Evolution and Identification of the WRKY Gene Family in Quinoa (Chenopodium quinoa)

RrWRKY1, a Transcription Factor, Is Involved in the Regulation of the Salt Stress Response in Rosa rugosa

Salt stress has become a major environmental problem affecting plant growth and development. Some WRKY transcription factors have been reported to be involved in the salt stress response in plants. However, there are few studies on the involvement of WRKYs in the salt stress response in Rosa rugosa. In this study, we isolated a salt tolerance gene, RrWRKY1, from R. rugosa. RrWRKY1 was found to belong to Group I of the WRKY family, and it was specifically expressed in leaves and petals. RrWRKY1 expression was upregulated under NaCl stress in rose leaves. After silencing RrWRKY1 in R. rugosa, transgenic plants showed dry leaves and black and brown veins, indicating sensitivity to salt stress. At the same time, the transcription levels of the salt tolerance-related genes RrNHX1, RrABF2, RrRD22, RrNCED1, and RrHKT1 also changed significantly. The superoxide dismutase (SOD) and peroxidase (POD) activities decreased, the proline content decreased, and the malondialdehyde (MDA) content in the gene-silenced plants increased, indicating that RrWRKY1 regulates the salt tolerance of R. rugosa. In addition, the overexpression of RrWRKY1 in Arabidopsis thaliana improved the germination rate and the average of the main root and lateral root lengths, and the transgenic plants had a larger number of lateral roots than the WT plants under salt stress. This study provides candidate gene resources for salinity tolerance breeding and a theoretical basis for analyzing the salinity tolerance mechanism of the WRKY gene.

Identification of WRKY transcription factors in Rosa chinensis and analysis of their expression response to alkali stress response

Breeding abiotic stress-tolerant varieties of Rosa chinensis is a paramount goal in horticulture. WRKY transcription factors, pivotal in plant responses to diverse stressors, offer potential targets for enhancing stress resilience in R. chinensis . Using bioinformatics and genomic data, we identified RcWRKY transcription factor genes, characterised their chromosomal distribution, phylogenetic relationships, structural attributes, collinearity, and expression patterns in response to saline stress. Leveraging bidirectional database searches, we pinpointed 66 RcWRKY genes, categorised into three groups. All except RcWRKY60 encoded DNA Binding Domain and Zinc Finger Motif regions of the WRKY domain. Expansion of the RcWRKY gene family was propelled by 19 segmental, and 2 tandem, duplications. We unveiled 41 and 15 RcWRKY genes corresponding to 50 AtWRKY and 17 OsWRKY orthologs respectively, indicating postdivergence expansion. Expression analyses under alkaline stress pinpointed significant alterations in 54 RcWRKY genes. Integration of functional roles from their Arabidopsis orthologs and cis -acting elements within their promoters, along with quantitative reverse transcription PCR validation, underscored the importance of RcWRKY27 and 29 in R. chinensis ' alkaline stress response. These findings offer insights into the biological roles of RcWRKY transcription factors, as well as the regulatory dynamics governing R. chinensis ' growth, development, and stress resilience.

Identification and Analysis of WRKY Transcription Factors in Response to Cowpea Fusarium Wilt in Cowpea

In plants, WRKY transcription factors play a crucial role in plant growth, development, and response to abiotic and biotic stress. Cowpea (Vigna unguiculata) is an important legume crop. However, cowpea Fusarium wilt (CFW), caused by Fusarium oxysporum f. sp. tracheiphilum (Fot), poses a serious threat to its production. In this study, we systematically identified members of the cowpea WRKY (VuWRKY) gene family and analyzed their expression patterns under CFW stress. A total of 91 WRKY transcription factors were identified in the cowpea genome. Phylogenetic and synteny analyses indicated that the expansion of VuWRKY genes in cowpea is primarily due to recent duplication events. Transcriptome analysis of cowpea inoculated with Fo revealed 31 differentially expressed VuWRKY genes, underscoring their role in the response to CFW infection. Four differentially expressed WRKY genes were selected for validation. Subcellular localization and Western blot assays showed their nuclear localization and normal expression in N. benthamiana. Additionally, yeast one-hybrid assays demonstrated that VuWRKY2 can bind to the promoter region of the Catalase (CAT) gene, indicating its potential role in transcriptional regulation. This study establishes a foundation for further exploration of the role and regulatory mechanisms of VuWRKY genes in response to CFW stress.

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.

Genome-wide analysis of AP2/ERF gene and functional analysis of CqERF24 gene in drought stress in quinoa

Quinoa is a crop with high nutritional value and strong stress resistance. AP2/ERF transcription factors play a key role in plant growth and development. In this study, 148 AP2/ERF genes were identified in quinoa, which were divided into 5 subfamilies, including ERF, AP2, DREB, RAV and Soloist. The results showed that the number of introns ranged from 0 to 11, and the Motif 1-Motif 4 was highly conserved in most CqAP2/ERF proteins. The 148 CqAP2/ERF genes were distributed on 19 chromosomes. There were 93 pairs of duplicating genes in this family, and gene duplication played a critical role in the expansion of this family. Protein-protein interaction indicated that the proteins in CqAP2/ERF subfamily exhibited complex interactions, and GO enrichment analysis indicated that 148 CqAP2/ERF proteins were involved in transcription factor activity. In addition, CqAP2/ERF gene contains a large number of elements related to hormones in promoter region (IAA, GA, SA, ABA and MeJA) and stresses (salt, drought, low temperature and anaerobic induction). Transcriptome analysis under drought stress indicated that most of the CqAP2/ERF genes were responsive to drought stress, and subcellular localization indicated that CqERF24 was location in the nucleus, qRT-PCR results also showed that most of the genes such as CqERF15, CqERF24, CqDREB03, CqDREB14, CqDREB37 and CqDREB43 also responded to drought stress in roots and leaves. Overexpression of CqERF24 in Arabidopsis thaliana enhanced drought resistance by increasing antioxidant enzyme activity and activation-related stress genes, and the gene is sensitive to ABA, while silencing CqERF24 in quinoa decreased drought tolerance. In addition, overexpression of CqERF24 in quinoa calli enhanced resistance to mannitol. These results lay a solid foundation for further study on the role of AP2/ERF family genes in quinoa under drought stress.

Genome-Wide Identification, Expression and Interaction Analyses of PP2C Family Genes in Chenopodium quinoa

Plant protein phosphatase 2Cs (PP2Cs) function as inhibitors in protein kinase cascades involved in various processes and are crucial participants in both plant development and signaling pathways activated by abiotic stress. In this study, a genome-wide study was conducted on the CqPP2C gene family. A total of putative 117 CqPP2C genes were identified. Comprehensive analyses of physicochemical properties, chromosome localization and subcellular localization were conducted. According to phylogenetic analysis, CqPP2Cs were divided into 13 subfamilies. CqPP2Cs in the same subfamily had similar gene structures, and conserved motifs and all the CqPP2C proteins had the type 2C phosphatase domains. The expansion of CqPP2Cs through gene duplication was primarily driven by segmental duplication, and all duplicated CqPP2Cs underwent evolutionary changes guided by purifying selection. The expression of CqPP2Cs in various tissues under different abiotic stresses was analyzed using RNA-seq data. The findings indicated that CqPP2C genes played a role in regulating both the developmental processes and stress responses of quinoa. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis of six CqPP2C genes in subfamily A revealed that they were up-regulated or down-regulated under salt and drought treatments. Furthermore, the results of yeast two-hybrid assays revealed that subfamily A CqPP2Cs interacted not only with subclass III CqSnRK2s but also with subclass II CqSnRK2s. Subfamily A CqPP2Cs could interact with CqSnRK2s in different combinations and intensities in a variety of biological processes and biological threats. Overall, our results will be useful for understanding the functions of CqPP2C in regulating ABA signals and responding to abiotic stress.

Molecular Characterization and Expression Analysis of YABBY Genes in Chenopodium quinoa

Plant-specific YABBY transcription factors play an important role in lateral organ development and abiotic stress responses. However, the functions of the YABBY genes in quinoa remain elusive. In this study, twelve YABBY (CqYAB) genes were identified in the quinoa genome, and they were distributed on nine chromosomes. They were classified into FIL/YAB3, YAB2, YAB5, INO, and CRC clades. All CqYAB genes consist of six or seven exons, and their proteins contain both N-terminal C2C2 zinc finger motifs and C-terminal YABBY domains. Ninety-three cis-regulatory elements were revealed in CqYAB gene promoters, and they were divided into six groups, such as cis-elements involved in light response, hormone response, development, and stress response. Six CqYAB genes were significantly upregulated by salt stress, while one was downregulated. Nine CqYAB genes were upregulated under drought stress, whereas six CqYAB genes were downregulated under cadmium treatment. Tissue expression profiles showed that nine CqYAB genes were expressed in seedlings, leaves, and flowers, seven in seeds, and two specifically in flowers, but no CqYAB expression was detected in roots. Furthermore, CqYAB4 could rescue the ino mutant phenotype in Arabidopsis but not CqYAB10, a paralog of CqYAB4, indicative of functional conservation and divergence among these YABBY genes. Taken together, these results lay a foundation for further functional analysis of CqYAB genes in quinoa growth, development, and abiotic stress responses.

Genome-wide identification and characterization of glutathione S-transferase gene family in quinoa (Chenopodium quinoa Willd.)

The present investigation was envisaged for large scale in-silico genome wide identification and characterization of glutathione S-transferases (GSTs) in Chenopodium quinoa. In this study, a total of 120 GST genes (CqGSTs) were identified and divided into 11 classes of which tau and phi were highest in numbers. The average protein length of protein was found to be 279.06 with their corresponding average molecular weight of 31,819.4 kDa. The subcellular localization analysis results showed that proteins were centrally localized in the cytoplasm followed by chloroplast, mitochondria and plastids. Structural analysis revealed the presence of 2 -14 exons in CqGST genes. Most of the proteins possessed two exon one intron organization. MEME analysis identified 15 significantly conserved motifs with a width of 6-50 amino acids. Motifs 1, 3, 2, 5, 6, 8, 9 and 13 were found specifically in tau class family; motifs 3, 4, 5, 6, 7 and 9 were found in phi class gene family, while motifs 3, 4, 13 and 14 were found in metaxin class. Multiple sequence alignment revealed highly conserved N-terminus with active site serine (Ser; S) or cysteine (Cys; C) residue for the activation of GSH binding and GST catalytic activity. The gene loci were found to be unevenly distributed across 18 different chromosomes with a maximum of 17 genes located on chromosome number 7. Dominance of alpha helix was followed by coil, extended strand and beta turns. Gene duplication analysis revealed that segmental duplication and purifying type selection were highest in number and found to be main source of expansion of GST gene family. Cis acting regulatory elements analysis showed the presence of 21 different elements involved in stress, hormone and light response and cellular development. The evolutionary relationship of CqGST proteins carried out using maximum likelihood method revealed that all the tau and phi class GSTs were closely associated with those of G. max, O. sativa and A. thaliana. Molecular docking of GST molecules with the fungicide metalaxyl showed that the CqGSTF1 had the lowest binding energy. The comprehensive study of CqGST gene family in quinoa provides groundwork for further functional analysis of CqGST genes in the species at molecular level and has potential applications in plant breeding.

Genome-Wide Analysis of WRKY Transcription Factors Involved in Abiotic Stress and ABA Response in Caragana korshinskii

The WRKY transcription factor family plays a vital role in plant development and environmental response. However, the information of WRKY genes at the genome-wide level is rarely reported in Caragana korshinskii. In this study, we identified and renamed 86 CkWRKY genes, which were further classified into three groups through phylogenetic analysis. Most of these WRKY genes were clustered and distributed on eight chromosomes. Multiple sequence alignment revealed that the conserved domain (WRKYGQK) of the CkWRKYs was basically consistent, but there were also six variation types (WRKYGKK, GRKYGQK, WRMYGQK, WRKYGHK, WKKYEEK and RRKYGQK) that appeared. The motif composition of the CkWRKYs was quite conservative in each group. In general, the number of WRKY genes gradually increased from lower to higher plant species in the evolutionary analysis of 28 species, with some exceptions. Transcriptomics data and RT-qPCR analysis showed that the CkWRKYs in different groups were involved in abiotic stresses and ABA response. Our results provided a basis for the functional characterization of the CkWRKYs involved in stress resistance in C. korshinskii.

Genome-wide identification and comparative expression profiling of the WRKY transcription factor family in two Citrus species with different Candidatus Liberibacter asiaticus susceptibility

BACKGROUND

Salicylic Acid (SA) is a pivotal phytohormone in plant innate immunity enhancement of triggered by various pathogens, such as Candidatus Liberibacter asiaticus (CLas), the causal agent of Huanglongbing (HLB). WRKY is a plant specific transcription factor (TF) family, which plays crucial roles in plant response to biotic stresses. So far, the evolutionary history, functions, and expression patterns under SA treatment and CLas infection of WRKY family are poorly understood in Citrus, despite the release of the genome of several Citrus species. A comprehensive genomic and expressional analysis is worth to conduct for this family.

RESULTS

Here, a genome-wide identification of WRKY TFs was performed in two Citrus species: Citrus sinensis (HLB-sensitive) and Poncirus trifoliata (HLB-tolerant). In total, 52 CsWRKYs and 51 PtrWRKYs were identified, whose physical and chemical properties, chromosome locations, phylogenetic relationships and structural characteristics were comparatively analyzed. Especially, expression patterns of these WRKY genes before and after SA treatment and CLas infection were compared. Based on this result, seven pairs of orthologous WRKY genes showing opposite expression patterns in two Citrus species were screened out. Moreover, two pairs of orthologous WRKY genes with significant differences in the number or type of stress-responsive cis-elements in the promoter regions were discovered. Subcellular localization and transcriptional activation activity assays revealed that these two pairs of orthologous genes are classic WRKY TFs localize in the nucleus and could function as transcriptional activators.

CONCLUSION

In this study, we systematically analyzed the genomic characterization of WRKY family in two Citrus species, together with the analyses of expression patterns under SA signaling and CLas infection. Our study laid a foundation for further study on the function of WRKY TFs in HLB response and SA signaling of Citrus.

Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by Penicillium digitatum

WRKY transcription factors (TFs) play a vital role in plant stress signal transduction and regulate the expression of various stress resistance genes. Sweet orange (Citrus sinensis) accounts for a large proportion of the world's citrus industry, which has high economic value, while Penicillium digitatum is a prime pathogenic causing postharvest rot of oranges. There are few reports on how CsWRKY TFs play their regulatory roles after P. digitatum infects the fruit. In this study, we performed genome-wide identification, classification, phylogenetic and conserved domain analysis of CsWRKY TFs, visualized the structure and chromosomal localization of the encoded genes, explored the expression pattern of each CsWRKY gene under P. digitatum stress by transcriptome data, and made the functional prediction of the related genes. This study provided insight into the characteristics of 47 CsWRKY TFs, which were divided into three subfamilies and eight subgroups. TFs coding genes were unevenly distributed on nine chromosomes. The visualized results of the intron-exon structure and domain are closely related to phylogeny, and widely distributed cis-regulatory elements on each gene played a global regulatory role in gene expression. The expansion of the CSWRKY TFs family was probably facilitated by twenty-one pairs of duplicated genes, and the results of Ka/Ks calculations indicated that this gene family was primarily subjected to purifying selection during evolution. Our transcriptome data showed that 95.7% of WRKY genes were involved in the transcriptional regulation of sweet orange in response to P. digitatum infection. We obtained 15 differentially expressed genes and used the reported function of AtWRKY genes as references. They may be involved in defense against P. digitatum and other pathogens, closely related to the stress responses during plant growth and development. Two interesting genes, CsWRKY2 and CsWRKY14, were expressed more than 60 times and could be used as excellent candidate genes in sweet orange genetic improvement. This study offers a theoretical basis for the response of CSWRKY TFs to P. digitatum infection and provides a vital reference for molecular breeding.

Genome-Wide Identification and Characterization of SPL Family Genes in Chenopodium quinoa

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode a large family of plant-specific transcription factors that play important roles in plant growth, development, and stress responses. However, there is little information available on SPL genes in Chenopodiaceae. Here, 23 SPL genes were identified and characterized in the highly nutritious crop Chenopodium quinoa. Chromosome localization analysis indicated that the 23 CqSPL genes were unevenly distributed on 12 of 18 chromosomes. Two zinc finger-like structures and a nuclear location signal were present in the SBP domains of all CqSPLs, with the exception of CqSPL21/22. Phylogenetic analysis revealed that these genes were classified into eight groups (group I–VIII). The exon–intron structure and motif composition of the genes in each group were similar. Of the 23 CqSPLs, 13 were potential targets of miR156/7. In addition, 5 putative miR156-encoding loci and 13 putative miR157-encoding loci were predicted in the quinoa genome, and they were unevenly distributed on chromosome 1–4. The expression of several Cqu-MIR156/7 loci was confirmed by reverse transcription polymerase chain reaction in seedlings. Many putative cis-elements associated with light, stress, and phytohormone responses were identified in the promoter regions of CqSPLs, suggesting that CqSPL genes are likely involved in the regulation of key developmental processes and stress responses. Expression analysis revealed highly diverse expression patterns of CqSPLs among tissues. Many CqSPLs were highly expressed in leaves, flowers, and seeds, and their expression levels were low in the roots, suggesting that CqSPLs play distinct roles in the development and growth of quinoa. The expression of 13 of 23 CqSPL genes responded to salt treatment (11 up-regulated and 2 down-regulated). A total of 22 of 23 CqSPL genes responded to drought stress (21 up-regulated and 1 down-regulated). Moreover, the expression of 14 CqSPL genes was significantly altered following cadmium treatment (3 up-regulated and 11 down-regulated). CqSPL genes are thus involved in quinoa responses to salt/drought and cadmium stresses. These findings provide new insights that will aid future studies of the biological functions of CqSPLs in C. quinoa.

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 Characterization of the WRKY Gene Family in Scutellaria baicalensis Georgi under Diverse Abiotic Stress

The WRKY gene family is an important inducible regulatory factor in plants, which has been extensively studied in many model plants. It has progressively become the focus of investigation for the secondary metabolites of medicinal plants. Currently, there is no systematic analysis of the WRKY gene family in Scutellaria baicalensis Georgi. For this study, a systematic and comprehensive bioinformatics analysis of the WRKY gene family was conducted based on the genomic data of S. baicalensis. A total of 77 WRKY members were identified and 75 were mapped onto nine chromosomes, respectively. Their encoded WRKY proteins could be classified into three subfamilies: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III, based on the characteristics of the amino acid sequences of the WRKY domain and genetic structure. Syntenic analysis revealed that there were 35 pairs of repetitive fragments. Furthermore, the transcriptome data of roots, stems, leaves, and flowers showed that the spatial expression profiles of WRKYs were different. qRT-PCR analysis revealed that 11 stress-related WRKYs exhibited specific expression patterns under diverse treatments. In addition, sub cellular localization analysis indicated that SbWRKY26 and SbWRKY41 were localized in nucleus. This study is the first to report the identification and characterization of the WRKY gene family in S. baicalensis, which is valuable for the further exploration of the biological function of SbWRKYs. It also provides valuable bioinformatics data for S. baicalensis and provides a reference for assessing the medicinal properties of the genus.

Approaches Involved in the Vegetable Crops Salt Stress Tolerance Improvement: Present Status and Way Ahead

Salt stress is one of the most important abiotic stresses as it persists throughout the plant life cycle. The productivity of crops is prominently affected by soil salinization due to faulty agricultural practices, increasing human activities, and natural processes. Approximately 10% of the total land area (950 Mha) and 50% of the total irrigated area (230 Mha) in the world are under salt stress. As a consequence, an annual loss of 12 billion US$ is estimated because of reduction in agriculture production inflicted by salt stress. The severity of salt stress will increase in the upcoming years with the increasing world population, and hence the forced use of poor-quality soil and irrigation water. Unfortunately, majority of the vegetable crops, such as bean, carrot, celery, eggplant, lettuce, muskmelon, okra, pea, pepper, potato, spinach, and tomato, have very low salinity threshold (ECt, which ranged from 1 to 2.5 dS m-1 in saturated soil). These crops used almost every part of the world and lakes' novel salt tolerance gene within their gene pool. Salt stress severely affects the yield and quality of these crops. To resolve this issue, novel genes governing salt tolerance under extreme salt stress were identified and transferred to the vegetable crops. The vegetable improvement for salt tolerance will require not only the yield influencing trait but also target those characters or traits that directly influence the salt stress to the crop developmental stage. Genetic engineering and grafting is the potential tool which can improve salt tolerance in vegetable crop regardless of species barriers. In the present review, an updated detail of the various physio-biochemical and molecular aspects involved in salt stress have been explored.

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

BACKGROUND

Liriodendron 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.

RESULTS

In 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.

CONCLUSIONS

This 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.

Rewilding staple crops for the lost halophytism: Toward sustainability and profitability of agricultural production systems

Abiotic stress tolerance has been weakened during the domestication of all major staple crops. Soil salinity is a major environmental constraint that impacts over half of the world population; however, given the increasing reliance on irrigation and the lack of available freshwater, agriculture in the 21st century will increasingly become saline. Therefore, global food security is critically dependent on the ability of plant breeders to create high-yielding staple crop varieties that will incorporate salinity tolerance traits and account for future climate scenarios. Previously, we have argued that the current agricultural practices and reliance on crops that exclude salt from uptake is counterproductive and environmentally unsustainable, and thus called for a need for a major shift in a breeding paradigm to incorporate some halophytic traits that were present in wild relatives but were lost in modern crops during domestication. In this review, we provide a comprehensive physiological and molecular analysis of the key traits conferring crop halophytism, such as vacuolar Na⁺ sequestration, ROS desensitization, succulence, metabolic photosynthetic switch, and salt deposition in trichomes, and discuss the strategies for incorporating them into elite germplasm, to address a pressing issue of boosting plant salinity tolerance.

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.

A cysteine-rich receptor-like protein kinase CaCKR5 modulates immune response against Ralstonia solanacearum infection in pepper

BACKGROUND

Cysteine-rich receptor-like kinases (CRKs) represent a large subfamily of receptor-like kinases and play vital roles in diverse physiological processes in regulating plant growth and development.

RESULTS

CaCRK5 transcripts were induced in pepper upon the infection of Ralstonia solanacearum and treatment with salicylic acid. The fusions between CaCRK5 and green fluorescence protein were targeted to the plasma membrane. Suppression of CaCRK5 via virus-induced gene silencing (VIGS) made pepper plants significantly susceptible to R. solanacearum infection, which was accompanied with decreased expression of defense related genes CaPR1, CaSAR8.2, CaDEF1 and CaACO1. Overexpression of CaCRK5 increased resistance against R. solanacearum in Nicotiana benthamiana. Furthermore, electrophoretic mobility shift assay and chromatin immunoprecipitation coupled with quantitative real-time PCR analysis revealed that a homeodomain zipper I protein CaHDZ27 can active the expression of CaCRK5 through directly binding to its promoter. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) analyses suggested that CaCRK5 heterodimerized with the homologous member CaCRK6 on the plasma membrane.

CONCLUSIONS

Our data revealed that CaCRK5 played a positive role in regulating immune responses against R. solanacearum infection in pepper.

Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)

Trehalose-6-phosphate synthase (TPS) is significant in the growth, development and stress resistance of plants. We identified the cucumber TPS family and its physicochemical properties, domains, gene structures, evolutionary relationships, gene locations, cis-acting elements, conserved motifs, and expression patterns using bioinformatics. Our results uncovered seven CsTPS genes in the cucumber genome and named CsTPS1-CsTPS7 according to their locations in the chromosomes. Seven CsTPS genes were randomly distributed in six cucumber chromosomes. Domain analysis showed that the TPS and TPP domains exist in all CsTPSs, and an additional hydrolase-3 domain exist in CsTPS3, CsTPS5 and CsTPS6. Phylogenetic analysis showed that TPS proteins from Arabidopsis, rice, soybean, and cucumber were divided into two subfamilies (Class I and Class II) and they were further divided into seven subgroups. TPS proteins from Arabidopsis and cucumber were grouped together, suggesting a close evolutionary relationship. Gene structure analysis indicated that most Class I genes contained 16-17 introns, while Class II genes (except CsTPS7) had two introns. Motif analysis showed that Class II genes had 10 complete conserved motifs, while Class I genes lacked motif 8 and motif 9. Furthermore, CsTPS genes possessed numerous cis-acting elements related to stress, hormone, and light response in the promoter regions. GO analysis indicated multiple functions for the CsTPS proteins. Expression analysis of CsTPS genes in different tissues found that they were expressed in roots, stems and leaves, with the highest expression levels in roots. The expression analysis of CsTPSs under different treatments showed that CsTPS genes may participate in the response to abiotic stress, plant hormones and sugar treatments.

Molecular Evolution and Local Root Heterogeneous Expression of the Chenopodium quinoa ARF Genes Provide Insights into the Adaptive Domestication of Crops in Complex Environments

Auxin response factors (ARFs) influence plant growth and development via the coupling of basic biological processes. However, the evolution, expansion, and regulatory mechanisms of ARFs in the domesticated crop quinoa after artificial selection remain elusive. In this study, we systematically identified 30 Chenopodium quinoa ARFs (CqARFs). In this typical domesticated crop, ARFs divided into three subfamilies are subjected to strong purification selection and have a highly conserved evolutionary pattern. Polyploidy is the primary reason for the expansion of the ARF family after quinoa domestication. The expression patterns of CqARFs in different tissues have been differentiated, and CqARF2, 5, 9 and 10 from class A have the characteristics of local heterogeneous expression in different regions of roots, which may be the key factors for crops to respond in complex environments. Overall, we examined the evolution and expansion of ARFs in representative domesticated crops using the genome, transcriptome, and molecular biology and discovered a class A ARF-centered heterogeneous expression network that played an important role in auxin signaling and environmental responses. We provide new insights into how ARFs promote domesticated crop adaptation to artificial selection by polyploid expansion.

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.