WRKY Gene Family Research Articles

Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata.

Background: Kandelia obovata, a dominant mangrove species, is widely distributed in tropical and subtropical areas. Low temperature is the major abiotic stress that seriously limits the survival and growth of mangroves. WRKY transcription factors (TFs) play vital roles in responses to biotic and abiotic stresses. However, genome-wide analysis of WRKY genes in K. obovata and their responses to chilling stress have not been reported. Methods: Bioinformatic analysis was used to identify and characterize the K. obovata WRKY (KoWRKY) gene family, RNA-seq and qRT–PCR analyses were employed to screen KoWRKYs that respond to chilling stress. Results: Sixty-four KoWRKYs were identified and they were unevenly distributed across all 18 K. obovata chromosomes. Many orthologous WRKY gene pairs were identified between Arabidopsis thaliana and K. obovata, showing high synteny between the two genomes. Segmental duplication events were found to be the major force driving the expansion for the KoWRKY gene family. Most of the KoWRKY genes contained several kinds of hormone- and stress-responsive cis-elements in their promoter. KoWRKY proteins belonged to three groups (I, II, III) according to their conserved WRKY domains and zinc-finger structure. Expression patterns derived from the RNA-seq and qRT–PCR analyses revealed that 9 KoWRKYs were significantly upregulated during chilling acclimation in the leaves. KEGG pathway enrichment analysis showed that the target genes of KoWRKYs were significantly involved in 11 pathways, and coexpression network analysis showed that 315 coexpressed pairs (KoWRKYs and mRNAs) were positively correlated. Conclusion: Sixty-four KoWRKYs from the K. obovata genome were identified, 9 of which exhibited chilling stress-induced expression patterns. These genes represent candidates for future functional analysis of KoWRKYs involved in chilling stress related signaling pathways in K. obovata. Our results provide a basis for further analysis of KoWRKY genes to determine their functions and molecular mechanisms in K. obovata in response to chilling stress.

Analysis of WRKY Resistance Gene Family in Boehmeria nivea (L.) Gaudich: Crosstalk Mechanisms of Secondary Cell Wall Thickening and Cadmium Stress.

A total of 60 WRKY family genes of ramie were identified in the ramie. The genes were unevenly distributed across 14 chromosomes in the specie and highly concentrated (72%) in the distal telomeric region. Phylogenetic analysis placed these genes into seven distinct subfamilies groups: I, II (a, b, c, d, e), and III, with group IIc containing only the variant of heptapetide sequence (WRKYGKK). Segmental duplication events (41.7%) was found to be the main driver of BnGWRKY evolution. Thirty eight from among the genes showed collinear relationships with WRKY genes from Arabidopsis thaliana, Cannabis sativa, Oryza sativa, and Zea mays. The number and density of stress and hormone responsives cis-acting elements were comparably higher than other elements, with abundant ARE and rare LTR cis-acting elements indicating the long-standing adaptability of ramie to its natural environment. GO and KEGG enrichment analysis of the WRKY target genes revealed their involvement in response to stimuli, immune system processes, transporter protein activity and antioxidant activity. Expression analysis show that most WRKYs were activated by the cadmium stress, more especially the BnGWRKY2, BnGWRKY15, BnGWRKY20, BnGWRKY50 and BnGWRKY58. Combining transcriptome, orthologous gene relationships and qPCR result, we established the possible involvement of BnGWRKY50 and BnGWRKY58 in crosstalk mechanism between secondary cell wall thickening and Cd2+ stress. This provided information into the role of BnGWRKY proteins in ramie secondary wall development and cadmium stress response to, and could serve as basis for improvement of the ramie.

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.

Characterization of the WRKY gene family in Akebia trifoliata and their response to Colletotrichum acutatum

BackgroundAkebia trifoliata, belonging to the Lardizabalaceae family, is a well-known Chinese traditional medicinal plant, susceptible to many diseases, such as anthracnose and powdery mildew. WRKY is one of the largest plant-specific transcription factor families and plays important roles in plant growth, development and stress response, especially in disease resistance. However, little was known about the numbers, characters, evolutionary relationship and expression of WRKY genes in A. trifoliata in response to plant disease due to lacking of A. trifoliata genome.ResultsA total of 42 putative AktWRKY genes were identified based on the full-length transcriptome-sequencing data of A. trifoliata. Then 42 AktWRKY genes were divided into three major groups (Group I-III) based on the WRKY domains. Motif analysis showed members within same group shared a similar motif composition, implying a functional conservation. Tissue-specific expression analysis showed that AktWRKY genes could be detected in all tissues, while few AktWRKY genes were tissue specific. We further evaluated the expression of AktWRKY genes in three varieties in response to Colletotrichum acutatum by qRT-PCR. The expression patterns of AktWRKY genes were similar between C01 and susceptible variety I02, but distinctly different in resistant variety H05. In addition, it showed that more than 64 percentages of AktWRKY genes were differentially expressed during fungal infection in I02 and H05. Furthermore, Gene ontology (GO) analysis showed that AktWRKY genes were categorized into 26 functional groups under cellular components, molecular functions and biological processes, and a predicted protein interaction network was also constructed.ConclusionsResults of bioinformation analysis and expression patterns implied that AktWRKYs might play multiple function in response to biotic stresses. Our study could facilitate to further investigate the function and regulatory mechanism of the WRKY in A. trifoliata during pathogen response.

Integrated Transcriptomics and Proteomics to Reveal Regulation Mechanism and Evolution of SmWRKY61 on Tanshinone Biosynthesis in Salvia miltiorrhiza and Salvia castanea.

Tanshinones found in Salvia species are the main active compounds for the treatment of cardiovascular and cerebrovascular diseases, but their contents are hugely different in different species. For example, tanshinone IIA content in Salvia castanea Diels f. tomentosa Stib. is about 49 times higher than that in Salvia miltiorrhiza Bunge. The molecular mechanism responsible for this phenomenon remains largely unknown. To address this, we performed comparative transcriptomic and proteomic analyses of S. miltiorrhiza and S. castanea. A total of 296 genes in S. castanea and 125 genes in S. miltiorrhiza were highly expressed at both the transcriptional and proteome levels, including hormone signal regulation, fungus response genes, transcription factors, and CYP450. Among these differentially expressed genes, the expression of SmWRKY61 was particularly high in S. castanea. Overexpression of SmWRKY61 in S. miltiorrhiza could significantly increase the content of tanshinone I and tanshinone IIA, which were 11.09 and 33.37 times of the control, respectively. Moreover, SmWRKY61 had a strong regulatory effect, elevating the expression levels of tanshinone pathway genes such as DXS2, CMK, HMGS2, 1, KSL1, KSL2, CYP76AH1, and CYP76AK3. For the WRKY family, 79 SmWRKYs were originally obtained and classified into three main groups. Collinearity analysis indicated a more specific extension of WRKY gene family in Salvia genus. In 55 Salvia species, only 37 species contained the WRKY61 sequence, and high SmWRKY61 expression in some Salvia L. species was often accompanied by high tanshinone accumulation. The above results suggest that SmWRKY61 is a highly effective regulator of tanshinone accumulation and may be a key factor resulting in high tanshinone accumulation in S. castanea.

The WRKY transcription factor family in cowpea: Genomic characterization and transcriptomic profiling under root dehydration

Cowpea [Vigna unguiculata (L.) Walp.] is one of the most tolerant legume crops to drought and salt stresses. WRKY transcription factor (TF) family members stand out among plant transcriptional regulators related to abiotic stress tolerance. However, little information is currently available on the expression of the cowpea WRKY gene family (VuWRKY) in response to water deficit. Thus, we analyzed genomic and transcriptomic data from cowpea to identify VuWRKY members and characterize their structure and transcriptional response under root dehydration stress. Ninety-two complete VuWRKY genes were found in the cowpea genome based on their domain characteristics. They were clustered into three groups: I (15 members), II (58), and III (16), while three genes were unclassified. Domain analysis of the encoded proteins identified four major variants of the conserved heptapeptide motif WRKYGQK. In silico analysis of VuWRKY gene promoters identified eight candidate binding motifs of cis-regulatory elements, regulated mainly by six TF families associated with abiotic stress responses. Ninety-seven VuWRKY modulated splicing variants associated with 55 VuWRKY genes were identified via RNA-Seq analysis available at the Cowpea Genomics Consortium (CpGC) database. qPCR analyses showed that 22 genes are induced under root dehydration, with VuWRKY18, 21, and 75 exhibiting the most significant induction levels. Given their central role in activating signal transduction cascades in abiotic stress response, the data provide a foundation for the targeted modification of specific VuWRKY family members to improve drought tolerance in this important climate-resilient legume in the developing world and beyond.

Genome-wide identification and expression analysis response to GA3 stresses of WRKY gene family in seed hemp (Cannabis sativa L)

WRKY transcription factor is one of the largest transcription factor families in higher plants. However, the investigations of the WRKY gene family have not yet been reported in seed hemp. In the present study, we identified 39 CasWRKYs at the genome-wide level and analyzed phylogenetic relationship, chromosome location, cis-acting elements, gene structure, conserved motif, and expression pattern. Based on the gene structure and phylogenetic analyses, CasWRKY proteins were divided into 3 groups and 7 subgroups. The gene duplication investigation revealed that 6 and 5 pairs of CasWRKY genes underwent tandem and segmental duplication events, respectively. These events may contribute to the diversity and expansion of the CasWRKY gene family. The regulatory elements in the promoter regions of CasWRKYs contained diverse cis-regulatory elements, among which P-box cis-regulatory elements showed high frequency, indicating that CasWRKYs can respond to the regulation of gibberellin. The expression profiles derived from RNA-seq and qRT-PCR showed that 13 CasWRKY genes could respond to GA3 stress and affect fiber development, as well as play significant roles in stem growth and development. This study will serve as molecular basis and practical reference for further exploring the genetic evolution and biological function of CasWRKY genes in seed hemp.

Identification and Expression Analysis of WRKY Gene Family in Response to Abiotic Stress in Dendrobium catenatum.

Dendrobium catenatum has become a rare and endangered medicinal plant due to habitat loss in China. As one of the most important and largest transcription factors, WRKY plays a critical role in response to abiotic stresses in plants. However, little is known regarding the functions of the WRKY family in D. catenatum. In this study, a total of 62 WRKY genes were identified from the D. catenatum genome. Phylogenetic analysis revealed that DcWRKY proteins could be divided into three groups, a division supported by the conserved motif compositions and intron/exon structures. DcWRKY gene expression and specific responses under drought, heat, cold and salt stresses were analyzed through RNA-seq data and RT-qPCR assay. The results showed that these genes had tissue-specificity and displayed different expression patterns in response to abiotic stresses. The expression levels of DcWRKY22, DcWRKY36 and DcWRKY45 were up-regulated by drought stress. Meanwhile, DcWRKY22 was highly induced by heat in roots, and DcWRKY45 was significantly induced by cold stress in leaves. Furthermore, DcWRKY27 in roots and DcWRKY58 in leaves were extremely induced under salt treatment. Finally, we found that all the five genes may function in ABA- and SA-dependent manners. This study identified candidate WRKY genes with possible roles in abiotic stress and these findings not only contribute to our understanding of WRKY family genes, but also provide valuable information for stress resistance development in D. catenatum.

Genome-wide identification of the Liriodendron chinense WRKY gene family and its diverse roles in response to multiple abiotic stress

BackgroundLiriodendron chinense (Lchi) is a tree species within the Magnoliaceae family and is considered a basal angiosperm. The too low or high temperature or soil drought will restrict its growth as the adverse environmental conditions, thus improving L. chinense abiotic tolerance was the key issues to study. WRKYs are a major family of plant transcription factors known to often be involved in biotic and abiotic stress responses. So far, it is still largely unknown if and how the LchiWRKY gene family is tied to regulating L. chinense stress responses. Therefore, studying the involvement of the WRKY gene family in abiotic stress regulation in L. chinense could be very informative in showing how this tree deals with such stressful conditions.ResultsIn this research, we performed a genome-wide analysis of the Liriodendron chinense (Lchi) WRKY gene family, studying their classification relationships, gene structure, chromosomal locations, gene duplication, cis-element, and response to abiotic stress. The 44 members of the LchiWRKY gene family contain a significant amount of sequence diversity, with their lengths ranging from 525 bp to 40,981 bp. Using classification analysis, we divided the 44 LchiWRKY genes into three phylogenetic groups (I, II, II), with group II then being further divided into five subgroups (IIa, IIb, IIc, IId, IIe). Comparative phylogenetic analysis including the WRKY families from 17 plant species suggested that LchiWRKYs are closely related to the Magnolia Cinnamomum kanehirae WRKY family, and has fewer family members than higher plants. We found the LchiWRKYs to be evenly distributed across 15 chromosomes, with their duplication events suggesting that tandem duplication may have played a major role in LchiWRKY gene expansion model. A Ka/Ks analysis indicated that they mainly underwent purifying selection and distributed in the group IId. Motif analysis showed that LchiWRKYs contained 20 motifs, and different phylogenetic groups contained conserved motif. Gene ontology (GO) analysis showed that LchiWRKYs were mainly enriched in two categories, i.e., biological process and molecular function. Two group IIc members (LchiWRKY10 and LchiWRKY37) contain unique WRKY element sequence variants (WRKYGKK and WRKYGKS). Gene structure analysis showed that most LchiWRKYs possess 3 exons and two different types of introns: the R- and V-type which are both contained within the WRKY domain (WD). Additional promoter cis-element analysis indicated that 12 cis-elements that play different functions in environmental adaptability occur across all LchiWRKY groups. Heat, cold, and drought stress mainly induced the expression of group II and I LchiWRKYs, some of which had undergone gene duplication during evolution, and more than half of which had three exons. LchiWRKY33 mainly responded to cold stress and LchiWRKY25 mainly responded to heat stress, and LchiWRKY18 mainly responded to drought stress, which was almost 4-fold highly expressed, while 5 LchiWRKYs (LchiWRKY5, LchiWRKY23, LchiWRKY14, LchiWRKY27, and LchiWRKY36) responded equally three stresses with more than 6-fold expression. Subcellular localization analysis showed that all LchiWRKYs were localized in the nucleus, and subcellular localization experiments of LchiWRKY18 and 36 also showed that these two transcription factors were expressed in the nucleus.ConclusionsThis study shows that in Liriodendron chinense, several WRKY genes like LchiWRKY33, LchiWRKY25, and LchiWRKY18, respond to cold or heat or drought stress, suggesting that they may indeed play a role in regulating the tree’s response to such conditions. This information will prove a pivotal role in directing further studies on the function of the LchiWRKY gene family in abiotic stress response and provides a theoretical basis for popularizing afforestation in different regions of China.

Genome-Wide Analysis of Snapdragon WRKY and VQ Gene Families and Their Expression in Response to Drought and Cold Stresses

Snapdragon (Antirrhinum majus) is one of the most widely cultivated grass flowers in the world. WRKY transcription factors, VQ proteins and their interactions play crucial roles in plant response to abiotic stresses. However, little is known about WRKY and VQ gene families in snapdragon. In the present study, WRKY and VQ genes and their interactions were comprehensively analyzed in snapdragon using bioinformatics approaches, and their expression in response to drought and cold stresses was examined using real-time PCR. A total of 67 AmWRKY genes were identified in snapdragon, which were classified into different groups or subgroups based on phylogenetic analysis. Members in the same group or sub-groups exhibited similar exon-intron structure and conserved motifs distribution. Among these WRKY genes, 16 and 22 genes were found to differentially express under drought and cold stresses, respectively. A total of 32 AmVQ genes were identified, of which 10 and 18 were found to differentially express under drought and cold stresses, respectively. The WRKY-VQ or WRKY-WRKY interaction relationships were predicted for 11 cold-responsive genes, suggesting that they might exist in the same response pathway to cold stress. These results lay a foundation for further studies on roles of WRKY and VQ genes and their interactions in regulating abiotic responses in snapdragon.

Characterization of <i>CsWRKY29</i> and <i>CsWRKY37</i> transcription factors and their functional roles in cold tolerance of tea plant

The WRKY gene family is most widely known as being the key plant transcription factor family involved in various stress responses and affecting plant growth and development. In this study, a total of 86 members of the <italic>CsWRKY</italic> genes were identified from the tea plant genome. Most of these genes contain several important <italic>Cis</italic>-regulatory elements in the promoter regions associated with multiple stress-responses. These genes were further classified into three groups, I, II, and III, each with 21, 58, and 7 members, respectively. We showed evidence that tandem duplications, but not the whole genome duplication, are likely to drive the amplification of <italic>CsWRKY</italic> genes in tea plants. All the 86 <italic>CsWRKY</italic> genes showed differential expression patterns either in different tissues, or under exposure to diverse abiotic stresses such as drought, cold acclimation, and MeJA treatments. Additionally, the functional roles of two genes, <italic>CsWRKY29</italic> and <italic>CsWRKY37</italic>, were examined under cold stress; and the silencing of these genes resulted in tea plant phenotypes susceptible to cold stress. Moreover, transgenic <italic>Arabidopsis</italic> lines overexpressing <italic>CsWRKY29</italic> and <italic>CsWRKY37</italic> genes showed higher survival rates and lower malondialdehyde levels under freezing treatment than the wild type plants. The core findings from this work provide valuable evolutionary pattern of WRKY gene family and underpinning the underlying regulatory roles of <italic>CsWRKY29</italic> and <italic>CsWRKY37</italic> from tea plants that conferred cold tolerance in transgenic <italic>Arabidopsis</italic> plants.

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

WRKY transcription factors comprise one of the largest gene families and serve as key regulators of plant defenses against herbivore attack. However, studies related to the roles of WRKY genes in response to herbivory are limited in maize. In this study, a total of 128 putative maize WRKY genes (ZmWRKYs) were identified from the new maize genome (v4). These genes were divided into seven subgroups (groups I, IIa–e, and III) based on phylogenomic analysis, with distinct motif compositions in each subgroup. Syntenic analysis revealed that 72 (56.3%) of the genes were derived from either segmental or tandem duplication events (69 and 3, respectively), suggesting a pivotal role of segmental duplication in the expansion of the ZmWRKY family. Importantly, transcriptional regulation prediction showed that six key WRKY genes contribute to four major defense-related pathways: L-phenylalanine biosynthesis II and flavonoid, benzoxazinoid, and jasmonic acid (JA) biosynthesis. These key WRKY genes were strongly induced in commercial maize (Jingke968) infested with the Asian corn borer, Ostrinia furnacalis, for 0, 2, 4, 12 and 24 h in the field, and their expression levels were highly correlated with predicted target genes, suggesting that these genes have important functions in the response to O. furnacalis. Our results provide a comprehensive understanding of the WRKY gene family based on the new assembly of the maize genome and lay the foundation for further studies into functional characteristics of ZmWRKY genes in commercial maize defenses against O. furnacalis in the field.

Identification of QTLs for stagnant flooding tolerance in rice employing genotyping by sequencing of a RIL population derived from Swarna × Rashpanjor.

The online version contains supplementary material available at 10.1007/s12298-021-01107-x.

Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum.

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng

BackgroundPanax ginseng is a well-known medicinal plant worldwide. As an herbal medicine, ginseng is also known for its long lifecycle, which can reach several decades. WRKY proteins play regulatory roles in many aspects of biological processes in plants, such as responses to biotic or abiotic stress, plant development, and adaptation to environmental challenges. Genome-wide analyses of WRKY genes in P. ginseng have not been reported.ResultsIn this study, 137 PgWRKY genes were identified from the ginseng genome. Phylogenetic analysis showed that the PgWRKYs could be clustered into three primary groups and five subgroups. Most of the PgWRKY gene promoters contained several kinds of hormone- and stress-related cis-regulatory elements. The expression patterns of PgWRKY genes in 14 different tissues were analyzed based on the available public RNA-seq data. The responses of the PgWRKY genes to heat, cold, salt and drought treatment were also investigated. Most of the PgWRKY genes were expressed differently after heat treatment, and expression trends changed significantly under drought and cold treatment but only slightly under salt treatment. The coexpression analysis of PgWRKY genes with the ginsenoside biosynthesis pathway genes identified 11 PgWRKYs that may have a potential regulatory role in the biosynthesis process of ginsenoside.ConclusionsThis work provides insights into the evolution, modulation and distribution of the WRKY gene family in ginseng and extends our knowledge of the molecular basis along with modulatory mechanisms of WRKY transcription factors in ginsenoside biosynthesis.

Genome-wide Identification and Expression Analysis of WRKY Gene Family in Dianthus caryophyllus

Genome-wide Identification and Expression Analysis of WRKY Gene Family in Dianthus caryophyllus

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

BackgroundThe 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.ResultsIn 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.ConclusionsTaken 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.

Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut (Juglans regia L.).

The transcription factor WRKY is widely distributed in the plant kingdom, playing a significant role in plant growth, development and response to stresses. Walnut is an economically important temperate tree species valued for both its edible nuts and high-quality wood, and its response to various stresses is an important factor that determines the quality of its fruit. However, in walnut trees themselves, information about the WRKY gene family remains scarce. In this paper, we perform a comprehensive study of the WRKY gene family in walnut. In total, we identified 103 WRKY genes in the common walnut that are clustered into 4 groups and distributed on 14 chromosomes. The conserved domains all contained a WRKY domain, and motif 2 was observed in most WRKYs, suggesting a high degree of conservation and similar functions within each subfamily. However, gene structure was significantly differentiated between different subfamilies. Synteny analysis indicates that there were 56 gene pairs in J. regia and A. thaliana, 76 in J. regia and J. mandshurica, 75 in J. regia and J. microcarpa, 76 in J. regia and P. trichocarpa, and 33 in J. regia and Q. robur, indicating that the WRKY gene family may come from a common ancestor. GO and KEGG enrichment analysis showed that the WRKY gene family was involved in resistance traits and the plant-pathogen interaction pathway. In anthracnose-resistant F26 fruits (AR) and anthracnose-susceptible F423 fruits (AS), transcriptome and qPCR analysis results showed that JrWRKY83, JrWRKY73 and JrWRKY74 were expressed significantly more highly in resistant cultivars, indicating that these three genes may be important contributors to stress resistance in walnut trees. Furthermore, we investigate how these three genes potentially target miRNAs and interact with proteins. JrWRKY73 was target by the miR156 family, including 12 miRNAs; this miRNA family targets WRKY genes to enhance plant defense. JrWRKY73 also interacted with the resistance gene AtMPK6, showing that it may play a crucial role in walnut defense.

PbWRKY75 promotes anthocyanin synthesis by activating PbDFR, PbUFGT, and PbMYB10b in pear.

Anthocyanins are common secondary metabolites in plants that impart red coloration to fruits and flowers. The important WRKY transcription factor family plays multifaceted roles in plant growth and development. In this study, we found a WRKY family gene, Pyrus bretschneideri WRKY75, that may be involved in anthocyanin synthesis in pear. Unlike Arabidopsis thaliana WRKY75, PbWRKY75 may be a positive regulator of anthocyanin synthesis. A transient expression assay indicated that PbWRKY75 promoted pear anthocyanin synthesis. The structural genes (PbANS, PbDFR, and PbUFGT) and positive regulators (PbMYB10 and PbMYB10b) of anthocyanin synthesis were significantly upregulated in the fruitlet skins of PbWRKY75-overexpressing "Zaosu" pears. Subsequently, yeast one-hybrid and dual-luciferase assays indicated that PbWRKY75 promoted PbDFR, PbUFGT, and PbMYB10b expression by activating their promoters. These results revealed that PbWRKY75 may promote the expression of both PbMYB10b and anthocyanin late biosynthetic genes (PbDFR and PbUFGT) by activating their promoters, thereby inducing anthocyanin synthesis in pear. This study enhanced our understanding of the mechanism of pear anthocyanin synthesis, which will be beneficial in the improvement of pear peel color.

Transcriptional regulation and functional analysis of Nicotiana tabacum under salt and ABA stress

Soil salinization is an important factor that restricts crop quality and yield and causes an enormous toll to human beings. Salt stress and abscisic acid (ABA) stress will occur in the process of soil salinization. In this study, transcriptome sequencing of tobacco leaves under salt and ABA stress in order to further study the resistance mechanism of tobacco. Compared with controlled groups, 1654 and 3306 DEGs were obtained in salt and ABA stress, respectively. The genes function enrichment analysis showed that the up-regulated genes in salt stress were mainly concentrated in transcription factor WRKY family and PAR1 resistance gene family, while the up-regulated genes were mainly concentrated on bHLH transcription factor, Kunitz-type protease inhibitor, dehydrin (Xero1) gene and CAT (Catalase) family protein genes in ABA stress. Tobacco MAPK cascade triggered stress response through up-regulation of gene expression in signal transduction. The expression products of these up-regulated genes can improve the abiotic stress resistance of plants. These results have an important implication for further understanding the mechanism of salinity tolerance in plants.