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Genes Function and Mechanism Identification in Plant Stress Resistance: 3rd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 May 2025) | Viewed by 6062

Special Issue Editor

Dr. Hengling Wei

E-Mail Website
Guest Editor
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
Interests: cotton breeding; cotton functional gene identification
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Global warming and its exacerbation of extreme weather events has increased the prevalence of factors that affect the development of plants. These include droughts, high temperatures and low temperatures, which have become the common forms of abiotic stress in the development of plants, particularly in areas that produce crops such as cotton. Creating plant germplasms that are resistant to such forms of abiotic stress is urgently required.

This Special Issue will address a selection of recent research topics and current review articles in the field of exploiting, cloning and verifying novel genes related to plant stress resistance, and will also consider the factors of drought, high temperature and low temperature, among others. Bioinformatics papers, up-to-date review articles and commentaries are also welcome.

This Special Issue is supervised by Dr. Hengling Wei and assisted by our Guest Editor’s Assistant Editor, Dr. Shoujiang Sun (China Agricultural University, Beijing, China).

Dr. Hengling Wei
Guest Editor

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

  • cotton
  • plant abiotic stresses
  • drought resistance
  • high-temperature resistance
  • low-temperature resistance
  • salt resistance

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Related Special Issues

Published Papers (5 papers)

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Research

11 pages, 594 KiB  
Article
Molecular Mass and Isoelectric Point Analysis of Cytokinin Sequences in the Wheat Genome
by Meshal M. Almutairi and Saad M. Alzahrani
Int. J. Mol. Sci. 2025, 26(11), 5270; https://doi.org/10.3390/ijms26115270 - 30 May 2025
Viewed by 330
Abstract
Cytokinins play an important role in plants and are targets of wheat breeding, particularly in terms of flowering and yield. The objective of this study was to determine relative synonymous codon usage (RSCU), molecular weight (g/mol), theoretical isoelectric point, instability index, aliphatic index, [...] Read more.
Cytokinins play an important role in plants and are targets of wheat breeding, particularly in terms of flowering and yield. The objective of this study was to determine relative synonymous codon usage (RSCU), molecular weight (g/mol), theoretical isoelectric point, instability index, aliphatic index, and hydrophobicity for the wheat cytokinin sequences from two different databases. The methods employed involved different formulas for calculations. The relative synonymous codon usage values were calculated as the ratio of the observed frequency to the expected frequency for the particular codon. The theoretical isoelectric point was calculated based on dissociation constant for groups of carboxylic acid and amino acids groups. The results showed that values of the relative synonymous codon usage divided amino acids of wheat into two groups. In the first group, values were above 1.6 (significant overrepresentation), such as those for phenylalanine (TTC), and Leucine (TTA). In the second group, values were below 0.6 (underrepresentation) such as those for leucine (CTA) and valine (GTT). In addition, the theoretical isoelectric point (pI) ranged from 4.81 to 6.6, and the instability index values were 34.3 and 38.16. A high degree of instability was observed at 1D and 5D of wheat genomes with values of 54.16 and 50.36, respectively. Principal component analysis (PCA) of the RSCU revealed that the main variation was attributed to PC1, accounting for a total variation of about 72.11%. The amino acids contributing to this variation included isoleucine, leucine, lysine, aspartic acid, and serine. PCA of the theoretical isoelectric point results found that the main variation was attributed to PC1, with a total variation of about 58.88%, and these chromosomes included 5D, 4D, 1A, 4B, and 3D of wheat genomes. Understanding the importance of RSCU in plant breeding helps breeders understand the mechanisms and functional aspects of wheat genomes, thereby enabling the development of wheat genomes for environmental adaptations. These results will provide a reference for nutrition and industrial applications, as well as supporting breeding programs. Full article
(This article belongs to the Special Issue Genes Function and Mechanism Identification in Plant Stress Resistance: 3rd Edition)
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18 pages, 8616 KiB  
Article
Exploring Metabolic Pathways and Gene Mining During Cotton Flower Bud Differentiation Stages Based on Transcriptomics and Metabolomics
by Miaoqian Yang, Wenjie Li, Xiaokang Fu, Jianhua Lu, Liang Ma, Hantao Wang and Hengling Wei
Int. J. Mol. Sci. 2025, 26(5), 2277; https://doi.org/10.3390/ijms26052277 - 4 Mar 2025
Viewed by 655
Abstract
Cotton is regarded as one of the significant economic crops in China, and its earliness is defined as one of the crucial traits influencing fiber quality and yield. To study the physiological and biochemical mechanisms related to early-maturing traits of cotton, cotton shoot [...] Read more.
Cotton is regarded as one of the significant economic crops in China, and its earliness is defined as one of the crucial traits influencing fiber quality and yield. To study the physiological and biochemical mechanisms related to early-maturing traits of cotton, cotton shoot apexes at the one-leaf, three-leaf, and five-leaf stages of the early-maturing cotton CCRI50 and late-maturing cotton Guoxinmian11 were collected for transcriptome sequencing and metabolomics, respectively. A total of 616, 782, and 842 differentially expressed genes (DEGs) at the one-leaf stage, three-leaf stage, and five-leaf stage were obtained through transcriptome sequencing, respectively. The metabolic detection results showed that 68, 56, and 62 differential metabolites (DMs) were obtained in the three periods, respectively. A total of 10 DMs were detected simultaneously from the one-leaf to five-leaf stage, 4 of which were phenolic acids and down-regulated in the early maturing variety CCRI50. A combined transcriptomic and metabolomic analysis revealed that phenylpropanoid biosynthesis, tyrosine metabolism, and phenylalanine metabolism might be important metabolic pathways in cotton bud differentiation. GhTYDC-A01 was identified in both the tyrosine metabolism and phenylalanine metabolism pathways, and it was highly expressed in pistils. To investigate the function of this gene in flowering, we overexpressed it in Arabidopsis thaliana. Compared to the wild type, the flowering time of the overexpression of GhTYDC-A01 in Arabidopsis was delayed. This study provides valuable resources and new insights into the relationship between metabolites and early-maturing cotton. Full article
(This article belongs to the Special Issue Genes Function and Mechanism Identification in Plant Stress Resistance: 3rd Edition)
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22 pages, 3999 KiB  
Article
Genome-Wide Identification and Expression Analysis of SlNRAMP Genes in Tomato under Nutrient Deficiency and Cadmium Stress during Arbuscular Mycorrhizal Symbiosis
by Junli Liu, Xiaoqi Bao, Gaoyang Qiu, Hua Li, Yuan Wang, Xiaodong Chen, Qinglin Fu and Bin Guo
Int. J. Mol. Sci. 2024, 25(15), 8269; https://doi.org/10.3390/ijms25158269 - 29 Jul 2024
Cited by 3 | Viewed by 1538
Abstract
Arbuscular mycorrhizal (AM) fungi are well known for enhancing phosphorus uptake in plants; however, their regulating roles in cation transporting gene family, such as natural resistance-associated macrophage protein (NRAMP), are still limited. Here, we performed bioinformatics analysis and quantitative expression assays of tomato [...] Read more.
Arbuscular mycorrhizal (AM) fungi are well known for enhancing phosphorus uptake in plants; however, their regulating roles in cation transporting gene family, such as natural resistance-associated macrophage protein (NRAMP), are still limited. Here, we performed bioinformatics analysis and quantitative expression assays of tomato SlNRAMP 1 to 5 genes under nutrient deficiency and cadmium (Cd) stress in response to AM symbiosis. These five SlNRAMP members are mainly located in the plasma or vacuolar membrane and can be divided into two subfamilies. Cis-element analysis revealed several motifs involved in phytohormonal and abiotic regulation in their promoters. SlNRAMP2 was downregulated by iron deficiency, while SlNRAMP1, SlNRAMP3, SlNRAMP4, and SlNRAMP5 responded positively to copper-, zinc-, and manganese-deficient conditions. AM colonization reduced Cd accumulation and expression of SlNRAMP3 but enhanced SlNRAMP1, SlNRAMP2, and SlNRMAP4 in plants under Cd stress. These findings provide valuable genetic information for improving tomato resilience to nutrient deficiency and heavy metal stress by developing AM symbiosis. Full article
(This article belongs to the Special Issue Genes Function and Mechanism Identification in Plant Stress Resistance: 3rd Edition)
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19 pages, 7974 KiB  
Article
Genome-Wide Identification of GRAS Transcription Factors and Their Functional Analysis in Salt Stress Response in Sugar Beet
by Xiaolin Hao, Yongyong Gong, Sixue Chen, Chunquan Ma and Huizi Duanmu
Int. J. Mol. Sci. 2024, 25(13), 7132; https://doi.org/10.3390/ijms25137132 - 28 Jun 2024
Cited by 3 | Viewed by 1467
Abstract
GAI-RGA-and-SCR (GRAS) transcription factors can regulate many biological processes such as plant growth and development and stress defense, but there are few related studies in sugar beet. Salt stress can seriously affect the yield and quality of sugar beet (Beta vulgaris). [...] Read more.
GAI-RGA-and-SCR (GRAS) transcription factors can regulate many biological processes such as plant growth and development and stress defense, but there are few related studies in sugar beet. Salt stress can seriously affect the yield and quality of sugar beet (Beta vulgaris). Therefore, this study used bioinformatics methods to identify GRAS transcription factors in sugar beet and analyzed their structural characteristics, evolutionary relationships, regulatory networks and salt stress response patterns. A total of 28 BvGRAS genes were identified in the whole genome of sugar beet, and the sequence composition was relatively conservative. According to the topology of the phylogenetic tree, BvGRAS can be divided into nine subfamilies: LISCL, SHR, PAT1, SCR, SCL3, LAS, SCL4/7, HAM and DELLA. Synteny analysis showed that there were two pairs of fragment replication genes in the BvGRAS gene, indicating that gene replication was not the main source of BvGRAS family members. Regulatory network analysis showed that BvGRAS could participate in the regulation of protein interaction, material transport, redox balance, ion homeostasis, osmotic substance accumulation and plant morphological structure to affect the tolerance of sugar beet to salt stress. Under salt stress, BvGRAS and its target genes showed an up-regulated expression trend. Among them, BvGRAS-15, BvGRAS-19, BvGRAS-20, BvGRAS-21, LOC104892636 and LOC104893770 may be the key genes for sugar beet’s salt stress response. In this study, the structural characteristics and biological functions of BvGRAS transcription factors were analyzed, which provided data for the further study of the molecular mechanisms of salt stress and molecular breeding of sugar beet. Full article
(This article belongs to the Special Issue Genes Function and Mechanism Identification in Plant Stress Resistance: 3rd Edition)
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13 pages, 1396 KiB  
Article
Temperature Effects on Expression Levels of hsp Genes in Eggs and Second-Stage Juveniles of Meloidogyne hapla Chitwood, 1949
by Łukasz Flis, Tadeusz Malewski and Renata Dobosz
Int. J. Mol. Sci. 2024, 25(9), 4867; https://doi.org/10.3390/ijms25094867 - 29 Apr 2024
Cited by 1 | Viewed by 1247
Abstract
Meloidogyne hapla is one of the most important nematode pathogens. It is a sedentary, biotrophic parasite of plants that overwinters in the soil or in diseased roots. The development of M. hapla is temperature dependent. Numerous studies have been performed on the effect [...] Read more.
Meloidogyne hapla is one of the most important nematode pathogens. It is a sedentary, biotrophic parasite of plants that overwinters in the soil or in diseased roots. The development of M. hapla is temperature dependent. Numerous studies have been performed on the effect of temperature on the development of M. hapla, but only a few of them analyzed the heat shock protein (hsp) genes. The aim of the study was to perform expression profiling of eight hsp genes (Mh-hsp90, Mh-hsp1, Mh-hsp4, Mh-hsp6, Mh-hsp60, Mh-dnj19, Mh-hsp43, and Mh-hsp12.2) at two development stages of M. hapla, i.e., in eggs and second-stage juveniles (J2). The eggs and J2 were incubated under cold stress (5 °C), heat stress (35 °C, 40 °C), and non-stress (10 °C, 20 °C, and 30 °C) conditions. Expression profiling was performed by qPCR. It was demonstrated that only two genes, Mh-hsp60 and Mh-dnj19, have been upregulated by heat and cold stress at both development stages. Heat stress upregulated the expression of more hsp genes than cold stress did. The level of upregulation of most hsp genes was more marked in J2 than in eggs. The obtained results suggest that the Mh-hsp90 and Mh-hsp1 genes can be used as bioindicators of environmental impacts on nematodes of the Meloidogyne genus. Full article
(This article belongs to the Special Issue Genes Function and Mechanism Identification in Plant Stress Resistance: 3rd Edition)
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