Genome-Wide Analysis of WRKY Gene Family and the Dynamic Responses of Key WRKY Genes Involved in Ostrinia furnacalis Attack in Zea mays

Functional characterisation of WRKY transcription factor CrWRKY48 involved in regulating seed abortion of Ponkan (Citrus reticulata)

Citrus fruits are one of the most important fruits in the world, and their seedless character is favored by consumers. WRKY is a plant-specific transcription factor family involved in all aspects of plant growth and development. However, the molecular mechanism of seedless fruit formation in citrus and the role of the WRKY gene family in seed abortion are still poorly understood. In this study, we identified 47 WRKY family genes in the citrus fruit Citrus reticulata and comprehensively characterized the WRKY gene family through gene structure and evolutionary relationships. The expression patterns and protein interaction networks of the WRKY gene family were analyzed based on citrus seed abortion transcriptome data, and several WRKY genes that may be involved in the seed abortion regulation were excavated. Furthermore, CrWRKY48 was verified to regulate seed abortion positively in Arabidopsis thaliana, and the rate of seed abortion caused by overexpression of CrWRKY48 reached 45.48%. Using terminal deoxynucleotidyl transferase-mediated dUTP nick-end labelling assays, DNA affinity purification sequencing and yeast-one-hybrid assays, we found that CrWRKY48 activated excessive programmed cell death by regulating the expression of programmed cell death-related genes such as SOBIR1. Our results show the potential regulation of the WRKY gene family for citrus seed abortion and provide novel insights into the role of CrWRKY48 in mediating citrus seed abortion by activating programmed cell death.

Identification of WRKY transcription factors in Ipomoea pes-caprae and functional role of IpWRKY16 in sweet potato salt stress response

BACKGROUND

WRKY transcription factors are plant-specific and play essential roles in growth, development, and stress responses, including reactions to salt, drought, and cold. Despite their significance, the WRKY genes in the wild sweet potato ancestor, Ipomoea pes-caprae, remain unexplored.

RESULTS

In this study, 65 WRKY genes were identified in the I. pes-caprae transcriptomic data. A phylogenetic tree incorporating Arabidopsis thaliana and Ipomoea batatas revealed seven major groups, each characterized by conserved gene structural features. Transcriptome data of I. pes-caprae under salt stress conditions identified 17 highly expressed WRKY genes, whose promoter regions contain cis-acting elements associated with plant growth, stress responses, and hormone signaling. Further analysis revealed that the 17 IpWRKY genes exhibited differential expression patterns under various abiotic stresses, suggesting their potential roles in specific stress responses. The gene IpWRKY16 was significantly up-expressed under salt stress, drought, salicylic acid (SA), and abscisic acid (ABA) treatments. Subcellular localization analysis confirmed that IpWRKY16 is located in the nucleus. Under salt stress, IpWRKY16 overexpressing roots showed high activity in superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and low content in malondialdehyde (MDA). Using non-invasive micro-test technology (NMT), a significant efflux of Na+ was observed in the elongation zones of sweet potato adventitious roots that overexpressed IpWRKY16. Quantitative reverse transcription PCR (qRT-PCR) revealed that several ion transporter genes were responsive to IpWRKY16 expression, with IbSOS3, IbAHA4-1, and IbAHA4-2 showing the highest expression levels. We hypothesize that IpWRKY16 responds to salt stress by forming a complex regulatory network involving these key genes.

CONCLUSIONS

This study provides a foundational understanding of WRKY transcription factors in I. pes-caprae, offering insights into their potential role in enhancing salt-tolerance in sweet potato. Our findings contribute valuable genetic knowledge that could aid in the molecular breeding of stress-resilient sweet potato varieties.

A CsWRKY48 Gene from Tea Plants Intercropped with Chinese Chestnut Plays an Important Role in Resistance to Biotic and Abiotic Stresses

Tea plant (Camellia sinensis) is an important horticultural crop. The quality and productivity of tea plants is always threatened by various adverse environmental factors. Numerous studies have shown that intercropping tea plants with other plants can greatly improve the quality of their products. The intercropping system of Chinese chestnut (Castanea mollissima) and tea plants is an agricultural planting model in which the two species are grown on the same piece of land following a specific spacing and cultivation method. Based on a comparative transcriptome analysis between Chinese chestnut tea intercropped plantations and a pure tea plantation, it was found that the expression levels of the WRKY genes were significantly upregulated under the intercropping pattern. In this study, we cloned a candidate gene, CsWRKY48, and verified its functions in tobacco (Nicotiana tabacum) via heterologous transformation. The contents of protective enzyme activities and osmoregulatory substances were significantly increased, and the trichomes length and density were improved in the transgenic tobacco lines. This phenotype offered an enhanced resistance to both low temperatures and aphids for transgenic lines overexpressing CsWRKY48. Further analysis indicated that the CsWRKY48 transcription factor might interact with other regulators, such as CBF, ERF, MYC, and MYB, to enhance the resistance of tea plants to biotic and abiotic stresses. These findings not only confirm the elevated resistance of tea plants under intercropping, but also indicate a potential regulatory network mediated by the WRKY transcription factor.

Genome-Wide Identification of the Maize Chitinase Gene Family and Analysis of Its Response to Biotic and Abiotic Stresses

BACKGROUND/OBJECTIVES

Chitinases, enzymes belonging to the glycoside hydrolase family, play a crucial role in plant growth and stress response by hydrolyzing chitin, a natural polymer found in fungal cell walls. This study aimed to identify and analyze the maize chitinase gene family, assessing their response to various biotic and abiotic stresses to understand their potential role in plant defense mechanisms and stress tolerance.

METHODS

We employed bioinformatics tools to identify 43 chitinase genes in the maize B73_V5 genome. These genes were characterized for their chromosomal positions, gene and protein structures, phylogenetic relationships, functional enrichment, and collinearity. Based on previous RNA-seq data, the analysis assessed the expression patterns of these genes at different developmental stages and under multiple stress conditions.

RESULTS

The identified chitinase genes were unevenly distributed across maize chromosomes with a history of tandem duplications contributing to their divergence. The ZmChi protein family was predominantly hydrophilic and localized mainly in chloroplasts. Expression analysis revealed that certain chitinase genes were highly expressed at specific developmental stages and in response to various stresses, with ZmChi31 showing significant responsiveness to 11 different abiotic and biotic stresses.

CONCLUSIONS

This study provides new insights into the role of chitinase genes in maize stress response, establishing a theoretical framework for exploring the molecular basis of maize stress tolerance. The identification of stress-responsive chitinase genes, particularly ZmChi31, offers potential candidates for further study in enhancing maize resistance to environmental challenges.

Genome-wide analysis of WRKY gene family and the dynamic responses of key WRKY genes involved in cadmium stress in Brassica juncea

The WRKY transcription factors comprise one of the most extensive gene families and serve as pivotal regulators of plant responses to heavy metal stress. They contribute significantly to maintaining plant growth and development by enhancing plant tolerance. However, research on the role of WRKY genes in response to cadmium (Cd) stress in mustard is minimal. In this study, we conducted a genome-wide analysis of the mustard WRKY gene family using bioinformatics. The results revealed that 291 WRKY putative genes (BjuWRKYs) were identified in the mustard genome. These genes were categorized into seven subgroups (I, IIa-e and III) through phylogenetic analysis, with differences in motif composition between each subgroup. Homology analysis indicated that 31.62% of the genes originated from tandem duplication events. Promoter analysis revealed an abundance of abiotic stress-related elements and hormone-related elements within the BjuWRKY genes. Transcriptome analysis demonstrated that most BjuWRKY genes exhibited differential expression patterns at different Cd treatment stages in mustard. Furthermore, 10 BjuWRKY genes were confirmed to respond to Cd stress through the construction of a BjuWRKY protein interaction network, prediction of hub genes, and real-time fluorescence quantitative PCR analysis, indicating their potential involvement in Cd stress. Our findings provide a comprehensive insight into the WRKY gene family in mustard and establish a foundation for further studies of the functional roles of BjuWRKY genes in Cd stress response.

Genome-scale identification, expression and evolution analysis of B-box members in Dendrobium huoshanense

B-box (BBX) proteins have been recognized as vital determinants in plant development, morphogenesis, and adaptive responses to a myriad of environmental stresses. These zinc-finger proteins play a pivotal role in various biological processes. Their influence spans photomorphogenesis, the regulation of flowering, and imparting resilience to a wide array of challenges, encompassing both biotic and abiotic factors. Chromosome localization, gene structure and conserved motifs, phylogenetic analysis, collinearity analysis, expression profiling, fluorescence quantitative analysis, and tobacco transient transformation methods were used for functional localization and expression pattern analysis of the DhBBX gene. A total of 23 DhBBX members were identified from Dendrobium huoshanense. Subsequent phylogenetic evaluations effectively segregated these genes into five discrete evolutionary subsets. The predictions of subcellular localizations revealed that all these proteins were localized in the nucleus. The genetic composition and patterns showed that the majority of these genes consisted of several exons, with a few variations that could be attributed to transposon insertion. A comprehensive analysis using qRT-PCR was conducted to unravel the expression patterns of these genes in D. huoshanense, with a specific concentration on their responses to various hormone treatments and cold stress. Subcellular localization reveals that DhBBX21 and DhBBX9 are located in the nucleus. Our results provide a deep comprehension of the complex regulatory mechanisms of BBXs in response to various environmental and hormonal stimuli. These discoveries encourage further detailed and focused investigations into the operational dynamics of the BBX gene family in a wider range of plant species.

The WRKY gene family in the halophyte Limonium bicolor: identification, expression analysis, and regulation of salt stress tolerance

KEY MESSAGE

63 L. bicolor WRKY genes were identified and their informatics was analyzed. The results suggested that the LbWRKY genes involved in the development and salt secretion of salt glands in L. bicolor. Salt stress, as a universal abiotic stress, severely inhibits the growth and development of plants. WRKY transcription factors play a vital role in plant growth and development, as well as in response to various stresses. Nevertheless, little is known of systematic genome-wide analysis of the WRKY genes in Limonium bicolor, a model recretohalophyte. In this study, 63 L. bicolor WRKY genes were identified (LbWRKY1-63), which were unevenly distributed across seven chromosomes and one scaffold. Based on the structural and phylogenetic characteristics, 63 LbWRKYs are divided into three main groups. Cis-elements in the LbWRKY promoters were related to growth and development, phytohormone responses, and stress responses. Colinearity analysis showed strong colinearity between LbWRKYs and GmWRKYs from soybean (Glycine max). Therefore, LbWRKY genes maybe have similar functions to GmWRKY genes. Expression analysis showed that 28 LbWRKY genes are highly expressed in roots, 9 in stems, 26 in leaves, and 12 in flowers and most LbWRKY genes responded to NaCl, ABA, and PEG6000. Silencing LbWRKY10 reduced salt gland density and salt secretion ability of leaves, and the salt tolerance of the species. Consistent with this, genes associated with salt gland development were markedly down-regulated in the LbWRKY10-silenced lines. Our findings suggested that the LbWRKY genes involved in the development and salt secretion of salt glands in L. bicolor. Our research provides new insights into the functions of the WRKY family in halophytes.

Pepper immunity against Ralstonia solanacearum is positively regulated by CaWRKY3 through modulation of different WRKY transcription factors

BACKGROUND

Several WRKY transcription factors (TFs), including CaWRKY6, CaWRKY22, CaWRKY27, and CaWRKY40 are known to govern the resistance of pepper (Capsicum annuum L.) plants to Ralstonia solanacearum infestation (RSI) and other abiotic stresses. However, the molecular mechanisms underlying these processes remain elusive.

METHODS

This study functionally described CaWRKY3 for its role in pepper immunity against RSI. The roles of phytohormones in mediating the expression levels of CaWRKY3 were investigated by subjecting pepper plants to 1 mM salicylic acid (SA), 100 µM methyl jasmonate (MeJA), and 100 µM ethylene (ETH) at 4-leaf stage. A virus-induced gene silencing (VIGS) approach based on the Tobacco Rattle Virus (TRV) was used to silence CaWRKY3 in pepper, and transiently over-expressed to infer its role against RSI.

RESULTS

Phytohormones and RSI increased CaWRKY3 transcription. The transcriptions of defense-associated marker genes, including CaNPR1, CaPR1, CaDEF1, and CaHIR1 were decreased in VIGS experiment, which made pepper less resistant to RSI. Significant hypersensitive (HR)-like cell death, H2O2 buildup, and transcriptional up-regulation of immunological marker genes were noticed in pepper when CaWRKY3 was transiently overexpressed. Transcriptional activity of CaWRKY3 was increased with overexpression of CaWRKY6, CaWRKY22, CaWRKY27, and CaWRKY40, and vice versa. In contrast, Pseudomonas syringae pv tomato DC3000 (Pst DC3000) was easily repelled by the innate immune system of transgenic Arabidopsis thaliana that overexpressed CaWRKY3. The transcriptions of defense-related marker genes like AtPR1, AtPR2, and AtNPR1 were increased in CaWRKY3-overexpressing transgenic A. thaliana plants.

CONCLUSION

It is concluded that CaWRKY3 favorably regulates phytohormone-mediated synergistic signaling, which controls cell death in plant and immunity of pepper plant against bacterial infections.

Nanoparticles as a Tool for Alleviating Plant Stress: Mechanisms, Implications, and Challenges

Plants, being sessile, are continuously exposed to varietal environmental stressors, which consequently induce various bio-physiological changes in plants that hinder their growth and development. Oxidative stress is one of the undesirable consequences in plants triggered due to imbalance in their antioxidant defense system. Biochemical studies suggest that nanoparticles are known to affect the antioxidant system, photosynthesis, and DNA expression in plants. In addition, they are known to boost the capacity of antioxidant systems, thereby contributing to the tolerance of plants to oxidative stress. This review study attempts to present the overview of the role of nanoparticles in plant growth and development, especially emphasizing their role as antioxidants. Furthermore, the review delves into the intricate connections between nanoparticles and plant signaling pathways, highlighting their influence on gene expression and stress-responsive mechanisms. Finally, the implications of nanoparticle-assisted antioxidant strategies in sustainable agriculture, considering their potential to enhance crop yield, stress tolerance, and overall plant resilience, are discussed.

Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation

Stem cells in plant shoots are a rare population of cells that produce leaves, fruits and seeds, vital sources for food and bioethanol. Uncovering regulators expressed in these stem cells will inform crop engineering to boost productivity. Single-cell analysis is a powerful tool for identifying regulators expressed in specific groups of cells. However, accessing plant shoot stem cells is challenging. Recent single-cell analyses of plant shoots have not captured these cells, and failed to detect stem cell regulators like CLAVATA3 and WUSCHEL . In this study, we finely dissected stem cell-enriched shoot tissues from both maize and arabidopsis for single-cell RNA-seq profiling. We optimized protocols to efficiently recover thousands of CLAVATA3 and WUSCHEL expressed cells. A cross-species comparison identified conserved stem cell regulators between maize and arabidopsis. We also performed single-cell RNA-seq on maize stem cell overproliferation mutants to find additional candidate regulators. Expression of candidate stem cell genes was validated using spatial transcriptomics, and we functionally confirmed roles in shoot development. These candidates include a family of ribosome-associated RNA-binding proteins, and two families of sugar kinase genes related to hypoxia signaling and cytokinin hormone homeostasis. These large-scale single-cell profiling of stem cells provide a resource for mining stem cell regulators, which show significant association with yield traits. Overall, our discoveries advance the understanding of shoot development and open avenues for manipulating diverse crops to enhance food and energy security.

The Multifaceted Role of Jasmonic Acid in Plant Stress Mitigation: An Overview

Plants, being sessile, have developed complex signaling and response mechanisms to cope with biotic and abiotic stressors. Recent investigations have revealed the significant contribution of phytohormones in enabling plants to endure unfavorable conditions. Among these phytohormones, jasmonic acid (JA) and its derivatives, collectively referred to as jasmonates (JAs), are of particular importance and are involved in diverse signal transduction pathways to regulate various physiological and molecular processes in plants, thus protecting plants from the lethal impacts of abiotic and biotic stressors. Jasmonic acid has emerged as a central player in plant defense against biotic stress and in alleviating multiple abiotic stressors in plants, such as drought, salinity, vernalization, and heavy metal exposure. Furthermore, as a growth regulator, JA operates in conjunction with other phytohormones through a complex signaling cascade to balance plant growth and development against stresses. Although studies have reported the intricate nature of JA as a biomolecular entity for the mitigation of abiotic stressors, their underlying mechanism and biosynthetic pathways remain poorly understood. Therefore, this review offers an overview of recent progress made in understanding the biosynthesis of JA, elucidates the complexities of its signal transduction pathways, and emphasizes its pivotal role in mitigating abiotic and biotic stressors. Moreover, we also discuss current issues and future research directions for JAs in plant stress responses.

Genotypic variation in field-grown maize eliminates trade-offs between resistance, tolerance and growth in response to high pressure from the Asian corn borer

Insect herbivory challenges plant survival, and coordination of the interactions between growth, herbivore resistance/tolerance is a key problem faced by plants. Based on field experiments into resistance to the Asian corn borer (ACB, Ostrinia furnacalis), we selected 10 inbred maize lines, of which five were resistant and five were susceptible to ACB. We conducted ACB larval bioassays, analysed defensive chemicals, phytohormones, and relative gene expression using RNA-seq and qPCR as well as agronomic traits, and found resistant lines had weaker inducibility, but were more resistant after ACB attack than susceptible lines. Resistance was related to high levels of major benzoxazinoids, but was not related to induced levels of JA or JA-Ile. Following combination analyses of transcriptome, metabolome and larval performance data, we discovered three benzoxazinoids biosynthesis-related transcription factors, NAC60, WRKY1 and WRKY46. Protoplast transformation analysis suggested that these may regulate maize defence-growth trade-offs by increasing levels of benzoxazinoids, JA and SA but decreasing IAA. Moreover, the resistance/tolerance-growth trade-offs were not observed in the 10 lines, and genotype-specific metabolic and genetic features probably eliminated the trade-offs. This study highlights the possibility of breeding maize varieties simultaneously with improved defences and higher yield under complex field conditions.

Metabolic and Molecular Rearrangements of Sauvignon Blanc (Vitis vinifera L.) Berries in Response to Foliar Applications of Specific Dry Yeast

Dry yeast extracts (DYE) are applied to vineyards to improve aromatic and secondary metabolic compound content and wine quality; however, systematic information on the underpinning molecular mechanisms is lacking. This work aimed to unravel, through a systematic approach, the metabolic and molecular responses of Sauvignon Blanc berries to DYE treatments. To accomplish this, DYE spraying was performed in a commercial vineyard for two consecutive years. Berries were sampled at several time points after the treatment, and grapes were analyzed for sugars, acidity, free and bound aroma precursors, amino acids, and targeted and untargeted RNA-Seq transcriptional profiles. The results obtained indicated that the DYE treatment did not interfere with the technological ripening parameters of sugars and acidity. Some aroma precursors, including cys-3MH and GSH-3MH, responsible for the typical aromatic nuances of Sauvignon Blanc, were stimulated by the treatment during both vintages. The levels of amino acids and the global RNA-seq transcriptional profiles indicated that DYE spraying upregulated ROS homeostatic and thermotolerance genes, as well as ethylene and jasmonic acid biosynthetic genes, and activated abiotic and biotic stress responses. Overall, the data suggested that the DYE reduced berry oxidative stress through the regulation of specific subsets of metabolic and hormonal pathways.

Wound-Induced Temporal Reprogramming of Gene Expression during Agarwood Formation in Aquilaria sinensis

Agarwood is a resinous heartwood of Aquilaria sinensis that is formed in response to mechanical wounding. However, the transcriptional response of A. sinensis to mechanical wounding during the agarwood formation process is still unclear. Here, three five-year-old A. sinensis trees were mechanically damaged by a chisel, and time-series transcriptomic analysis of xylem tissues in the treated area (TA) was performed at 15 (TA1), 70 (TA2) and 180 days after treatment (TA3). Samples from untreated areas at the corresponding time points (UA1, UA2, UA3, respectively) were collected as controls. A total of 1862 (TA1 vs. UA1), 961 (TA2 vs. UA2), 1370 (TA3 vs. UA3), 3305 (TA2 vs. TA1), 2625 (TA3 vs. TA1), 2899 (TA3 vs. TA2), 782 (UA2 vs. UA1), 4443 (UA3 vs. UA1) and 4031 (UA3 vs. UA2) genes were differentially expressed (DEGs). Functional enrichment analysis showed that DEGs were significantly enriched for secondary metabolic processes, signal transduction and transcriptional regulation processes. Most of the genes involved in lignin biosynthesis were more abundant in the TA groups, which included phenylalanine ammonia-lyase, 4-coumarate CoA ligase, cinnamate 4-hydroxylase, caffeoyl-CoA O-methyltransferase and cinnamoyl-CoA reductase. DEGs involved in sesquiterpene biosynthesis were also identified. Hydroxymethylglutaryl-CoA synthase, 3-hydroxy-3-methylglutaryl-coenzyme A reductase, phosphomevalonate kinase and terpene synthase genes were significantly increased in the TA groups, promoting sesquiterpene biosynthesis in the wounded xylem tissues. The TF-gene transcriptomic networks suggested that MYB DNA-binding, NAM, WRKY, HLH and AP2 TFs co-expressed with genes related to lignin and sesquiterpene synthesis, indicating their critical regulatory roles in the biosynthesis of these compounds. Overall, our study reveals a dynamic transcriptional response of A. sinensis to mechanical wounding, provides a resource for identifying candidate genes for molecular breeding of agarwood quality, and sheds light on the molecular mechanisms of agarwood formation in A. sinensis.

Genome-wide identification of candidate chemosensory receptors in the bean bug Riptortus pedestris (Hemiptera: Alydidae) and the functional verification of its odorant receptor co-receptor (Orco) in recognizing aggregation pheromone

A sophisticated and sensitive olfactory system plays a vital role in the survival and reproduction of insects. Chemosensory receptors are indispensable for the molecular recognition and discrimination of semiochemicals. Riptortus pedestris is a notorious pest of legume plants, resulting in yield losses and quality decreases in soybeans. It is well accepted that R. pedestris highly relies on its olfactory system in detecting aggregation pheromones, host volatiles, and pesticides; however, little research focused on its chemosensory receptors. In the present study, we identified 237 odorant receptors (ORs), 42 gustatory receptors (GRs), and 31 ionotropic receptors (IRs) from the reported genome of R. pedestris, and analyzed their phylogenetic relationship with other hemipteran species. Through the results of RNA-seq and real-time quantitative PCR (qRT-PCR), we found that RpedORs displayed different expression levels in the antennae of R. pedestris at different development stages. To further verify the function of odorant receptor co-receptor (Orco), an obligate and unique insect OR, we silenced RpedOrco by RNA interference (RNAi) method. The results showed that silencing RpedOrco could significantly impair the response to aggregation pheromone in R. pedestris, indicating that RpedOrco plays an essential role in odorant detection. Our results can provide the theoretical foundations for revealing the olfactory recognition mechanism of R. pedestris and help explore and develop novel olfactory-based agents against this pest.

Genome-Wide Identification and Expression Analysis of WRKY Gene Family in Neolamarckia cadamba

The WRKY transcription factor family plays important regulatory roles in multiple biological processes in higher plants. They have been identified and functionally characterized in a number of plant species, but very little is known in Neolamarckia cadamba, a 'miracle tree' for its fast growth and potential medicinal resource in Southeast Asia. In this study, a total of 85 WRKY genes were identified in the genome of N. cadamba. They were divided into three groups according to their phylogenetic features, with the support of the characteristics of gene structures and conserved motifs of protein. The NcWRKY genes were unevenly distributed on 22 chromosomes, and there were two pairs of segmentally duplicated events. In addition, a number of putative cis-elements were identified in the promoter regions, of which hormone- and stress-related elements were shared in many NcWRKYs. The transcript levels of NcWRKY were analyzed using the RNA-seq data, revealing distinct expression patterns in various tissues and at different stages of vascular development. Furthermore, 16 and 12 NcWRKY genes were confirmed to respond to various hormone treatments and two different abiotic stress treatments, respectively. Moreover, the content of cadambine, the active metabolite used for the various pharmacological activities found in N. cadamba, significantly increased after Methyl jasmonate treatment. In addition, expression of NcWRKY64/74 was obviously upregulated, suggesting that they may have a potential function of regulating the biosynthesis of cadambine in response to MeJA. Taken together, this study provides clues into the regulatory roles of the WRKY gene family in N. cadamba.

Comprehensive genomic analysis of the Rho GTPases regulators in seven Rosaceae species revealed that PbrGDI1 controls pollen tube growth in Pyrus via mediating cellulose deposition

The primary regulators of Rho GTPases are GTPase-activating protein (GAP), guanine nucleotide exchange factor (GEF), and GDP dissociation inhibitor (GDI), which function as signaling switches in several physiological processes involved in plant growth and development. This study compared how the Rho GTPase regulators functioned in seven Rosaceae species. Seven Rosaceae species, divided into three subgroups, had a total of 177 regulators of Rho GTPases. According to duplication analysis, the expansion of GEF, GAP, and GDI families was facilitated by whole genome duplication or a dispersed duplication event. The balance of cellulose deposition to control the growth of the pear pollen tube, as demonstrated by the expression profile and antisense oligonucleotide approach. Moreover, protein-protein interactions indicated that PbrGDI1 and PbrROP1 could directly interact, suggesting that PbrGDI1 regulated the growth of the pear pollen tube through PbrROP1 signaling downstream. These results lay the foundations for future functional characterization of the GAP, GEF, and GDI gene families in Pyrus bretschneideri.

In-depth analysis of large-scale screening of WRKY members based on genome-wide identification

With the rapid advancement of high-throughput sequencing technology, it is now possible to identify individual gene families from genomes on a large scale in order to study their functions. WRKY transcription factors are a key class of regulators that regulate plant growth and abiotic stresses. Here, a total of 74 WRKY genes were identified from Dendrobium officinale Kimura et Migo genome. Based on the genome-wide analysis, an in-depth analysis of gene structure and conserved motif was performed. The phylogenetic analysis indicated that DoWRKYs could be classified into three main groups: I, II, and III, with group II divided into five subgroups: II-a, II-b, II-c, II-d, and II-e. The sequence alignment indicated that these WRKY transcriptional factors contained a highly conserved WRKYGQK heptapeptide. The localization analysis of chromosomes showed that WRKY genes were irregularly distributed across several chromosomes of D. officinale. These genes comprised diverse patterns in both number and species, and there were certain distinguishing motifs among subfamilies. Moreover, the phylogenetic tree and chromosomal location results indicated that DoWRKYs may have undergone a widespread genome duplication event. Based on an evaluation of expression profiles, we proposed that DoWRKY5, 54, 57, 21, etc. may be involved in the transcriptional regulation of the JA signaling pathway. These results provide a scientific reference for the study of DoWRKY family genes.

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

WRKY transcription factors, as the largest gene family in higher plants, play an important role in various biological processes including growth and development, regulation of secondary metabolites, and stress response. In this study, we performed genome-wide identification and analysis of WRKY transcription factors in S. siamensis. A total of 59 SsWRKY genes were identified that were distributed on all 14 chromosomes, and these were classified into three major groups based on phylogenetic relationships. Each of these groups had similar conserved motifs and gene structures. We compared all the S. siamensis SsWRKY genes with WRKY genes identified from three diverse plant species, and the results implied that segmental duplication and tandem duplication play an important roles in the evolution processes of the WRKY gene family. Promoter region analysis revealed that SsWRKY genes included many cis-acting elements related to plant growth and development, phytohormone response, and both abiotic and biotic stress. Expression profiles originating from the transcriptome database showed expression patterns of these SsWRKY genes in four different tissues and revealed that most genes are expressed in plant roots. Fifteen SsWRKY genes with low-temperature response motifs were surveyed for their gene expression under cold stress, showing that most genes displayed continuous up-regulation during cold treatment. Our study provides a foundation for further study on the function and regulatory mechanism of the SsWRKY gene family.

Genome-Wide Analysis of the WRKY Gene Family in Malus domestica and the Role of MdWRKY70L in Response to Drought and Salt Stresses

The WRKY transcription factors are unique regulatory proteins in plants, which are important in the stress responses of plants. In this study, 113 WRKY genes were identified from the apple genome GDDH13 and a comprehensive analysis was performed, including chromosome mapping, and phylogenetic, motif and collinearity analysis. MdWRKYs are expressed in different tissues, such as seeds, flowers, stems and leaves. We analyzed seven WRKY proteins in different groups and found that all of them were localized in the nucleus. Among the 113 MdWRKYs, MdWRKY70L was induced by both drought and salt stresses. Overexpression of it in transgenic tobacco plants conferred enhanced stress tolerance to drought and salt. The malondialdehyde content and relative electrolyte leakage values were lower, while the chlorophyll content was higher in transgenic plants than in the wild-type under stressed conditions. In conclusion, this study identified the WRKY members in the apple genome GDDH13, and revealed the function of MdWRKY70L in the response to drought and salt stresses.

WRKY Gene Family Drives Dormancy Release in Onion Bulbs

Onion (Allium cepa L.) is an important bulb crop grown worldwide. Dormancy in bulbous plants is an important physiological state mainly regulated by a complex gene network that determines a stop of vegetative growth during unfavorable seasons. Limited knowledge on the molecular mechanisms that regulate dormancy in onion were available until now. Here, a comparison between uninfected and onion yellow dwarf virus (OYDV)-infected onion bulbs highlighted an altered dormancy in the virus-infected plants, causing several symptoms, such as leaf striping, growth reduction, early bulb sprouting and rooting, as well as a lower abscisic acid (ABA) level at the start of dormancy. Furthermore, by comparing three dormancy stages, almost five thousand four hundred (5390) differentially expressed genes (DEGs) were found in uninfected bulbs, while the number of DEGs was significantly reduced (1322) in OYDV-infected bulbs. Genes involved in cell wall modification, proteolysis, and hormone signaling, such as ABA, gibberellins (GAs), indole-3-acetic acid (IAA), and brassinosteroids (BRs), that have already been reported as key dormancy-related pathways, were the most enriched ones in the healthy plants. Interestingly, several transcription factors (TFs) were up-regulated in the uninfected bulbs, among them three genes belonging to the WRKY family, for the first time characterized in onion, were identified during dormancy release. The involvement of specific WRKY genes in breaking dormancy in onion was confirmed by GO enrichment and network analysis, highlighting a correlation between AcWRKY32 and genes driving plant development, cell wall modification, and division via gibberellin and auxin homeostasis, two key processes in dormancy release. Overall, we present, for the first time, a detailed molecular analysis of the dormancy process, a description of the WRKY-TF family in onion, providing a better understanding of the role played by AcWRKY32 in the bulb dormancy release. The TF co-expressed genes may represent targets for controlling the early sprouting in onion, laying the foundations for novel breeding programs to improve shelf life and reduce postharvest.