deepening climate crisis, has led to the need for alternative energy sources. One of these is the cultivation of energy crops. In turn, issues related to the deepening problem of soil salinization are an important aspect of environmental protection on a global scale. New species and innovative solutions are sought to support the effective cultivation of energy crops, including in saline areas. The purpose of the study was to evaluate the effect of the foliar application of an aqueous quercetin solution applied in different doses (1%, 3% and 5%) on the physiological properties of Virginia Mallow plants subjected to salt stress conditions. The experiment was carried out as a pot experiment. The results obtained were related to two types of plants treated as a control sample. In one case, they were grown with the addition of quercetin alone, without salt stress. The other group was grown without quercetin and without salt. Quercetin is a phenolic compound that plays an important physiological and biochemical role in plants. Salinity caused a significant decrease in physiological indices in Virginia Mallow leaves. Foliar application of an aqueous quercetin solution mitigated the negative impact of salt on plants, the most stimulating effect being demonstrated at a dose of 5.0%. Full article
(This article belongs to the Special Issue Functional Genomics of Energy Crops 2.0)
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11 pages, 2798 KiB  
Article
Genetic Diversity Analysis and Core Collection Construction of Ancient Sophora japonica L. Using SSR Markers
by Yinyin Fu, Shuangyun Li, Bingyao Ma, Cuilan Liu, Yukun Qi and Caihong Pang
Int. J. Mol. Sci. 2024, 25(23), 12776; https://doi.org/10.3390/ijms252312776 - 28 Nov 2024
Cited by 1 | Viewed by 896
Abstract
Sophora japonica is an important native tree species in northern China, with high ornamental, medicinal, and ecological value. In order to elucidate the genetic resources of ancient S. japonica, 16 simple sequence repeat (SSR) markers were used to evaluate its genetic diversity [...] Read more.
Sophora japonica is an important native tree species in northern China, with high ornamental, medicinal, and ecological value. In order to elucidate the genetic resources of ancient S. japonica, 16 simple sequence repeat (SSR) markers were used to evaluate its genetic diversity and population structure and build a core collection of 416 germplasms from the Shandong, Shanxi, and Hebei provinces. A total of 160 alleles were detected, the mean major allele frequency (MAF)was 0.39, and the mean effective number of alleles (Ne) was 4.08. Shannon’s information index (I), the observed heterozygosity (Ho), the expected heterozygosity (He), and the polymorphism information content (PIC) were 1.58, 0.64, 0.74, and 0.70, respectively, indicating relatively high genetic diversity in ancient S. japonica germplasms. Low genetic differentiation coefficient (Fst = 0.04) and frequent gene flow (Nm = 9.74) were found in the tested S. japonica populations, and an analysis of molecular variance (AMOVA) indicated that the genetic variation mainly came from within individuals (84%). A genetic structure and cluster analysis indicated that 416 ancient S. japonica germplasms could be divided into five subgroups, and there were obvious genetic exchanges among different subgroups. A core collection consisting of 104 (25% of the original collection) germplasms was constructed using the R language package Genetic Subsetter version 0.8 based on the stepwise regression method. The retention rates of the number of alleles (Na), Ne, I, He, and PIC were 87.50%, 106.24%, 103.02%, 102.50%, and 102.74%, respectively. The t-test analysis suggested that there were no significant differences between the core collection and the original collection. The principal coordinate analysis (PCoA) showed that the core collection was uniformly distributed within the initial collection and was able to fully represent the genetic diversity of the original collection. These results provide a scientific basis for the conservation and utilization of ancient S. japonica germplasms. Full article
(This article belongs to the Special Issue Functional Genomics of Energy Crops 2.0)
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18 pages, 8739 KiB  
Article
Genome-Wide Identification of the SPP/SPPL Gene Family and BnaSPPL4 Regulating Male Fertility in Rapeseed (Brassica napus L.)
by Guangze Li, Wenjun Zhu, Minyu Tian, Rong Liu, Ying Ruan and Chunlin Liu
Int. J. Mol. Sci. 2024, 25(7), 3936; https://doi.org/10.3390/ijms25073936 - 1 Apr 2024
Viewed by 1519
Abstract
Signal peptide peptidase (SPP) and its homologs, signal peptide peptidase-like (SPPL) proteases, are members of the GxGD-type aspartyl protease family, which is widespread in plants and animals and is a class of transmembrane proteins with significant biological functions. SPP/SPPLs have been identified; however, [...] Read more.
Signal peptide peptidase (SPP) and its homologs, signal peptide peptidase-like (SPPL) proteases, are members of the GxGD-type aspartyl protease family, which is widespread in plants and animals and is a class of transmembrane proteins with significant biological functions. SPP/SPPLs have been identified; however, the functions of SPP/SPPL in rapeseed (Brassica napus L.) have not been reported. In this study, 26 SPP/SPPLs were identified in rapeseed and categorized into three groups: SPP, SPPL2, and SPPL3. These members mainly contained the Peptidase_A22 and PA domains, which were distributed on 17 out of 19 chromosomes. Evolutionary analyses indicated that BnaSPP/SPPLs evolved with a large number of whole-genome duplication (WGD) events and strong purifying selection. Members are widely expressed and play a key role in the growth and development of rapeseed. The regulation of rapeseed pollen fertility by the BnaSPPL4 gene was further validated through experiments based on bioinformatics analysis, concluding that BnaSPPL4 silencing causes male sterility. Cytological observation showed that male infertility caused by loss of BnaSPPL4 gene function occurs late in the mononucleate stage due to microspore dysplasia. Full article
(This article belongs to the Special Issue Functional Genomics of Energy Crops 2.0)
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21 pages, 21484 KiB  
Article
MsHDZ23, a Novel Miscanthus HD-ZIP Transcription Factor, Participates in Tolerance to Multiple Abiotic Stresses
by Naixu Liu, Ruikang Yu, Wendi Deng, Ruibo Hu, Guo He, Kang He, Yingzhen Kong, Xianfeng Tang, Gongke Zhou and Congpeng Wang
Int. J. Mol. Sci. 2024, 25(6), 3253; https://doi.org/10.3390/ijms25063253 - 13 Mar 2024
Cited by 7 | Viewed by 1504
Abstract
The homeodomain-leucine zipper (HD-ZIP) transcription factors, representing one of the largest plant-specific superfamilies, play important roles in the response to various abiotic stresses. However, the functional roles of HD-ZIPs in abiotic stress tolerance and the underlying mechanisms remain relatively limited in Miscanthus sinensis [...] Read more.
The homeodomain-leucine zipper (HD-ZIP) transcription factors, representing one of the largest plant-specific superfamilies, play important roles in the response to various abiotic stresses. However, the functional roles of HD-ZIPs in abiotic stress tolerance and the underlying mechanisms remain relatively limited in Miscanthus sinensis. In this study, we isolated an HD-ZIP TF gene, MsHDZ23, from Miscanthus and ectopically expressed it in Arabidopsis. Transcriptome and promoter analyses revealed that MsHDZ23 responded to salt, alkali, and drought treatments. The overexpression (OE) of MsHDZ23 in Arabidopsis conferred higher tolerance to salt and alkali stresses compared to wild-type (WT) plants. Moreover, MsHDZ23 was able to restore the hb7 mutant, the ortholog of MsHDZ23 in Arabidopsis, to the WT phenotype. Furthermore, MsHDZ23-OE lines exhibited significantly enhanced drought stress tolerance, as evidenced by higher survival rates and lower water loss rates compared to WT. The improved drought tolerance may be attributed to the significantly smaller stomatal aperture in MsHDZ23-OE lines compared to WT. Furthermore, the accumulation of the malondialdehyde (MDA) under abiotic stresses was significantly decreased, accompanied by dramatically enhanced activities in several antioxidant enzymes, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in the transgenic plants. Collectively, these results demonstrate that MsHDZ23 functions as a multifunctional transcription factor in enhancing plant resistance to abiotic stresses. Full article
(This article belongs to the Special Issue Functional Genomics of Energy Crops 2.0)
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