Overexpression of ZmWRKY65 transcription factor from maize confers stress resistances in transgenic Arabidopsis

Strigolactones alleviate AlCl3 stress by vacuolar compartmentalization and cell wall blocking in apple

Poor management and excess fertilization of apple (Malus domestica Borkh.) orchards are causing increasingly serious soil acidification, resulting in Al toxicity and direct poisoning of roots. Strigolactones (SLs) are reported to be involved in plant responses to abiotic stress, but their role and mechanism under AlCl3 stress remain unknown. Here, we found that applying 1 μm GR24 (an SL analoge) significantly alleviated AlCl3 stress of M26 apple rootstock, mainly by blocking the movement of Al through cell wall and by vacuolar compartmentalization of Al. RNA-seq analysis identified the core transcription factor gene MdWRKY53, and overexpressing MdWRKY53 enhanced AlCl3 tolerance in transgenic apple plants through the same mechanism as GR24. Subsequently, we identified MdPMEI45 (encoding pectin methylesterase inhibitor) and MdALS3 (encoding an Al transporter) as downstream target genes of MdWRKY53 using chromatin immunoprecipitation followed by sequencing (ChIP-seq). GR24 enhanced the interaction between MdWRKY53 and the transcription factor MdTCP15, further increasing the binding of MdWRKY53 to the MdPMEI45 promoter and inducing MdPMEI45 expression to prevent Al from crossing cell wall. MdWRKY53 also bound to the promoter of MdALS3 and enhanced its transcription to compartmentalize Al in vacuoles under AlCl3 stress. We therefore identified two modules involved in alleviating AlCl3 stress in woody plant apple: the SL-WRKY+TCP-PMEI module required for excluding external Al by blocking the entry of Al3+ into cells and the SL-WRKY-ALS module allowing internal detoxification of Al through vacuolar compartmentalization. These findings lay a foundation for the practical application of SLs in agriculture.

Genome-Wide Identification of WRKY Transcription Factor Family in Chinese Rose and Response to Drought, Heat, and Salt Stress

The WRKY gene family is a key transcription factor family for plant development and the stress response. However, few studies have investigated the WRKY gene family in Chinese rose (Rosa chinensis). In this study, 68 RcWRKY genes were identified from the Chinese rose genome and classified into three primary groups and five subgroups based on the structural and phylogenetic characteristics. The analysis of the conserved domains, motifs, and gene structure revealed that the RcWRKY genes within the same group had the same exon-intron organization and composition. Chromosome mapping and gene duplication revealed that the RcWRKY genes were randomly dispersed across seven chromosomes. Fragment duplication and refined selection may have influenced the evolution of the WRKY gene family in Chinese rose. The cis-acting elements in the WRKY promoter region revealed that the RcWRKY genes contained numerous abiotic stress response elements. The results of qRT-PCR revealed that the expression of RcWRKY was tissue-specific, with high expression being observed under drought, heat, and salt stress. Notably, RcWRKY49's expression increased more than fivefold following salt stress, indicating that it is a crucial gene mediating the salt stress response of Chinese rose. These findings shed light on the regulatory role of RcWRKY in the growth and development of Chinese rose, and they serve as a foundation for future molecular breeding programs and gene discovery.

Deciphering the Interaction between Coniella granati and Pomegranate Fruit Employing Transcriptomics

Pomegranate fruit dry rot is caused by Coniella granati, also referred as Pilidiella granati. In order to decipher the induced responses of mature pomegranates inoculated with the pathogen, an RNA-seq analysis was employed. A high number of differentially expressed genes (DEGs) were observed through a three-time series inoculation period. The transcriptional reprogramming was time-dependent, whereas the majority of DEGs were suppressed and the expression patterns of specific genes may facilitate the pathogen colonization at 1 day after inoculation (dai). In contrast, at 2 dai and mainly thereafter at 3 dai, defense responses were partially triggered in delay. Particularly, DEGs were mainly upregulated at the latest time point. Among them, specific DEGs involved in cell wall modification and degradation processes, pathogen recognition and signaling transduction cascades, activation of specific defense and metabolite biosynthesis-related genes, as well in induction of particular families of transcriptional factors, may constitute crucial components of a defense recruiting strategy employed by pomegranate fruit upon C. granati challenge. Overall, our findings provide novel insights to the compatible interaction of pomegranates-C. granati and lay the foundations for establishing integrated pest management (IPM) strategies involving advanced approaches, such as gene editing or molecular breeding programs for disease resistance, according to European Union (EU) goals.

Genome-wide identification of ZmMYC2 binding sites and target genes in maize

BACKGROUND

Jasmonate (JA) is the important phytohormone to regulate plant growth and adaption to stress signals. MYC2, an bHLH transcription factor, is the master regulator of JA signaling. Although MYC2 in maize has been identified, its function remains to be clarified.

RESULTS

To understand the function and regulatory mechanism of MYC2 in maize, the joint analysis of DAP-seq and RNA-seq is conducted to identify the binding sites and target genes of ZmMYC2. A total of 3183 genes are detected both in DAP-seq and RNA-seq data, potentially as the directly regulating genes of ZmMYC2. These genes are involved in various biological processes including plant growth and stress response. Besides the classic cis-elements like the G-box and E-box that are bound by MYC2, some new motifs are also revealed to be recognized by ZmMYC2, such as nGCATGCAnn, AAAAAAAA, CACGTGCGTGCG. The binding sites of many ZmMYC2 regulating genes are identified by IGV-sRNA.

CONCLUSIONS

All together, abundant target genes of ZmMYC2 are characterized with their binding sites, providing the basis to construct the regulatory network of ZmMYC2 and better understanding for JA signaling in maize.

Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated with pear petal defense responses against Monilinia laxa infection

Pear brown rot and blossom blight caused by Monilinia laxa seriously affect pear production worldwide. Here, we compared the transcriptomic profiles of petals after inoculation with M. laxa using two pear cultivars with different levels of sensitivity to disease (Sissy, a relatively tolerant cultivar, and Kristalli, a highly susceptible cultivar). Physiological indexes were also monitored in the petals of both cultivars at 2 h and 48 h after infection (2 HAI and 48 HAI). RNA-seq data and weighted gene co-expression network analysis (WGCNA) allowed the identification of key genes and pathways involved in immune- and defense-related responses that were specific for each cultivar in a time-dependent manner. In particular, in the Kristalli cultivar, a significant transcriptome reprogramming occurred early at 2 HAI and was accompanied either by suppression of key differentially expressed genes (DEGs) involved in the modulation of any defense responses or by activation of DEGs acting as sensitivity factors promoting susceptibility. In contrast to the considerably high number of DEGs induced early in the Kristalli cultivar, upregulation of specific DEGs involved in pathogen perception and signal transduction, biosynthesis of secondary and primary metabolism, and other defense-related responses was delayed in the Sissy cultivar, occurring at 48 HAI. The WGCNA highlighted one module that was significantly and highly correlated to the relatively tolerant cultivar. Six hub genes were identified within this module, including three WRKY transcription factor-encoding genes: WRKY 65 (pycom05g27470), WRKY 71 (pycom10g22220), and WRKY28 (pycom17g13130), which may play a crucial role in enhancing the tolerance of pear petals to M. laxa. Our results will provide insights into the interplay of the molecular mechanisms underlying immune responses of petals at the pear-M. laxa pathosystem.

Comprehensive transcriptome analyses of Fusarium-infected root xylem tissues to decipher genes involved in chickpea wilt resistance

Fusarium wilt is the most destructive soil-borne disease that poses a major threat to chickpea production. To comprehensively understand the interaction between chickpea and Fusarium oxysporum, the xylem-specific transcriptome analysis of wilt-resistant (WR315) and wilt-susceptible (JG62) genotypes at an early timepoint (4DPI) was investigated. Differential expression analysis showed that 1368 and 348 DEGs responded to pathogen infection in resistant and susceptible genotypes, respectively. Both genotypes showed transcriptional reprogramming in response to Foc2, but the responses in WR315 were more severe than in JG62. Results of the KEGG pathway analysis revealed that most of the DEGS in both genotypes with enrichment in metabolic pathways, secondary metabolite biosynthesis, plant hormone signal transduction, and carbon metabolism. Genes associated with defense-related metabolites synthesis such as thaumatin-like protein 1b, cysteine-rich receptor-like protein kinases, MLP-like proteins, polygalacturonase inhibitor 2-like, ethylene-responsive transcription factors, glycine-rich cell wall structural protein-like, beta-galactosidase-like, subtilisin-like protease, thioredoxin-like protein, chitin elicitor receptor kinase-like, proline transporter-like, non-specific lipid transfer protein and sugar transporter were mostly up-regulated in resistant as compared to susceptible genotypes. The results of this study provide disease resistance genes, which would be helpful in understanding the Foc resistance mechanism in chickpea.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03803-9.

Genome-wide identification and comprehensive analysis of WRKY transcription factor family in safflower during drought stress

The WRKY family is an important family of transcription factors in plant development and stress response. Currently, there are few reports on the WRKY gene family in safflower (Carthamus tinctorius L.). In this study, a total of 82 CtWRKY genes were identified from the safflower genome and could be classified into 3 major groups and 5 subgroups based on their structural and phylogenetic characteristics. The results of gene structure, conserved domain and motif analyses indicated that CtWRKYs within the same subfamily maintained a consistent exon/intron organization and composition. Chromosomal localization and gene duplication analysis results showed that CtWRKYs were randomly localized on 12 chromosomes and that fragment duplication and purification selection may have played an important role in the evolution of the WRKY gene family in safflower. Promoter cis-acting element analysis revealed that the CtWRKYs contain many abiotic stress response elements and hormone response elements. Transcriptome data and qRT-PCR analyses revealed that the expression of CtWRKYs showed tissue specificity and a strong response to drought stress. Notably, the expression level of the CtWRKY55 gene rapidly increased more than eightfold under drought treatment and rehydration, indicating that it may be a key gene in response to drought stress. These results provide useful insights for investigating the regulatory function of the CtWRKY gene in safflower growth and development, as well as identifying key genes for future molecular breeding programmes.

Maize Phytocytokines Modulate Pro-Survival Host Responses and Pathogen Resistance

Phytocytokines are signaling peptides that alert plant cells of danger. However, the downstream responses triggered by phytocytokines and their effect on plant survival are still largely unknown. Here, we have identified three biologically active maize orthologues of phytocytokines previously described in other plants. The maize phytocytokines show common features with microbe-associated molecular patterns (MAMPs), including the induction of immune-related genes and activation of papain-like cysteine proteases. In contrast to MAMPs, phytocytokines do not promote cell death in the presence of wounding. In infection assays with two fungal pathogens, we found that phytocytokines affect the development of disease symptoms, likely due to the activation of phytohormonal pathways. Collectively, our results show that phytocytokines and MAMPs trigger unique and antagonistic features of immunity. We propose a model in which phytocytokines activate immune responses partially similar to MAMPs but, in contrast to microbial signals, they act as danger and survival molecules to the surrounding cells. Future studies will focus on the components determining the divergence of signaling outputs upon phytocytokine activation. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Linking plant functional genes to rhizosphere microbes: a review

The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.

Cellobiose elicits immunity in lettuce conferring resistance to Botrytis cinerea

Cellobiose is the primary product of cellulose hydrolysis and is expected to function as a type of pathogen/damage-associated molecular pattern in evoking plant innate immunity. In this study, cellobiose was demonstrated to be a positive regulator in the immune response of lettuce, but halted autoimmunity when lettuce was exposed to concentrations of cellobiose >60 mg l-1. When lettuce plants were infected by Botrytis cinerea, cellobiose endowed plants with enhanced pre-invasion resistance by activating high β-1,3-glucanase and antioxidative enzyme activities at the initial stage of pathogen infection. Cellobiose-activated core regulatory factors such as EDS1, PTI6, and WRKY70, as well as salicylic acid signaling, played an indispensable role in modulating plant growth-defense trade-offs. Transcriptomics data further suggested that the cellobiose-activated plant-pathogen pathways are involved in microbe/pathogen-associated molecular pattern-triggered immune responses. Genes encoding receptor-like kinases, transcription factors, and redox homeostasis, phytohormone signal transduction, and pathogenesis-related proteins were also up- or down-regulated by cellobiose. Taken together, the findings of this study demonstrated that cellobiose serves as an elicitor to directly activate disease-resistance-related cellular functions. In addition, multiple genes have been identified as potential modulators of the cellobiose-induced immune response, which could aid understanding of underlying molecular events.

RNA-seq study reveals the signaling and carbohydrate metabolism regulators involved in dormancy release by warm stratification in Paris polyphylla var. yunnanensis

Long-term seed dormancy of Paris polyphylla var. yunnanensis limits its large-scale artificial cultivation. It is crucial to understand the regulatory genes involving in dormancy release for artificial cultivation in this species. In this study, seed dormancy of Paris polyphylla var. yunnanensis was effectively released by warm stratification (20°C) for 90 days. The freshly harvested seeds (dormant) and stratified seeds (non-dormant) were used to sequence, and approximately 147 million clean reads and 28,083 annotated unigenes were detected. In which, a total of 10,937 differentially expressed genes (DEGs) were identified between dormant and non-dormant seeds. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) classification revealed that the majority unigenes involved in signaling transduction and carbohydrate metabolism. Of them, the signaling transduction-related DEGs were mainly hormones-, reactive oxygen species (ROS)-, and transcription factor (TF)-related genes. The largest number of signaling transduction-related DEGs were auxin-responsive genes (SAUR, AUX/IAA, and ARF) and AP2-like ethylene-responsive transcription factor (ERF/AP2). Moreover, at least 29 DEGs such as α-amylase (AMY), β-glucosidase (Bglb/Bglu/Bglx), and endoglucanase (Glu) were identified involving in carbohydrate metabolism. These identified genes provide a valuable resource to investigate the molecular basis of dormancy release in Paris polyphylla var. yunnanensis.

Occurrence of simple sequence repeats in cDNA sequences of safflower (Carthamus tinctorius) reveals the importance of SSR-containing genes for cell biology and dynamic response to environmental cues

Safflower (Carthamus tinctorius) is a diploid crop plant belonging to the family Asteraceae and is well known as one of important oilseed crops due to edible oil containing unsaturated fatty acids. In recent years it is gaining increased attention for food, pharmaceutical and industrial uses, and hence the updating its breeding methods is necessary. Genic simple sequence repeats (SSRs) in addition of being desire molecular markers, are supposed to influence gene function and the respective phenotype. This study aimed to identify SSRs in cDNA sequences and further analysis of the functional features of the SSR-containing genes to elucidate their role in biological and cellular processes. We identified 1,841 SSR regions in 1,667 cDNA sequences. Among all types of repeats, trinucleotide repeats were the most abundant (35.7%), followed by hexanucleotide (29.6%) and dinucleotide repeats (22.0%). Thirty five SSR primer pairs were validated by PCR reaction, detected a high rate of polymorphism (>57%) among safflower accessions, physically mapped on safflower genome and could clearly discriminate the cultivated accessions from wild relatives. The cDNA-derived SSR markers are suitable for evaluation of genetic diversity, linkage and association mapping studies and genome-based breeding programmes. Occurrence of SSR repeats in biologically-important classes of proteins such as kinases, transferases and transcription factors was inferred from functional analyses, which along with variability of their repeat copies, can endow the cell and whole organism the flexibility of facing with continuously changing environment, and indicate a structure-based evolution mechanism of the genome which acts as an up-to-dating tool for the cell and whole origanism, which is realized in GO terms such as involvement of most SSR-containing genes in biological, cellular and metabolic processes, especially in response to stimulus, response to stress, interaction to other organisms and defense responses.

Multiomic Data Integration in the Analysis of Drought-Responsive Mechanisms in Quercus ilex Seedlings

The integrated analysis of different omic layers can provide new knowledge not provided by their individual analysis. This approach is also necessary to validate data and reveal post-transcriptional and post-translational mechanisms of gene expression regulation. In this work, we validated the possibility of applying this approach to non-model species such as Quercus ilex. Transcriptomics, proteomics, and metabolomics from Q. ilex seedlings subjected to drought-like conditions under the typical summer conditions in southern Spain were integrated using a non-targeted approach. Two integrative approaches, PCA and DIABLO, were used and compared. Both approaches seek to reduce dimensionality, preserving the maximum information. DIABLO also allows one to infer interconnections between the different omic layers. For easy visualization and analysis, these interconnections were analyzed using functional and statistical networks. We were able to validate results obtained by analyzing the omic layers separately. We identified the importance of protein homeostasis with numerous protease and chaperones in the networks. We also discovered new key processes, such as transcriptional control, and identified the key function of transcription factors, such as DREB2A, WRKY65, and CONSTANS, in the early response to drought.

Overexpression of ZmSRG7 Improves Drought and Salt Tolerance in Maize (Zea mays L.)

Osmotic stress caused by drought and high salinity is the key factor limiting plant growth. However, its underlying molecular regulatory mechanism remains unclear. In this study, we found the stress-related gene Zm00001d019704 (ZmSRG7) based on transcriptome sequencing results previously obtained in the laboratory and determined its biological function in maize. We found that ZmSRG7 was significantly expressed in both roots and leaves under 10% PEG6000 or 150 mM NaCl. Subcellular localization showed that the gene was localized in the nucleus. The germination rate and root length of the ZmSRG7 overexpressing lines were significantly increased under drought or salt stress compared with the control. However, after drought stress, the survival rate and relative water content of maize were increased, while the water loss rate was slowed down. Under salt stress, the Na⁺ concentration and Na⁺: K⁺ ratio of maize was increased. In addition, the contents of antioxidant enzymes and proline in maize under drought or salt stress were higher than those in the control, while the contents of MDA, H₂O₂ and O₂⁻ were lower than those in the control. The results showed that the ZmSRG7 gene played its biological function by regulating the ROS signaling pathway. An interaction between ZmSRG7 and the Zmdhn1 protein was found using a yeast two-hybrid experiment. These results suggest that the ZmSRG7 gene can improve maize tolerance to drought or salt by regulating hydrogen peroxide homeostasis.

Genome-wide identification and analysis of WRKY gene family in maize provide insights into regulatory network in response to abiotic stresses

BACKGROUND

The WRKY transcription factor family plays significant roles in biotic and abiotic stress responses, which has been associated with various biological processes in higher plants. However, very little is known regarding the structure and function of WRKY genes in maize.

RESULTS

In this study, a total of 140 ZmWRKY proteins encoded by 125 ZmWRKY genes were eventually identified in maize. On the basis of features of molecular structure and a comparison of phylogenetic relationships of WRKY transcription factor families from Arabidopsis, rice and maize, all 140 ZmWRKY proteins in maize were divided into three main groups (Groups I, II and III) and the Group II was further classified into five subgroups. The characteristics of exon-intron structure of these putative ZmWRKY genes and conserved protein motifs of their encoded ZmWRKY proteins were also presented respectively, which was in accordance with the group classification results. Promoter analysis suggested that ZmWRKY genes shared many abiotic stress-related elements and hormone-related elements. Gene duplication analysis revealed that the segmental duplication and purifying selection might play a significant role during the evolution of the WRKY gene family in maize. Using RNA-seq data, transcriptome analysis indicated that most of ZmWRKY genes displayed differential expression patterns at different developmental stages of maize. Further, by quantitative real-time PCR analysis, twenty-one ZmWRKY genes were confirmed to respond to two different abiotic stress treatments, suggesting their potential roles in various abiotic stress responses. In addition, RNA-seq dataset was used to conduct weighted gene co-expression network analysis (WGCNA) in order to recognize gene subsets possessing similar expression patterns and highly correlated with each other within different metabolic networks. Further, subcellular localization prediction, functional annotation and interaction analysis of ZmWRKY proteins were also performed to predict their interactions and associations involved in potential regulatory network.

CONCLUSIONS

Taken together, the present study will serve to present an important theoretical basis for further exploring function and regulatory mechanism of ZmWRKY genes in the growth, development, and adaptation to abiotic stresses in maize.