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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: 31 May 2023 | Viewed by 3230

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Special Issue Editor

Dr. Hengling Wei

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Guest Editor

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Interests: cotton breeding; cotton functional gene identification

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 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, by exploiting, cloning, and verifying novel genes, is urgently required.

This Special Issue, ‘Genes Function and Mechanism Identification in Plant Stress Resistance’, 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.

Dr. Hengling Wei
Guest Editor

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Keywords

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

Published Papers (7 papers)

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Research

Open AccessArticle

Transcriptome Reveals the Molecular Mechanism of the ScALDH21 Gene from the Desert Moss Syntrichia caninervis Conferring Resistance to Salt Stress in Cotton

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Int. J. Mol. Sci. 2023, 24(6), 5822; https://doi.org/10.3390/ijms24065822 - 18 Mar 2023

Viewed by 162

Abstract

The desert moss Syntrichia caninervis has proven to be an excellent plant material for mining resistance genes. The aldehyde dehydrogenase 21 (ScALDH21) gene from S. caninervis has been shown to confer tolerance to salt and drought, but it is unclear how the transgene ScALDH21 regulates tolerance to abiotic stresses in cotton. In the present work, we studied the physiological and transcriptome analyses of non-transgenic (NT) and transgenic ScALDH21 cotton (L96) at 0 day, 2 days, and 5 days after salt stress. Through intergroup comparisons and a weighted correlation network analysis (WGCNA), we found that there were significant differences between NT and L96 cotton in the plant hormone, Ca²⁺, and mitogen-activated protein kinase (MAPK) signaling pathways as well as for photosynthesis and carbohydrate metabolism. Overexpression of ScALDH21 significantly increased the expression of stress-related genes in L96 compared to NT cotton under both normal growth and salt stress conditions. These data suggest that the ScALDH21 transgene can scavenge more reactive oxygen species (ROS) in vivo relative to NT cotton and improve cotton resistance to salt stress by increasing the expression of stress-responsive genes, responding quickly to stress stimuli, enhancing photosynthesis and improving carbohydrate metabolism. Therefore, ScALDH21 is a promising candidate gene to improve resistance to salt stress, and the application of this gene in cotton provides new insights into molecular plant breeding. Full article

(This article belongs to the Special Issue Genes Function and Mechanism Identification in Plant Stress Resistance)

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Open AccessArticle

Genome-Wide Identification and Expression Analysis of Cysteine-Rich Polycomb-like Protein (CPP) Gene Family in Tomato

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Int. J. Mol. Sci. 2023, 24(6), 5762; https://doi.org/10.3390/ijms24065762 - 17 Mar 2023

Viewed by 196

Abstract

The cysteine-rich polycomb-like protein (CPP) gene family is a class of transcription factors containing conserved cysteine-rich CRC structural domains that is involved in the regulation of plant growth and stress tolerance to adversity. Relative to other gene families, the CPP gene family has not received sufficient attention. In this study, six SlCPPs were identified for the first time using the most recent genome-wide identification data of tomato. Subsequently, a phylogenetic analysis classified SlCPPs into four subfamilies. The analysis of cis-acting elements in the promoter indicates that SlCPPs are involved in plant growth and development and also stress response. We present for the first time the prediction of the tertiary structure of these SlCPPs proteins using the AlphaFold2 artificial intelligence system developed by the DeepMind team. Transcriptome data analysis showed that SlCPPs were differentially expressed in different tissues. Gene expression profiling showed that all SlCPPs except SlCPP5 were up-regulated under drought stress; SlCPP2, SlCPP3 and SlCPP4 were up-regulated under cold stress; SlCPP2 and SlCPP5 were up-regulated under salt stress; all SlCPPs were up-regulated under inoculation with Cladosporium fulvum; and SlCPP1, SlCPP3, and SlCPP4 were up-regulated under inoculation with Stemphylium lycopersici. We performed a virus-induced gene silencing experiment on SlCPP3, and the results indicated that SlCPP3 was involved in the response to drought stress. Finally, we predicted the interaction network of the key gene SlCPP3, and there was an interaction relationship between SlCPP3 and 10 genes, such as RBR1 and MSI1. The positive outcome showed that SlCPPs responded to environmental stress. This study provides a theoretical and empirical basis for the response mechanisms of tomato in abiotic stresses. Full article

(This article belongs to the Special Issue Genes Function and Mechanism Identification in Plant Stress Resistance)

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Open AccessArticle

Transcriptome and Metabolome Profiling Unveil Pigment Formation Variations in Brown Cotton Lines (Gossypium hirsutum L.)

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Int. J. Mol. Sci. 2023, 24(6), 5249; https://doi.org/10.3390/ijms24065249 - 09 Mar 2023

Viewed by 252

Abstract

Naturally brown colored cotton (NBCC) is becoming increasingly popular due to its natural properties of coloration. However, poor fiber quality and color fading are key issues that are hindering the cultivation of naturally colored cotton. In this study, based on transcriptome and metabolome of 18 days post-anthesis (DPA), we compared the variations of pigment formation in two brown cotton fibers (DCF and LCF), with white cotton fiber (WCF) belonging to a near-isogenic line. A transcriptome study revealed a total of 15,785 differentially expressed genes significantly enriched in the flavonoid biosynthesis pathway. Furthermore, for flavonoid biosynthesis-related genes, such as flavonoid 3′5′-hydroxylase (F3′5′H), anthocyanidin synthase (ANS), anthocyanidin reductase (ANR), chalcone synthase (CHS), dihydroflavonol 4-reductase (DFR), and chalcone isomerase (CHI), their expressions significantly increased in LCF compared with DCF and WCF. Moreover, transcription factors MYB and bHLH were significantly expressed in LCF and DCF. Most flavonoid-related metabolites (myricetin naringenin, catechin, epicatechin-epiafzelechin, and epigallocatechin) were found to be more highly up-regulated in LCF and DCF than WCF. These findings reveal the regulatory mechanism controlling different brown pigmentation in cotton fibers and elucidate the need for the proper selection of high-quality brown cotton fiber breeding lines for promising fiber quality and durable brown color pigmentation. Full article

(This article belongs to the Special Issue Genes Function and Mechanism Identification in Plant Stress Resistance)

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Open AccessArticle

The CCCH-Type Zinc-Finger Protein GhC3H20 Enhances Salt Stress Tolerance in Arabidopsis thaliana and Cotton through ABA Signal Transduction Pathway

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Int. J. Mol. Sci. 2023, 24(5), 5057; https://doi.org/10.3390/ijms24055057 - 06 Mar 2023

Viewed by 507

Abstract

The CCCH zinc-finger protein contains a typical C3H-type motif widely existing in plants, and it plays an important role in plant growth, development, and stress responses. In this study, a CCCH zinc-finger gene, GhC3H20, was isolated and thoroughly characterized to regulate salt stress in cotton and Arabidopsis. The expression of GhC3H20 was up-regulated under salt, drought, and ABA treatments. GUS activity was detected in the root, stem, leaves, and flowers of ProGhC3H20::GUS transgenic Arabidopsis. Compared with the control, the GUS activity of ProGhC3H20::GUS transgenic Arabidopsis seedlings under NaCl treatment was stronger. Through the genetic transformation of Arabidopsis, three transgenic lines of 35S-GhC3H20 were obtained. Under NaCl and mannitol treatments, the roots of the transgenic lines were significantly longer than those of the wild-type (WT) Arabidopsis. The leaves of the WT turned yellow and wilted under high-concentration salt treatment at the seedling stage, while the leaves of the transgenic Arabidopsis lines did not. Further investigation showed that compared with the WT, the content of catalase (CAT) in the leaves of the transgenic lines was significantly higher. Therefore, compared with the WT, overexpression of GhC3H20 enhanced the salt stress tolerance of transgenic Arabidopsis. A virus-induced gene silencing (VIGS) experiment showed that compared with the control, the leaves of pYL156-GhC3H20 plants were wilted and dehydrated. The content of chlorophyll in pYL156-GhC3H20 leaves was significantly lower than those of the control. Therefore, silencing of GhC3H20 reduced salt stress tolerance in cotton. Two interacting proteins (GhPP2CA and GhHAB1) of GhC3H20 have been identified through a yeast two-hybrid assay. The expression levels of PP2CA and HAB1 in transgenic Arabidopsis were higher than those in the WT, and pYL156-GhC3H20 had expression levels lower than those in the control. GhPP2CA and GhHAB1 are the key genes involved in the ABA signaling pathway. Taken together, our findings demonstrate that GhC3H20 may interact with GhPP2CA and GhHAB1 to participate in the ABA signaling pathway to enhance salt stress tolerance in cotton. Full article

(This article belongs to the Special Issue Genes Function and Mechanism Identification in Plant Stress Resistance)

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Open AccessArticle

Genome-Wide Identification, Characterization and Experimental Expression Analysis of CNGC Gene Family in Gossypium

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Int. J. Mol. Sci. 2023, 24(5), 4617; https://doi.org/10.3390/ijms24054617 - 27 Feb 2023

Viewed by 419

Abstract

Cyclic nucleotide-gated ion channels (CNGCs) are channel proteins for calcium ions, and have been reported to play important roles in regulating survival and environmental response of various plants. However, little is known about how the CNGC family works in Gossypium. In this study, 173 CNGC genes, which were identified from two diploid and five tetraploid Gossypium species, were classified into four groups by phylogenetic analysis. The collinearity results demonstrated that CNGC genes are integrally conservative among Gossypium species, but four gene losses and three simple translocations were detected, which is beneficial to analyzing the evolution of CNGCs in Gossypium. The various cis-acting regulatory elements in the CNGCs’ upstream sequences revealed their possible functions in responding to multiple stimuli such as hormonal changes and abiotic stresses. In addition, expression levels of 14 CNGC genes changed significantly after being treated with various hormones. The findings in this study will contribute to understanding the function of the CNGC family in cotton, and lay a foundation for unraveling the molecular mechanism of cotton plants’ response to hormonal changes. Full article

(This article belongs to the Special Issue Genes Function and Mechanism Identification in Plant Stress Resistance)

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Open AccessArticle

Transcriptome Analysis Reveals the Defense Mechanism of Cotton against Verticillium dahliae Induced by Hypovirulent Fungus Gibellulopsis nigrescens CEF08111

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Int. J. Mol. Sci. 2023, 24(2), 1480; https://doi.org/10.3390/ijms24021480 - 12 Jan 2023

Cited by 2 | Viewed by 565

Abstract

Verticillium wilt is a kind of plant vascular disease caused by the soilborne fungus Verticillium dahliae, which severely limits cotton production. Our previous studies showed that the endophytic fungus Gibellulopsis nigrescens CEF08111 can effectively control Verticillium wilt and induce a defense response in cotton plants. However, the comprehensive molecular mechanism governing this response is not yet clear. To study the signaling mechanism induced by strain CEF08111, the transcriptome of cotton seedlings pretreated with CEF08111 was sequenced. The results revealed 249, 3559 and 33 differentially expressed genes (DEGs) at 3, 12 and 48 h post inoculation with CEF08111, respectively. At 12 h post inoculation with CEF08111, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that the DEGs were enriched mainly in the plant–pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathway-plant, and plant hormone signal transduction pathways. Gene ontology (GO) analysis revealed that these DEGs were enriched mainly in the following terms: response to external stimulus, systemic acquired resistance, kinase activity, phosphotransferase activity, xyloglucan: xyloglucosyl transferase activity, xyloglucan metabolic process, cell wall polysaccharide metabolic process and hemicellulose metabolic process. Moreover, many genes, such as calcium-dependent protein kinase (CDPK), flagellin-sensing 2 (FLS2), resistance to Pseudomonas syringae pv. maculicola 1(RPM1) and myelocytomatosis protein 2 (MYC2), that regulate crucial points in defense-related pathways were identified and may contribute to V. dahliae resistance in cotton. Seven DEGs of the pathway phenylpropanoid biosynthesis were identified by weighted gene co-expression network analysis (WGCNA), and these genes are related to lignin synthesis. The above genes were compared and analyzed, a total of 710 candidate genes that may be related to the resistance of cotton to Verticillium wilt were identified. These results provide a basis for understanding the molecular mechanism by which the biocontrol fungus CEF08111 increases the resistance of cotton to Verticillium wilt. Full article

(This article belongs to the Special Issue Genes Function and Mechanism Identification in Plant Stress Resistance)

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Open AccessArticle

A Comprehensive Analysis of the DUF4228 Gene Family in Gossypium Reveals the Role of GhDUF4228-67 in Salt Tolerance

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Int. J. Mol. Sci. 2022, 23(21), 13542; https://doi.org/10.3390/ijms232113542 - 04 Nov 2022

Viewed by 733

Abstract

Soil salinization conditions seriously restrict cotton yield and quality. Related studies have shown that the DUF4228 proteins are pivotal in plant resistance to abiotic stress. However, there has been no systematic identification and analysis of the DUF4228 gene family in cotton and their role in abiotic stress. In this study, a total of 308 DUF4228 genes were identified in four Gossypium species, which were divided into five subfamilies. Gene structure and protein motifs analysis showed that the GhDUF4228 proteins were conserved in each subfamily. In addition, whole genome duplication (WGD) events and allopolyploidization might play an essential role in the expansion of the DUF4228 genes. Besides, many stress-responsive (MYB, MYC) and hormone-responsive (ABA, MeJA) related cis-elements were detected in the promoters of the DUF4228 genes. The qRT-PCR results showed that GhDUF4228 genes might be involved in the response to abiotic stress. VIGS assays and the measurement of relative water content (RWC), Proline content, POD activity, and malondialdehyde (MDA) content indicated that GhDUF4228-67 might be a positive regulator of cotton response to salt stress. The results in this study systematically characterized the DUF4228s in Gossypium species and will provide helpful information to further research the role of DUF4228s in salt tolerance. Full article

(This article belongs to the Special Issue Genes Function and Mechanism Identification in Plant Stress Resistance)

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