Genome-Wide Identification and Analysis of the WRKY Gene Family in Asparagus officinalis

In recent years, the related research of the WRKY gene family has been gradually promoted, which is mainly reflected in the aspects of environmental stress and hormone response. However, to make the study of the WRKY gene family more complete, we also need to focus on the whole-genome analysis and identification of the family. In previous studies, the whole WRKY gene family of Arabidopsis, legumes and other plants has been thoroughly studied. However, since the publication of Asparagus officinalis genome-wide data, there has never been an analysis of the whole WRKY gene family. To understand more broadly the function of the WRKY gene family, the whole genome and salt stress transcriptome data of asparagus were used for comprehensive analysis in this study, including WRKY gene family identification, phylogenetic tree construction, analysis of conserved mods and gene domains, extraction of cis-acting elements, intron/exon analysis, species collinearity analysis, and WRKY expression analysis under salt stress. The results showed that a total of 70 genes were selected and randomly distributed on 10 chromosomes and one undefined chromosome. According to the functional classification of Arabidopsis thaliana, the WRKY family of asparagus was divided into 11 subgroups (C1-C9, U1, U2). It is worth considering that the distribution rules of gene-conserved motifs, gene domains and introns/exons in the same subfamily are similar, which suggests that genes in the same subfamily may regulate similar physiological processes. In this study, 11 cis-acting elements of WRKY family were selected, among which auxin, gibberellin, abscisic acid, salicylic acid and other hormone-regulated induction elements were involved. In addition, environmental stress (such as drought stress and low-temperature response) also accounted for a large proportion. Interestingly, we analyzed a total of two tandem duplicate genes and 13 segmental duplication genes, suggesting that this is related to the amplification of the WRKY gene family. Transcriptome data analysis showed that WRKY family genes could regulate plant growth and development by up-regulating and down-regulating gene expression under salt stress. Volcanic maps showed that 3 and 15 AoWRKY genes were significantly up-regulated or down-regulated in NI&NI+S and AMF&AMF+S, respectively. These results provide a new way to analyze the evolution and function of the WRKY gene family, and can provide a reference for the production and research of asparagus.

Effects of low molecular weight polysaccharides from Ulva prolifera on the tolerance of Triticum aestivum to osmotic stress

Polysaccharides derived from seaweeds can be used as biostimulants to enhance plant resistance to different stressors. In this study, we investigated the effects of applying low molecular weight polysaccharides (LPU) derived from Ulva prolifera with 14.2 kDa on the responses of wheat (Triticum aestivum) to osmotic stress. The results showed that osmotic stress simulated using polyethylene glycol inhibited seedling growth, whereas we observed increases in the fresh weights and shoot lengths of seedlings treated with polysaccharide for 120 h. Furthermore, we observed enhanced activities of antioxidant enzymes, and significant reductions in malondialdehyde content of 23.13%, 19.82%, and 20.04% in response treatment for 120 h with 0.01%, 0.03%, and 0.05% LPU, respectively, relative to those in the group treated with polyethylene glycol alone. In all treatments, expression of the P5CS gene was upregulated to promote proline accumulation. Moreover, after 120 h, exogenously applied LPU induced the expression of stress-related genes, including SnRK2, Wabi5, Wrab18, and Wdhn13. Collectively, these findings indicate that LPU might have the effect of regulating the abscisic acid-dependent pathway in wheat, thereby increasing seedling antioxidant capacity and growth. Application of LPU may accordingly represent an effective approach for enhancing the resistance to osmotic stress in wheat.

Heterologous expression of wheat WRKY transcription factor genes transcriptionally activated in hybrid necrosis strains alters abiotic and biotic stress tolerance in transgenic Arabidopsis

Hybrid necrosis and hybrid chlorosis are sometimes observed in interspecific hybrids between the tetraploid wheat cultivar Langdon and diploid wild wheat Aegilops tauschii. Many WRKY transcription factor genes are dramatically upregulated in necrosis and chlorosis wheat hybrids. Here, we isolated cDNA clones for four wheat WRKY transcription factor genes, TaWRKY49, TaWRKY92, TaWRKY112, and TaWRKY142, that were commonly upregulated in the hybrid necrosis and hybrid chlorosis and belonged to the same clade of the WRKY gene family. Expression patterns of the four TaWRKY genes in response to several stress conditions were similar in wheat seeding leaves. The four TaWRKY-GFP fusion proteins were targeted to the nucleus in onion epidermal cells. The TaWRKY gene expression levels were increased by high salt, dehydration, darkness, and blast fungus treatment in common wheat. Expression of either of the TaWRKY genes increased salinity and osmotic stress tolerance accompanied with overexpression of STZ/Zat10, and induced overexpression of the salicylic acid-signal pathway marker gene AtPR1 in transgenic Arabidopsis. TaWRKY142 expression also induced the jasmonic acid-pathway marker gene AtPDF1.2 and enhanced resistance against the fungal pathogen Colletotrichum higginsianum in transgenic Arabidopsis. These results suggest that the four TaWRKY genes act as integrated hubs of multiple stress signaling pathways in wheat and play important roles in autoimmune response-inducing hybrid necrosis and hybrid chlorosis.

Cytosolic glyceraldehyde-3-phosphate dehydrogenase 2/5/6 increase drought tolerance via stomatal movement and reactive oxygen species scavenging in wheat

Drought is a major threat to wheat growth and crop productivity. However, there has been only limited success in developing drought-hardy cultivars. This lack of progress is due, at least in part, to a lack of understanding of the molecular mechanisms of drought tolerance in wheat. Here, we evaluated the potential role of three cytosolic glyceraldehyde-3-phosphate dehydrogenases (TaGAPC2/5/6) under drought stress in wheat and Arabidopsis. We found that TaGAPC2/5/6 all positively responded to drought stress via reactive oxygen species (ROS) scavenging and stomatal movement. The results of yeast co-transformation and electrophoretic mobility shift assay showed that TaWRKY33 acted as a direct regulator of TaGAPC2/5/6 genes. The dual luciferase reporter assay indicated that TaWRKY33 positively activated the expression of TaGAPC2/5/6. The results of bimolecular fluorescence complementation and yeast two-hybrid system demonstrated that TaGAPC2/5/6 interacted with phospholipase Dδ (PLDδ). We then demonstrated that TaGAPC2/5/6 positively promoted the activity of TaPLDδ in vitro and in vivo. Furthermore, lower PLDδ activity in RNAi wheat could lead to less PA accumulation, causing higher stomatal aperture sizes under drought stress. In summary, our results establish a new positive regulatory mechanism of TaGAPCs which helps wheat fine-tune their drought responses.

Genome-wide identification and expression analysis of the WRKY genes in sugar beet (Beta vulgaris L.) under alkaline stress

Background

The WRKY transcription factor family plays crucial roles in many aspects of physiological processes and adaption to environment. Although the WRKY genes have been widely identified in various plant species, the structure and function of the WRKY family in sugar beet (Beta vulgaris L.) remains unknown.

Methods

In the present study, the WRKY genes were identified from the sugar beet genome by bioinformatics. A phylogenetic tree was constructed by MEGA7.0. A distribution map of these genes was displayed by MapInspect 1.0. Furthermore, the exon-intron structure and the conserved motifs were predicted by GSDS 2.0 and MEME 5.0.5, respectively. Additionally, the expression levels of nine selected genes in shoots and roots of sugar beet seedlings exposed to alkaline stress were assayed by qRT-PCR.

Results

A total of 58 putative BvWRKY genes are identified in the sugar beet genome. The coding sequences of these genes ranged from 558 to 2,307 bp and molecular weights (MWs) varied from 21.3 to 84. The BvWRKY genes are clustered into three major groups I, II, and III, with 11, 40, and seven members, based on the primary amino acid sequences. The number of introns in the BvWRKY genes ranged from 1 to 5, with a majority of BvWRKY (27/58) containing three exons. All the BvWRKY genes have one or two conserved WRKY domains and zinc-finger structure. Moreover, the selected BvWRKY genes showed a variety of expression patterns in shoots and roots of seedlings under various concentrations of NaHCO₃. Importantly, BvWRKY10 in shoots and BvWRKY16 in roots were remarkably up-regulated by alkaline stress. Taken together, our findings extend understandings of the BvWRKY genes family and provide useful information for subsequent research on their functions in sugar beet under alkaline stress.

Genome-wide identification of the potato WRKY transcription factor family

WRKY transcription factors play pivotal roles in regulation of stress responses. This study identified 79 WRKY genes in potato (Solanum tuberosum). Based on multiple sequence alignment and phylogenetic relationships, WRKY genes were classified into three major groups. The majority of WRKY genes belonged to Group II (52 StWRKYs), Group III had 14 and Group I consisted of 13. The phylogenetic tree further classified Group II into five sub-groups. All StWRKY genes except StWRKY79 were mapped on potato chromosomes, with eight tandem duplication gene pairs and seven segmental duplication gene pairs found from StWRKY family genes. The expression analysis of 22 StWRKYs showed their differential expression levels under various stress conditions. Cis-element prediction showed that a large number of elements related to drought, heat and salicylic acid were present in the promotor regions of StWRKY genes. The expression analysis indicated that seven StWRKYs seemed to respond to stress (heat, drought and salinity) and salicylic acid treatment. These genes are candidates for abiotic stress signaling for further research.

Overexpression of TaWRKY146 Increases Drought Tolerance through Inducing Stomatal Closure in Arabidopsis thaliana

As a superfamily of transcription factors, the tryptophan-arginine-lysine-tyrosine (WRKY) transcription factors have been found to be essential for abiotic and biotic stress responses in plants. Currently, only 76 WRKY transcription factors in wheat could be identified in the NCBI database, among which only a few have been functionally analyzed. Herein, a total of 188 WRKY transcription factors were identified from the wheat genome database, which included 123 full-length coding sequences, and all of them were used for detailed evolution studies. By bioinformatics analysis, a WRKY transcription factor, named TaWRKY146, was found to be the homologous gene of AtWRKY46, overexpression of which leads to hypersensitivity to drought and salt stress in Arabidopsis. Consequently, the full length of TaWRKY146 was cloned, and the expression levels of TaWRKY146 were found significantly up-regulated in the leaves and roots of wheat seedlings, which were subjected to osmotic stress. Overexpression of TaWRKY146 in Arabidopsis was shown to enhance drought tolerance by the induction of stomatal closure that reduced the transpiration rate. All these results provide a firm foundation for further identification of WRKY transcription factors with important functions in wheat.

Proteomic profiling analysis reveals that glutathione system plays important roles responding to osmotic stress in wheat (Triticum aestivum L.) roots

Wheat is one of the most important crops in the world, and osmotic stress has become one of the main factors affecting wheat production. Understanding the mechanism of the response of wheat to osmotic stress would be greatly significant. In the present study, isobaric tag for relative and absolute quantification (iTRAQ) was used to analyze the changes of protein expression in the wheat roots exposed to different osmotic stresses. A total of 2,228 expressed proteins, including 81 differentially expressed proteins, between osmotic stress and control, were found. The comprehensive analysis of these differentially expressed proteins revealed that osmotic stress increased the variety of expressed proteins and suppressed the quantity of expressed proteins in wheat roots. Furthermore, the proteins for detoxifying and reactive oxygen species scavenging, especially the glutathione system, played important roles in maintaining organism balance in response to osmotic stress in wheat roots. Thus, the present study comprehensively describes the protein expression changes in wheat roots in response to osmotic stress, providing firmer foundation to further study the mechanism of osmotic resistance in wheat.

Genome-wide identification of WRKY family genes in peach and analysis of WRKY expression during bud dormancy

Bud dormancy in deciduous fruit trees is an important adaptive mechanism for their survival in cold climates. The WRKY genes participate in several developmental and physiological processes, including dormancy. However, the dormancy mechanisms of WRKY genes have not been studied in detail. We conducted a genome-wide analysis and identified 58 WRKY genes in peach. These putative genes were located on all eight chromosomes. In bioinformatics analyses, we compared the sequences of WRKY genes from peach, rice, and Arabidopsis. In a cluster analysis, the gene sequences formed three groups, of which group II was further divided into five subgroups. Gene structure was highly conserved within each group, especially in groups IId and III. Gene expression analyses by qRT-PCR showed that WRKY genes showed different expression patterns in peach buds during dormancy. The mean expression levels of six WRKY genes (Prupe.6G286000, Prupe.1G393000, Prupe.1G114800, Prupe.1G071400, Prupe.2G185100, and Prupe.2G307400) increased during endodormancy and decreased during ecodormancy, indicating that these six WRKY genes may play a role in dormancy in a perennial fruit tree. This information will be useful for selecting fruit trees with desirable dormancy characteristics or for manipulating dormancy in genetic engineering programs.