Stress Response Element Research Articles

Genome-wide analysis of calmodulin binding Protein60 candidates in the important crop plants.

Efficient management of environmental stresses is essential for sustainable crop production. Calcium (Ca²⁺) signaling plays a crucial role in regulating responses to both biotic and abiotic stresses, particularly during host-pathogen interactions. In Arabidopsis thaliana, calmodulin-binding protein 60 (CBP60) family members, such as AtCBP60g, AtCBP60a, and AtSARD1, have been well characterized for their involvement in immune regulation. However, a comprehensive understanding of CBP60 genes in major crops remains limited. In this study, we utilized the Phytozome v12.1 database to identify and analyze CBP60 genes in agriculturally important crops. Expression patterns of a Oryza sativa (rice) CBP60 gene, OsCBP60bcd-1, were assessed in resistant and susceptible rice genotypes in response to infection by the bacterial pathogen Xanthomonas oryzae. Localization of CBP60 proteins was analyzed to predict their functional roles, and computational promoter analysis was performed to identify stress-responsive cis-regulatory elements. Phylogenetic analysis revealed that most CBP60 genes in crops belong to the immune-related clade. Expression analysis showed that OsCBP60bcd-1 was significantly upregulated in the resistant rice genotype upon pathogen infection. Subcellular localization studies suggested that the majority of CBP60 proteins are nuclear-localized, indicating a potential role as transcription factors. Promoter analysis identified diverse stress-responsive cis-regulatory elements in the promoters of CBP60 genes, highlighting their regulatory potential under stress conditions. The upregulation of OsCBP60bcd-1 in response to Xanthomonas oryzae and the presence of stress-responsive elements in its promoter underscore the importance of CBP60 genes in pathogen defense. These findings provide a basis for further investigation into the functional roles of CBP60 genes in crop disease resistance, with implications for enhancing stress resilience in agricultural species.

Genome-Wide Analysis and Expression Profiling of Glyoxalase Gene Families Under Abiotic Stresses in Cucumber (Cucumis sativus L.)

The glyoxalase pathway, consisting of glyoxalase I (GLYI) and glyoxalase II (GLYII), is an enzymatic system that converts cytotoxic methylglyoxal to non-toxic S-D-lactoylglutathione. Although the GLY gene family has been analyzed in Arabidopsis, rice, grape, cabbage, and soybean, cucumber studies are lacking. Here, we analyzed the cucumber GLY gene family, identifying 13 CsGLYI and 2 CsGLYII genes. Furthermore, we investigated the physicochemical properties, phylogenetic relationships, chromosomal localization and colinearity, gene structure, conserved motifs, cis-regulatory elements, and protein–protein interaction networks of the CsGLY family. They were primarily localized in the cytoplasm, chloroplasts, and mitochondria, with a minor presence in the nucleus. The classification of CsGLYI and CsGLYII genes into five classes closely resembled the homologous genes in Arabidopsis and soybean. Additionally, hormone-responsive elements dominated the promoter region of GLY genes, alongside light- and stress-responsive elements. The predicted interaction proteins of CsGLYIs and CsGLYIIs exerted a significant role in cellular respiration, amino acid synthesis, and metabolism, as well as methylglyoxal catabolism. In addition, the expression profiles of GLY genes were distinct in different tissues of cucumber as well as under diverse abiotic stresses. This study is conducive to the further exploration of the functional diversity among glyoxalase genes and the mechanisms of stress responses in cucumber.

Comprehensive Analysis of BrDUF506 Genes Across the Brassica rapa Genome Uncovers Potential Functions in Sexual Reproduction and Abiotic Stress Tolerance.

The Domain of Unknown Function 506 (DUF506) belongs to the PD-(D/E) XK nuclease superfamily and has been reported to play critical roles in growth and development as well as responses to abiotic stresses. However, the function of DUF506 genes in Brassica rapa (B. rapa) remains unclear. In this study, a total of 18 BrDUF506 genes were identified and randomly distributed across eight chromosomes, categorized into four subfamilies. Analyzing their promoter sequences has uncovered various stress-responsive elements, such as those for drought, methyl jasmonate (MeJA), and abscisic acid (ABA). Bra000098 and Bra017099 exhibit significantly enhanced expression in response to heat and drought stress. Protein interaction predictions indicate that Bra000098 homolog, At2g38820, is interacting with ERF012 and PUB48 and is involved in abiotic stress regulation. Furthermore, gene expression profiling has identified Bra026262 with a high expression level in flowers and significantly decreased in female sterile mutants. Protein interaction prediction further revealed that its homolog, At4g32480, interacts with MYB and AGL proteins, suggesting the potential roles in female gametophyte development. The current study enhances our understanding of the functional roles of BrDUF506s, providing significant insights that are valuable in investigating sexual reproduction and abiotic stress responses in B. rapa.

Genome-Wide Identification and Expression Analysis of the ALKB Homolog Gene Family in Potato (Solanum tuberosum L.).

N6-methyladenosine (m6A) is an abundant and pervasive post-transcriptional modification in eukaryotic mRNAs. AlkB homolog (ALKBH) proteins play crucial roles in RNA metabolism and translation, participating in m6A methylation modification to regulate plant development. However, no comprehensive investigations have been conducted on ALKBH in potato. Here, 11 StALKBH family genes were identified in potato and renamed according to BLASTP and phylogenetic analyses following the Arabidopsis genome. The characteristics, sequence structures, motif compositions, phylogenetics, chromosomal locations, synteny, and promoter cis-acting element predictions were analyzed, revealing distinct evolutionary relationships between potato and other species (tomato and Arabidopsis). Homologous proteins were classified into seven groups depending on similar conserved domains, which implies that they possess a potentially comparable function. Moreover, the StALKBHs were ubiquitous, and their expression was examined in the various tissues of a whole potato, in which the StALKBH genes, except for StALKBH2, were most highly expressed in the stolon and flower. Multiple hormone and stress-response elements were found to be located in the promoters of the StALKBH genes. Further qRT-PCR results suggest that they may be significantly upregulated in response to phytohormones and abiotic stress (except for cold), and the expression of most of the StALKBH genes exhibited positively modulated trends. Overall, this study is the first to report a genome-wide assessment of the ALKBH family in potato, providing valuable insights into candidate gene selection and facilitating in-depth functional analyses of ALKBH-mediated m6A methylation mechanisms in potato.

Genome-wide characterization and expression analysis of WRKY transcription factors reveals biotic stress response potential mechanisms in Panax notoginseng

WRKY transcription factors (TFs), among the largest families of transcriptional regulators, are essential players in defense responses in plants. Panax notoginseng, a traditional and precious herbal medicine in China, is widely cultivated due to its excellent medicinal and edible value. However, P. notoginseng is frequently affected by various diseases (like Black blot disease, Root rot disease and Viral diseases). Therefore, the present study aimed to identify and characterize PnWRKYs in the P. notoginseng genome, reveal their structural attributes, regulatory elements, and potential functions in defense responses. 68 PnWRKY TFs that have conserved domains and different physicochemical characteristics were identified in the genome. They can be divided into four groups according to phylogenetic relationships and conserved domain structures. Furthermore, Group II WRKY TFs can be classified into five subgroups (IIa, IIb, IIc, IId, and IIe) according to their zinc finger-like motif. The PnWRKY family expands mainly via segmental duplication. Additionally, the promoter regions of PnWRKYs contain many hormone-responsive and stress-responsive elements. Expression patterns under different hormones (salicylic acid, methyl jasmonate, and melatonin) and disease (root rot disease, black blot disease, and virus disease) treatment analysis highlighted their wide involvement in plant hormone-induced disease defense responses. These findings affirmed the potential functions of PnWRKY TFs in disease-mediated defense responses and provided valuable insights for future agricultural applications.

Systematic analysis of the ARF gene family in Fagopyrum dibotrys and its potential roles in stress tolerance.

The auxin response factor (ARF) is a plant-specific transcription factor that regulates the expression of auxin response genes by binding directly to their promoters. They play an important role in the regulation of plant growth and development, as well as in the response to biotic and abiotic stresses. However, the identification and functional analysis of ARFs in Fagopyrum dibotrys are still unclear. In this study, a total of 26 FdARF genes were identified using bioinformatic methods. Their chromosomal location, gene structure, physical and chemical properties of their encoded protein, subcellular location, phylogenetic tree, conserved motifs and cis-acting elements in FdARF promoters were analyzed. The results showed that 26 FdARF genes were unevenly distributed on 8 chromosomes, with the largest distribution on chromosome 4 and the least distribution on chromosome 3. Most FdARF proteins are located in the nucleus, except for the proteins FdARF7 and FdARF21 located to the cytoplasm and nucleus, while FdARF14, FdARF16, and FdARF25 proteins are located outside the chloroplast and nucleus. According to phylogenetic analysis, 26 FdARF genes were divided into 6 subgroups. Duplication analysis indicates that the expansion of the FdARF gene family was derived from segmental duplication rather than tandem duplication. The prediction based on cis-elements of the promoter showed that 26 FdARF genes were rich in multiple stress response elements, suggesting that FdARFs may be involved in the response to abiotic stress. Expression profiling analysis showed that most of the FdARF genes were expressed in the roots, stems, leaves, and tubers of F. dibotrys, but their expression exhibits a certain degree of tissue specificity. qRT-PCR analysis revealed that most members of the FdARF gene were up- or down-regulated in response to abiotic stress. The results of this study expand our understanding of the functional role of FdARFs in response to abiotic stress and lay a theoretical foundation for further exploration of other functions of FdARF genes.

Comprehensive analysis of ankyrin repeat gene family revealed SbANK56 confers drought tolerance in sorghum

Ankyrin repeat (ANK) proteins are crucial for cell growth, development, and response to hormones and environmental stress. However, there has been little research done to clarify the roles of ANK proteins in sorghum. In this study, 142 ANK genes of sorghum were identified and classified into 12 subfamilies according to the conserved domains. The cis-elements analysis revealed a substantial presence of stress-responsive elements within the promoter region of SbANK genes. After treated with drought, salt, and abscisic acid, SbANK56 showed the highest expression levels among family members by using quantitative real-time PCR (qRT-PCR) analysis. The survival rate was significantly improved by the overexpression of SbANK56 compared to wild type (WT) under drought conditions. SbANK56 overexpressing plants displayed lower malondialdehyde and higher proline contents compared to WT plants under drought conditions. Additionally, the expression levels of drought-associated genes were significantly increased in SbANK56 transgenic plants. Importantly, the analysis of natural variation in SbANK56 revealed a significant positive correlation between SbANK56Hap4 and both its differential expression and drought stress tolerance. Taken together, our results provide some evidence for improving drought tolerance in sorghum through breeding initiatives while also advancing our knowledge of the evolutionary trends and functional mechanisms underlying ANK genes.

Bioinformatics Analysis of the Panax ginseng Cyclophilin Gene and Its Anti-Phytophthora cactorum Activity.

In this paper, Panax ginseng cyclophilin (PgCyP) was successfully obtained through a genetic engineering technique. A bioinformatics method was used to analyze the physicochemical properties and structure of PgCyP. The results showed that PgCyP belongs to the cyclophilin gene family. The protein encoded by the PgCyP gene contains the active site of PPIase (R62, F67, and H133) and a binding site for cyclosporine A (W128). The relative molecular weight of PgCyP is 187.11 bp; its theoretical isoelectric point is 7.67, and it encodes 174 amino acids. The promoter region of PgCyP mainly contains the low-temperature environmental stress response (LTR) element, abscisic acid-responsive cis-acting element (ABRE), and light-responsive cis-acting element (G-Box). PgCyP includes a total of nine phosphorylation sites, comprising four serine phosphorylation sites, three threonine phosphorylation sites, and two tyrosine phosphorylation sites. PgCyP was recombined and expressed in vitro, and its recombinant expression was investigated. Furthermore, it was found that the recombinant PgCyP protein could effectively inhibit the germination of Phytophthora cactorum spores and the normal growth of Phytophthora cactorum mycelia in vitro. Further experiments on the roots of susceptible Arabidopsis thaliana showed that the PgCyP protein could improve the resistance of arabidopsis to Phytophthora cactorum. The findings of this study provide a basis for the use of the PgCyP protein as a new type of green biopesticide.

Genome-Wide Identification of the Auxin Response Factor Gene Family in Maple (Acer truncatum) and Transcriptional Expression Analysis at Different Coloration Stages of Leaves

Auxin response factors (ARFs) are involved in the mechanism of plant leaf color regulation, inhibiting chlorophyll synthesis while promoting anthocyanin production. However, it is not clear whether the ARF gene family is involved in autumn leaf color changes in maple. The differentially expressed genes for autumn leaf discoloration were obtained by transcriptome sequencing, and the AtARF family was constructed by homologous gene search. The results show that the AtARFs consist of 21 members distributed on 11 chromosomes and can be divided into three subfamilies, which are mainly distributed in the nucleus. The promoter regions of the AtARFs contain light-responsive elements, abiotic stress-responsive elements, and hormone-responsive elements. The analyses presented in this paper provide comprehensive information on ARFs and help to elucidate their functional roles in leaf color change in Acer truncatum.

Transcription factor gene TaWRKY76 confers plants improved drought and salt tolerance through modulating stress defensive-associated processes in Triticum aestivum L.

WRKY transcription factor (TF) family acts as essential regulators in plant growth and abiotic stress responses. This study reported the function of TaWRKY76, a member of WRKY TF family in Triticum aestivum L., in regulating plant osmotic stress tolerance. TaWRKY76 transcripts were significantly upregulated upon drought and salt signaling, with dose extent- and stress temporal-dependent manners. Plant GUS activity assays suggested that stress responsive cis-acting elements, such as DRE and ABRE, exert essential roles in defining gene transcription under osmotic stress conditions. The TaWRKY76 protein targeted onto nucleus and possessed ability interacting with TaMYC2, a MYC TF member of wheat. TaWRKY76 and TaMYC2 positively regulated plant drought and salt adaptation by modulating osmotic stress-related physiological indices, including osmolyte contents, stomata movement, root morphology, and reactive oxygen species (ROS) homeostasis. Yeast one-hybrid assay indicated the binding ability of TaWRKY76 with promoters of TaDREB1;1, TaNCEB3, and TaCOR15;4. ChIP-PCR analysis confirmed that the osmotic stress genes are transcriptionally regulated by TaWRKY76. Moreover, the transgenic lines with knockdown of these stress-response genes displayed lowered plant biomass together with worsened root growth traits, decreased proline contents, and elevated ROS amounts. These results suggested that these stress defensive genes contributed to TaWRKY76-modulated osmotic stress tolerance. Highly positive correlations were observed between yield and the transcripts of TaWRKY76 in a wheat variety panel under field drought condition. A major haplotype TaWRKY76 Hap1 conferred improved drought tolerance. Our results suggested that TaWRKY76 is essential in plant drought and salt adaptation and a valuable target for molecular breeding stress-tolerant cultivars in Triticum aestivum L..

Genome-wide identification, expression pattern and interacting protein analysis of INDETERMINATE DOMAIN (IDD) gene family in Phalaenopsis equestris

The plant-specific INDETERMINATE DOMAIN (IDD) gene family is important for plant growth and development. However, a comprehensive analysis of the IDD family in orchids is limited. Based on the genome data of Phalaenopsis equestris, the IDD gene family was identified and analyzed by bioinformatics methods in this study. Ten putative P. equestris IDD genes (PeIDDs) were characterized and phylogenetically classified into two groups according to their full amino acid sequences. Protein motifs analysis revealed that overall structures of PeIDDs in the same group were relatively conserved. Its promoter regions harbored a large number of responsive elements, including light responsive, abiotic stress responsive elements, and plant hormone cis-acting elements. The transcript level of PeIDD genes under cold and drought conditions, and by exogenous auxin (NAA) and abscisic acid (ABA) treatments further confirmed that most PeIDDs responded to various conditions and might play essential roles under abiotic stresses and hormone responses. In addition, distinct expression profiles in different tissues/organs suggested that PeIDDs might be involved in various development processes. Furthermore, the prediction of protein-protein interactions (PPIs) revealed some PeIDDs (PeIDD3 or PeIDD5) might function via cooperating with chromatin remodeling factors. The results of this study provided a reference for further understanding the function of PeIDDs.

Identification of the ribosomal protein L18 (RPL18) gene family reveals that TaRPL18-1 positively regulates powdery mildew resistance in wheat

The Ribosomal protein L18 (RPL18) protein gene family plays an important role in plant growth, development and stress response. Although the RPL18 genes have been identified in several plant species, the RPL18 gene family in wheat (Triticum aestivum) is still unexplored. This study found 8 TaRPL18 genes, each of which has a significantly different gene sequence length and is evenly distributed on the chromosome; Additionally, these proteins have similar physicochemical characteristics as well as secondary and tertiary structures. 17 RPL18 genes in 4 species (wheat, Arabidopsis, rice, and maize) were classified into 5 groups, and the TaRPL18 genes within the same group showed similar structures and conserved motifs. Analysis of the cis-acting elements in the TaRPL18 genes promoter regions revealed the presence of developmental and stress-responsive elements in the majority of the genes. Through yeast two-hybrid (Y2H) experiments, it was confirmed that the powdery mildew resistance protein TaPm46 physically interacts with the Class IV TaRPL18-1. Functional analysis indicated that TaRPL18-1-silenced wheat plants show reduced resistance to powdery mildew compared to the wild type (WT), with decreased expression levels of PAL and PPO genes, and increased expression levels of the PR gene. The findings of this study provide a basis for clarifying the function of the TaRPL18 genes and will be useful for the selection of disease-resistant varieties of wheat.

Genome-Wide Analysis of Aquaporins Gene Family in Populus euphratica and Its Expression Patterns in Response to Drought, Salt Stress, and Phytohormones.

Aquaporins (AQPs) play an essential role in membrane water transport during plant responses to water stresses centered on conventional upstream signals. Phytohormones (PHs) regulate plant growth and yield, working with transcription factors to help plants withstand environmental challenges and regulate physiological and chemical processes. The AQP gene family is important, so researchers have studied its function and regulatory system in numerous species. Yet, there is a critical gap the understanding of many of their molecular features, thus our full knowledge of AQPs is far-off. In this study, we undertook a broad examination of the AQP family gene in Populus euphratica via bioinformatics tools and analyzed the expression patterns of certain members in response to drought, salt, and hormone stress. A total of 22 AQP genes were examined in P. euphratica, and were categorized into four main groups, including TIPs, PIPs, SIPs, and NIPs based on phylogenetic analysis. Comparable exon-intron gene structures were found by gene structure examination, and similarities in motif number and pattern within the same subgroup was determined by motif analysis. The PeuAQP gene family has numerous duplications, and there is a distinct disparity in how the members of the PeuAQP family react to post-translational modifications. Abiotic stress and hormone responses may be mediated by AQPs, as indicated by the abundance of stress response elements found in 22 AQP genes, as revealed by the promoter's cis-elements prediction. Expression pattern analysis reveals that selected six AQP genes from the PIP subgroup were all expressed in the leaves, stem, and roots with varying expression levels. Moreover, qRT-PCR analysis discovered that the majority of the selected AQP members were up- or down-regulated in response to hormone treatment and abiotic stress. Remarkably, PeuAQP14 and PeuAQP15 appeared to be highly responsive to drought stress and PeuAQP15 exhibited a high response to salt stress. The foliar application of the phytohormones (SA, IAA, GA3, MeJA, and ABA) were found to either activate or inhibit PeuAQP, suggesting that they may mitigate the effects of water shortage of poplar water stress. The present work enhances our knowledge of the practical roles of AQPs in stress reactions and offers fundamental information for the AQP genes in poplar species. It also highlights a direction for producing new varieties of poplar species with drought, salt, and hormone tolerance and holds substantial scientific and ecological importance, offering a potential contribution to the conservation of poplar species in arid regions.

Genome-wide analysis of two repeats containing MYB transcription factors in groundnut identifies drought-inducible genes involved as a negative regulator of root nodulation

The MYB gene superfamily encompasses a group of related genes found in all eukaryotes. In contrast to animals, higher plants contain large numbers of two-repeat MYB genes, which have been established in regulating crucial developmental, biotic, and abiotic stress responses that profoundly affect the plant's yield. However, a comprehensive analysis of the two-repeat MYB gene family in groundnut and its progenitors, especially the role of two-repeat MYB genes in response to drought stress, and the effect of those genes in nodulation have not been reported so far. Our recent analysis of the groundnut genome has identified 79 (Arachis duranensis), 84 (Arachis ipaensis), and 161 (Arachis hypogaea) two-repeat MYB genes, which belong to multiple distinct subgroups based on their architecture. Here, we provided a complete overview of the gene structure, protein motif organization, chromosome localization, gene duplication events, and synteny analysis to clarify evolutionary perspectives. Members of the same subgroup showed highly conserved structure and motif compositions. The whole-genome duplication and segmental duplication likely contributed to the expansion of two-repeat MYB genes in Arachis hypogaea. The upstream sequences of most genes contained phytohormone-responsive, stress-responsive, light-responsive, and plant growth-related elements. The genes not only have diverse expression profiles across different development stages but as shown in our experimental findings, most of them were induced by ABA and drought-related stress. Further gene silencing experiments demonstrated that two drought-inducible MYB genes, homologs of Arabidopsis MYB96 and MYB94, function as a negative regulator of root nodulation. The results of this study can serve as a strong foundation for further elucidation of the physiological and molecular function of two-repeat MYB genes in groundnut.

Whole genome regulatory effect of MoISW2 and consequences for the evolution of the rice plant pathogenic fungus Magnaporthe oryzae.

Isw2 proteins, ubiquitous across eukaryotes, exhibit a propensity for DNA binding and exert dynamic influences on local chromosome condensation in an ATP-dependent fashion, thereby modulating the accessibility of neighboring genes to transcriptional machinery. Here, we report the deletion of a putative MoISW2 gene, yielding substantial ramifications on plant pathogenicity. Subsequent gene complementation and chromatin immunoprecipitation sequencing (ChIP-seq) analyses were conducted to delineate binding sites. RNA sequencing (RNA-seq) assays revealed discernible impacts on global gene regulation along chromosomes in both mutant and wild-type strains, with comparative analyses against 55 external RNA-seq data sets corroborating these findings. Notably, MoIsw2-mediated binding and activities delineate genomic loci characterized by pronounced gene expression variability proximal to MoIsw2 binding sites, juxtaposed with comparatively stable expression in surrounding regions. The contingent genes influenced by MoIsw2 activity predominantly encompass niche-determinant genes, including those encoding secreted proteins, secondary metabolites, and stress-responsive elements, alongside avirulence genes. Furthermore, our investigations unveil a spatial correlation between MoIsw2 binding motifs and known transposable elements (TEs), suggesting a potential interplay wherein TE transposition at these loci could modulate the transcriptional landscape of Magnaporthe oryzae in a strain-specific manner. Collectively, these findings position MoIsw2 as a plausible master regulator orchestrating the delicate equilibrium between genes vital for biomass proliferation, akin to housekeeping genes, and niche-specific determinants crucial for ecological adaptability. Stress-induced TE transposition, in conjunction with MoIsw2 activity, emerges as a putative mechanism fostering enhanced mutagenesis and accelerated evolution of niche-determinant genes relative to housekeeping counterparts.IMPORTANCEIsw2 proteins are conserved in plants, fungi, animals, and other eukaryotes. We show that a fungal Isw2 protein in the rice pathogen Magnaporthe oryzae binds to retrotransposon (RT) DNA motifs and affects the epigenetic gene expression landscape of the fungal genome. Mainly ecological niche determinant genes close to the binding motifs are affected. RT elements occur frequently in DNA between genes in most organisms. They move place and multiply in the genome, especially under physiological stress. We further discuss the Isw2 and RT combined activities as a possible sought-after mechanism that can cause biased mutation rates and faster evolution of genes necessary for reacting to abiotic and biotic challenges. The most important biotic challenges for plant pathogens are the ones from the host plants' innate immunity. The overall result of these combined activities will be an adaptation-directed evolution of niche-determinant genes.

The Genome-Wide Identification of the Dihydroflavonol 4-Reductase (DFR) Gene Family and Its Expression Analysis in Different Fruit Coloring Stages of Strawberry.

Dihydroflavonol 4-reductase (DFR) significantly influences the modification of flower color. To explore the role of DFR in the synthesis of strawberry anthocyanins, in this study, we downloaded the CDS sequences of the DFR gene family from the Arabidopsis genome database TAIR; the DFR family of forest strawberry was compared; then, a functional domain screen was performed using NCBI; the selected strawberry DFR genes were analyzed; and the expression characteristics of the family members were studied by qRT-PCR. The results showed that there are 57 members of the DFR gene family in strawberry, which are mainly expressed in the cytoplasm and chloroplast; most of them are hydrophilic proteins; and the secondary structure of the protein is mainly composed of α-helices and random coils. The analysis revealed that FvDFR genes mostly contain light, hormone, abiotic stress, and meristem response elements. From the results of the qRT-PCR analysis, the relative expression of each member of the FvDFR gene was significantly different, which was expressed throughout the process of fruit coloring. Most genes had the highest expression levels in the full coloring stage (S4). The expression of FvDFR30, FvDFR54, and FvDFR56 during the S4 period was 8, 2.4, and 2.4 times higher than during the S1 period, indicating that the DFR gene plays a key role in regulating the fruit coloration of strawberry. In the strawberry genome, 57 members of the strawberry DFR gene family were identified. The higher the DFR gene expression, the higher the anthocyanin content, and the DFR gene may be the key gene in anthocyanin synthesis. Collectively, the DFR gene is closely related to fruit coloring, which lays a foundation for further exploring the function of the DFR gene family.

Identification, characterization, and expression analysis of WRKY transcription factors in Cardamine violifolia reveal the key genes involved in regulating selenium accumulation

BackgroundCardamine violifolia is a significant Brassicaceae plant known for its high selenium (Se) accumulation capacity, serving as an essential source of Se for both humans and animals. WRKY transcription factors play crucial roles in plant responses to various biotic and abiotic stresses, including cadmium stress, iron deficiency, and Se tolerance. However, the molecular mechanism of CvWRKY in Se accumulation is not completely clear.ResultsIn this study, 120 WRKYs with conserved domains were identified from C. violifolia and classified into three groups based on phylogenetic relationships, with Group II further subdivided into five subgroups. Gene structure analysis revealed WRKY variations and mutations within the CvWRKYs. Segmental duplication events were identified as the primary driving force behind the expansion of the CvWRKY family, with numerous stress-responsive cis-acting elements found in the promoters of CvWRKYs. Transcriptome analysis of plants treated with exogenous Se and determination of Se levels revealed a strong positive correlation between the expression levels of CvWRKY034 and the Se content. Moreover, CvWRKY021 and CvWRKY099 exhibited high homology with AtWRKY47, a gene involved in regulating Se accumulation in Arabidopsis thaliana. The WRKY domains of CvWRKY021 and AtWRKY47 were highly conserved, and transcriptome data analysis revealed that CvWRKY021 responded to Na2SeO4 induction, showing a positive correlation with the concentration of Na2SeO4 treatment. Under the induction of Na2SeO3, CvWRKY021 and CvWRKY034 were significantly upregulated in the roots but downregulated in the shoots, and the Se content in the roots increased significantly and was mainly concentrated in the roots. CvWRKY021 and CvWRKY034 may be involved in the accumulation of Se in roots.ConclusionsThe results of this study elucidate the evolution of CvWRKYs in the C. violifolia genome and provide valuable resources for further understanding the functional characteristics of WRKYs related to Se hyperaccumulation in C. violifolia.

Genome-Wide Characterization of IQD Family Proteins in Apple and Functional Analysis of the Microtubule-Regulating Abilities of MdIQD17 and MdIQD28 under Cold Stress.

Microtubules undergo dynamic remodeling in response to diverse abiotic stress in plants. The plant-specific IQ67 DOMAIN (IQD) family proteins serve as microtubule-associated proteins, playing multifaceted roles in plant development and response to abiotic stress. However, the biological function of IQD genes in apple remains unclear. In this study, we conducted a comprehensive analysis of the Malus domestica genome, identifying 42 IQD genes distributed across 17 chromosomes and categorized them into four subgroups. Promoter analysis revealed the presence of stress-responsive elements. Subsequent expression analysis highlighted the significant upregulation of MdIQD17 and MdIQD28 in response to cold treatments, prompting their selection for further functional investigation. Subcellular localization studies confirmed the association of MdIQD17 and MdIQD28 with microtubules. Crucially, confocal microscopy and quantification revealed diminished microtubule depolymerization in cells transiently overexpressing MdIQD17 and MdIQD28 compared to wild-type cells during cold conditions. In conclusion, this study provides a comprehensive analysis of IQD genes in apple, elucidating their molecular mechanism in response to cold stress.

Identification and Characterization of Shaker Potassium Channel Gene Family and Response to Salt and Chilling Stress in Rice.

Shaker potassium channel proteins are a class of voltage-gated ion channels responsible for K+ uptake and translocation, playing a crucial role in plant growth and salt tolerance. In this study, bioinformatic analysis was performed to identify the members within the Shaker gene family. Moreover, the expression patterns of rice Shaker(OsShaker) K+ channel genes were analyzed in different tissues and salt treatment by RT-qPCR. The results revealed that there were eight OsShaker K+ channel genes distributed on chromosomes 1, 2, 5, 6 and 7 in rice, and their promoters contained a variety of cis-regulatory elements, including hormone-responsive, light-responsive, and stress-responsive elements, etc. Most of the OsShaker K+ channel genes were expressed in all tissues of rice, but at different levels in different tissues. In addition, the expression of OsShaker K+ channel genes differed in the timing, organization and intensity of response to salt and chilling stress. In conclusion, our findings provide a reference for the understanding of OsShaker K+ channel genes, as well as their potential functions in response to salt and chilling stress in rice.

Genome-Wide Analysis of the Nramp Gene Family in Kenaf (Hibiscus cannabinus): Identification, Expression Analysis, and Response to Cadmium Stress.

Kenaf (Hibiscus cannabinu) is a grass bast fiber crop that has the ability to tolerate and accumulate heavy metals, and it has been considered as a potential heavy metal accumulator and remediation plant. Nramp is a natural resistance-related macrophage, which plays an important role in the transport of divalent metal ions, plant growth and development, and abiotic stress. In this study, the Nramp gene family of kenaf was analyzed at the whole genome level. A total of 15 HcNramp genes were identified. They are distributed unevenly on chromosomes. Phylogenetic analysis classified 15 HcNramp proteins into 3 different subfamilies. All proteins share specific motif 4 and motif 6, and the genes belonging to the same subfamily are similar in structure and motif. The promoters are rich in hormone response, meristem expression, and environmental stress response elements. Under different treatments, the expression levels of HcNramp genes vary in different tissues, and most of them are expressed in roots first. These findings can provide a basis for understanding the potential role of the Nramp gene family in kenaf in response to cadmium (Cd) stress, and are of great significance for screening related Cd tolerance genes in kenaf.