Genome-wide characterization of JASMONATE-ZIM DOMAIN transcription repressors in wheat (Triticum aestivum L.)

Identification of Salt-Stress-Responding Genes by Weighted Gene Correlation Network Analysis and Association Analysis in Wheat Leaves

The leaf is not only the main site of photosynthesis, but also an important organ reflecting plant salt tolerance. Discovery of salt-stress-responding genes in the leaf is of great significance for the molecular improvement of salt tolerance in wheat varieties. In this study, transcriptome sequencing was conducted on the leaves of salt-tolerant wheat germplasm CH7034 seedlings at 0, 1, 6, 24, and 48 h after NaCl treatment. Based on weighted gene correlation network analysis of differentially expressed genes (DEGs) under salt stress, 12 co-expression modules were obtained, of which, 9 modules containing 4029 DEGs were related to the salt stress time-course. These DEGs were submitted to the Wheat Union database, and a total of 904,588 SNPs were retrieved from 114 wheat germplasms, distributed on 21 wheat chromosomes. Using the R language package and GAPIT program, association analysis was performed between 904,588 SNPs and leaf salt injury index of 114 wheat germplasms. The results showed that 30 single nucleotide polymorphisms (SNPs) from 15 DEGs were associated with salt tolerance. Then, nine candidate genes, including four genes (TaBAM, TaPGDH, TaGluTR, and TaAAP) encoding enzymes as well as five genes (TaB12D, TaS40, TaPPR, TaJAZ, and TaWRKY) encoding functional proteins, were identified by converting salt tolerance-related SNPs into Kompetitive Allele-Specifc PCR (KASP) markers for validation. Finally, interaction network prediction was performed on TaBAM and TaAAP, both belonging to the Turquoise module. Our results will contribute to a further understanding of the salt stress response mechanism in plant leaves and provide candidate genes and molecular markers for improving salt-tolerant wheat varieties.

The wheat pathogenesis-related protein (TdPR1.2) enhanced tolerance to abiotic and biotic stresses in transgenic Arabidopsis plants

In plants, the pathogenesis-related (PR) proteins have been identified as important regulators of biotic and abiotic stresses. PR proteins branch out into 19 different classes (PR1-PR19). Basically, all PR proteins display a well-established method of action, with the notable exception of PR1, which is a member of a large superfamily of proteins with a common CAP domain. We have previously isolated and characterized the first PR1 from durum wheat, called TdPR-1.2. In the current research work, TdPR1.2 gene was used to highlight its functional activities under various abiotic (sodium chloride (100 mM NaCl) and oxidative stresses (3 mM H2O2), hormonal salicylic acid (SA), abscisic acid (ABA) and jasmonic acid (JA), and abiotic stresses (Botrytis cinerea and Alternaria solani). Enhancement survival index was detected in Arabidopsis transgenic plants expressing TdPR1.2 gene. Moreover, quantitative real-time reverse transcription PCR (qRT-PCR) analysis demonstrated induction of antioxidant enzymes such as catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD). It equally revealed a decrease of malondialdehyde (MDA) as well as hydrogen peroxide (H2O2) levels in transgenic Arabidopsis plants compared to control lines, confirming the role of TdPR1.2 in terms of alleviating biotic and abiotic stresses in transgenic Arabidopsis plants. Eventually, RT-qPCR results showed a higher expression of biotic stress-related genes (PR1 and PDF1.2) in addition to a downregulation of the wound-related gene (LOX3 and VSP2) in transgenic lines treated with jasmonic acid (JA). Notably, these findings provide evidence for the outstanding functions of PR1.2 from durum wheat which can be further invested to boost tolerance in crop plants to abiotic and biotic stresses.

CwJAZ4/9 negatively regulates jasmonate-mediated biosynthesis of terpenoids through interacting with CwMYC2 and confers salt tolerance in Curcuma wenyujin

Plant JASMONATE ZIM-DOMAIN (JAZ) genes play crucial roles in regulating the biosynthesis of specialized metabolites and stressful responses. However, understanding of JAZs controlling these biological processes lags due to numerous JAZ copies. Here, we found that two leaf-specific CwJAZ4/9 genes from Curcuma wenyujin are strongly induced by methyl-jasmonate (MeJA) and negatively correlated with terpenoid biosynthesis. Yeast two-hybrid, luciferase complementation imaging and in vitro pull-down assays confirmed that CwJAZ4/9 proteins interact with CwMYC2 to form the CwJAZ4/9-CwMYC2 regulatory cascade. Furthermore, transgenic hairy roots showed that CwJAZ4/9 acts as repressors of MeJA-induced terpenoid biosynthesis by inhibiting the terpenoid pathway and jasmonate response, thus reducing terpenoid accumulation. In addition, we revealed that CwJAZ4/9 decreases salt sensitivity and sustains the growth of hairy roots under salt stress by suppressing the salt-mediated jasmonate responses. Transcriptome analysis for MeJA-mediated transgenic hairy root lines further confirmed that CwJAZ4/9 negatively regulates the terpenoid pathway genes and massively alters the expression of genes related to salt stress signaling and responses, and crosstalks of multiple phytohormones. Altogether, our results establish a genetic framework to understand how CwJAZ4/9 inhibits terpenoid biosynthesis and confers salt tolerance, which provides a potential strategy for producing high-value pharmaceutical terpenoids and improving resistant C. wenyujin varieties by a genetic approach.

Genome-wide identification of JAZ gene family members in autotetraploid cultivated alfalfa (Medicago sativa subsp. sativa) and expression analysis under salt stress

BACKGROUND

Jasmonate ZIM-domain (JAZ) proteins, which act as negative regulators in the jasmonic acid (JA) signalling pathway, have significant implications for plant development and response to abiotic stress.

RESULTS

Through a comprehensive genome-wide analysis, a total of 20 members of the JAZ gene family specific to alfalfa were identified in its genome. Phylogenetic analysis divided these 20 MsJAZ genes into five subgroups. Gene structure analysis, protein motif analysis, and 3D protein structure analysis revealed that alfalfa JAZ genes in the same evolutionary branch share similar exon‒intron, motif, and 3D structure compositions. Eight segmental duplication events were identified among these 20 MsJAZ genes through collinearity analysis. Among the 32 chromosomes of the autotetraploid cultivated alfalfa, there were 20 MsJAZ genes distributed on 17 chromosomes. Extensive stress-related cis-acting elements were detected in the upstream sequences of MsJAZ genes, suggesting that their response to stress has an underlying function. Furthermore, the expression levels of MsJAZ genes were examined across various tissues and under the influence of salt stress conditions, revealing tissue-specific expression and regulation by salt stress. Through RT‒qPCR experiments, it was discovered that the relative expression levels of these six MsJAZ genes increased under salt stress.

CONCLUSIONS

In summary, our study represents the first comprehensive identification and analysis of the JAZ gene family in alfalfa. These results provide important information for exploring the mechanism of JAZ genes in alfalfa salt tolerance and identifying candidate genes for improving the salt tolerance of autotetraploid cultivated alfalfa via genetic engineering in the future.

Comprehensive Comparative Analysis of the JAZ Gene Family in Common Wheat (Triticum aestivum) and Its D-Subgenome Donor Aegilops tauschii

JASMONATE-ZIM DOMAIN (JAZ) repressor proteins work as co-receptors in the jasmonic acid (JA) signalling pathway and are essential for plant development and environmental adaptation. Despite wheat being one of the main staple food crops, until recently, comprehensive analysis of its JAZ gene family has been limited due to the lack of complete and high-quality reference genomes. Here, using the latest reference genome, we identified 17 JAZ genes in the wheat D-genome donor Aegilops tauschii. Then, 54 TaJAZs were identified in common wheat. A systematic examination of the gene structures, conserved protein domains, and phylogenetic relationships of this gene family was performed. Five new JAZ genes were identified as being derived from tandem duplication after wheat divergence from other species. We integrated RNA-seq data and yield QTL information and found that tandemly duplicated TaJAZ genes were prone to association with spike-related traits. Moreover, 12 TaJAZ genes were located within breeding selection sweeps, including 9 tandemly duplicated ones. Haplotype variation analysis of selected JAZ genes showed significant association of TaJAZ7A and TaJAZ13A with thousand-grain weight. Our work provides a clearer picture of wheat JAZ gene evolution and puts forward the possibility of using these genes for wheat yield improvement.

Comprehensive analysis of JAZ family members in Ginkgo biloba reveals the regulatory role of the GbCOI1/GbJAZs/GbMYC2 module in ginkgolide biosynthesis

Ginkgo biloba L., an ancient relict plant known as a 'living fossil', has a high medicinal and nutritional value in its kernels and leaves. Ginkgolides are unique diterpene lactone compounds in G. biloba, with favorable therapeutic effects on cardiovascular and cerebrovascular diseases. Thus, it is essential to study the biosynthesis and regulatory mechanism of ginkgolide, which will contribute to quality improvement and medication requirements. In this study, the regulatory roles of the JAZ gene family and GbCOI1/GbJAZs/GbMYC2 module in ginkgolide biosynthesis were explored based on genome and methyl jasmonate-induced transcriptome. Firstly, 18 JAZ proteins were identified from G. biloba, and the gene characteristics and expansion patterns along with evolutionary relationships of these GbJAZs were analyzed systematically. Expression patterns analysis indicated that most GbJAZs expressed highly in the fibrous root and were induced significantly by methyl jasmonate. Mechanistically, yeast two-hybrid assays suggested that GbJAZ3/11 interacted with both GbMYC2 and GbCOI1, and several GbJAZ proteins could form homodimers or heterodimers between the GbJAZ family. Moreover, GbMYC2 is directly bound to the G-box element in the promoter of GbLPS, to regulate the biosynthesis of ginkgolide. Collectively, these results systematically characterized the JAZ gene family in G. biloba and demonstrated that the GbCOI1/GbJAZs/GbMYC2 module could regulate ginkgolides biosynthesis, which provides a novel insight for studying the mechanism of JA regulating ginkgolide biosynthesis.

OsRuvBL1a DNA helicase boost salinity and drought tolerance in transgenic indica rice raised by in planta transformation

RuvBL, is a member of SF6 superfamily of helicases and is conserved among the various model systems. Recently, rice (Oryza sativa L.) homolog of RuvBL has been biochemically characterized for its ATPase and DNA helicase activities; however its involvement in stress has not been studied so far. Present investigation reports the detailed functional characterization of OsRuvBL under abiotic stresses through genetic engineering. An efficient Agrobacterium-mediated in planta transformation protocol was developed in indica rice to generate the transgenic lines and study was focused on optimization of factors to achieve maximum transformation efficiency. Overexpressing OsRuvBL1a transgenic lines showed enhanced tolerance under in vivo salinity stress as compared to WT plants. The physiological and biochemical analysis of the OsRuvBL1a transgenic lines showed better performance under salinity and drought stresses. Several stress responsive interacting partners of OsRuvBL1a were identified using Y2H system revealed to its role in stress tolerance. Functional mechanism for boosting stress tolerance by OsRuvBL1a has been proposed in this study. This integration of OsRuvBL1a gene in rice genome using in planta transformation method helped to achieve the abiotic stress resilient smart crop. This study is the first direct evidence to show the novel function of RuvBL in boosting abiotic stress tolerance in plants.

Genome-Wide Identification and Functional Analysis of the TIFY Family Genes in Response to Abiotic Stresses and Hormone Treatments in Tartary Buckwheat (Fagopyrum tataricum)

TIFY is a plant-specific gene family with four subfamilies: ZML, TIFY, PPD, and JAZ. Recently, this family was found to have regulatory functions in hormone stimulation, environmental response, and development. However, little is known about the roles of the TIFY family in Tartary buckwheat (Fagopyrum tataricum), a significant crop for both food and medicine. In this study, 18 TIFY family genes (FtTIFYs) in Tartary buckwheat were identified. The characteristics, motif compositions, and evolutionary relationships of the TIFY proteins, as well as the gene structures, cis-acting elements, and synteny of the TIFY genes, are discussed in detail. Moreover, we found that most FtTIFYs responded to various abiotic stresses (cold, heat, salt, or drought) and hormone treatments (ABA, MeJA, or SA). Through yeast two-hybrid assays, we revealed that two FtTIFYs, FtTIFY1 and FtJAZ7, interacted with FtABI5, a homolog protein of AtABI5 involved in ABA-mediated germination and stress responses, implying crosstalk between ABA and JA signaling in Tartary buckwheat. Furthermore, the overexpression of FtJAZ10 and FtJAZ12 enhanced the heat stress tolerance of tobacco. Consequently, our study suggests that the FtTIFY family plays important roles in responses to abiotic stress and provides two candidate genes (FtJAZ10 and FtJAZ12) for the cultivation of stress-resistant crops.

Revealing the Roles of the JAZ Family in Defense Signaling and the Agarwood Formation Process in Aquilaria sinensis

Jasmonate ZIM-domain family proteins (JAZs) are repressors in the signaling cascades triggered by jasmonates (JAs). It has been proposed that JAs play essential roles in the sesquiterpene induction and agarwood formation processes in Aquilaria sinensis. However, the specific roles of JAZs in A. sinensis remain elusive. This study employed various methods, including phylogenetic analysis, real-time quantitative PCR, transcriptomic sequencing, yeast two-hybrid assay, and pull-down assay, to characterize A. sinensis JAZ family members and explore their correlations with WRKY transcription factors. The bioinformatic analysis revealed twelve putative AsJAZ proteins in five groups and sixty-four putative AsWRKY transcription factors in three groups. The AsJAZ and AsWRKY genes exhibited various tissue-specific or hormone-induced expression patterns. Some AsJAZ and AsWRKY genes were highly expressed in agarwood or significantly induced by methyl jasmonate in suspension cells. Potential relationships were proposed between AsJAZ4 and several AsWRKY transcription factors. The interaction between AsJAZ4 and AsWRKY75n was confirmed by yeast two-hybrid and pull-down assays. This study characterized the JAZ family members in A. sinensis and proposed a model of the function of the AsJAZ4/WRKY75n complex. This will advance our understanding of the roles of the AsJAZ proteins and their regulatory pathways.

Goss's Wilt Resistance in Corn Is Mediated via Salicylic Acid and Programmed Cell Death but Not Jasmonic Acid Pathways

A highly aggressive strain (CMN14-5-1) of Clavibacter nebraskensis bacteria, which causes Goss's wilt in corn, induced severe symptoms in a susceptible corn line (CO447), resulting in water-soaked lesions followed by necrosis within a few days. A tolerant line (CO450) inoculated with the same strain exhibited only mild symptoms such as chlorosis, freckling, and necrosis that did not progress after the first six days following infection. Both lesion length and disease severity were measured using the area under the disease progression curve (AUDPC), and significant differences were found between treatments. We analyzed the expression of key genes related to plant defense in both corn lines challenged with the CMN14-5-1 strain. Allene oxide synthase (ZmAOS), a gene responsible for the production of jasmonic acid (JA), was induced in the CO447 line in response to CMN14-5-1. Following inoculation with CMN14-5-1, the CO450 line demonstrated a higher expression of salicylic acid (SA)-related genes, ZmPAL and ZmPR-1, compared to the CO447 line. In the CO450 line, four genes related to programmed cell death (PCD) were upregulated: respiratory burst oxidase homolog protein D (ZmrbohD), polyphenol oxidase (ZmPPO1), ras-related protein 7 (ZmRab7), and peptidyl-prolyl cis-trans isomerase (ZmPPI). The differential gene expression in response to CMN14-5-1 between the two corn lines provided an indication that SA and PCD are involved in the regulation of corn defense responses against Goss's wilt disease, whereas JA may be contributing to disease susceptibility.

Combating powdery mildew: Advances in molecular interactions between Blumeria graminis f. sp. tritici and wheat

Wheat powdery mildew caused by a biotrophic fungus Blumeria graminis f. sp. tritici (Bgt), is a widespread airborne disease which continues to threaten global wheat production. One of the most chemical-free and cost-effective approaches for the management of wheat powdery mildew is the exploitation of resistant cultivars. Accumulating evidence has reported that more than 100 powdery mildew resistance genes or alleles mapping to 63 different loci (Pm1-Pm68) have been identified from common wheat and its wild relatives, and only a few of them have been cloned so far. However, continuous emergence of new pathogen races with novel degrees of virulence renders wheat resistance genes ineffective. An essential breeding strategy for achieving more durable resistance is the pyramiding of resistance genes into a single genotype. The genetics of host-pathogen interactions integrated with temperature conditions and the interaction between resistance genes and their corresponding pathogen a virulence genes or other resistance genes within the wheat genome determine the expression of resistance genes. Considerable progress has been made in revealing Bgt pathogenesis mechanisms, identification of resistance genes and breeding of wheat powdery mildew resistant cultivars. A detailed understanding of the molecular interactions between wheat and Bgt will facilitate the development of novel and effective approaches for controlling powdery mildew. This review gives a succinct overview of the molecular basis of interactions between wheat and Bgt, and wheat defense mechanisms against Bgt infection. It will also unleash the unsung roles of epigenetic processes, autophagy and silicon in wheat resistance to Bgt.

Overexpression of TaMYC2 confers freeze tolerance by ICE-CBF-COR module in Arabidopsis thaliana

Dongnongdongmai No.1 (Dn1) is one of the few winter wheat varieties that can successfully overwinter at temperatures as low as -25°C or even lower. To date, few researches were carried to identify the freeze tolerance genes in Dn1 and applied them to improve plant resistance to extreme low temperatures. The basic helix-loop-helix (bHLH) transcription factor MYC2 is a master regulator in JA signaling, which has been reported to involve in responses to mild cold stress (2°C and 7°C). We hypothesized that MYC2 might be part of the regulatory network responsible for the tolerance of Dn1 to extreme freezing temperatures. In this study, we showed that wheat MYC2 (TaMYC2) was induced under both extreme low temperature (-10°C and-25°C) and JA treatments. The ICE-CBF-COR transcriptional cascade, an evolutionary conserved cold resistance pathway downstream of MYC2, was also activated in extreme low temperatures. We further showed that overexpression of any of the MYC2 genes from Dn1 TaMYC2A, B, D in Arabidopsis led to enhanced freeze tolerance. The TaMYC2 overexpression lines had less electrolyte leakage and lower malondialdehyde (MDA) content, and an increase in proline content, an increases antioxidant defences, and the enhanced expression of ICE-CBF-COR module under the freezing temperature. We further verified that TaMYC2 might function through physical interaction with TaICE41 and TaJAZ7, and that TaJAZ7 physically interacts with TaICE41. These results elucidate the molecular mechanism by which TaMYC2 regulates cold tolerance and lay the foundation for future studies to improve cold tolerance in plants.

Comparative Transcriptome Analysis Reveals Hormone Signal Transduction and Sucrose Metabolism Related Genes Involved in the Regulation of Anther Dehiscence in Photo-Thermo-Sensitive Genic Male Sterile Wheat

Anther dehiscence is an important process to release pollen and then is a critical event in pollination. In the wheat photo-thermo-sensitive genic male sterility (PTGMS) line, pollen cannot release from anther since the anther cannot dehisce during anther dehiscence stage in a sterile condition. In this study, we carried out RNA-sequencing to analyze the transcriptome of one wheat PTGMS line BS366 during anther dehiscence under fertile and sterile conditions to explore the mechanism. We identified 6306 differentially expressed genes (DEGs). Weighted gene co-expression network analysis (WGCNA) and KEGG analysis showed that DEGs were mainly related to “hormone signal transduction pathway” and “starch and sucrose metabolism”. We identified 35 and 23 DEGs related hormone signal transduction and sucrose metabolism, respectively. Compared with conventional wheat Jing411, there were some changes in the contents of hormones, including JA, IAA, BR, ABA and GA3, and sucrose, during three anther dehiscence stages in the sterile condition in BS366. We performed qRT-PCR to verify the expression levels of some critical DEGs of the hormone signaling pathway and the starch and sucrose metabolism pathway. The results showed disparate expression patterns of the critical DEGs of the hormone signaling pathway and the starch and sucrose metabolism pathway in different conditions, suggesting these genes may be involved in the regulation of the anther dehiscence in BS366. Finally, we conducted a hypothesis model to reveal the regulation pathway of hormones and sucrose on anther dehiscence. The information provided new clues to the molecular mechanisms of anther dehiscence in wheat and improved wheat hybrid breeding.

Genome wide Identification and Characterization of Wheat GH9 Genes Reveals Their Roles in Pollen Development and Anther Dehiscence

Glycoside hydrolase family 9 (GH9) is a key member of the hydrolase family in the process of cellulose synthesis and hydrolysis, playing important roles in plant growth and development. In this study, we investigated the phenotypic characteristics and gene expression involved in pollen fertility conversion and anther dehiscence from a genomewide level. In total, 74 wheat GH9 genes (TaGH9s) were identified, which were classified into Class A, Class B and Class C and unevenly distributed on chromosomes. We also investigated the gene duplication and reveled that fragments and tandem repeats contributed to the amplification of TaGH9s. TaGH9s had abundant hormone-responsive elements and light-responsive elements, involving JA–ABA crosstalk to regulate anther development. Ten TaGH9s, which highly expressed stamen tissue, were selected to further validate their function in pollen fertility conversion and anther dehiscence. Based on the cell phenotype and the results of the scanning electron microscope at the anther dehiscence period, we found that seven TaGH9s may target miRNAs, including some known miRNAs (miR164 and miR398), regulate the level of cellulose by light and phytohormone and play important roles in pollen fertility and anther dehiscence. Finally, we proposed a hypothesis model to reveal the regulation pathway of TaGH9 on fertility conversion and anther dehiscence. Our study provides valuable insights into the GH9 family in explaining the male sterility mechanism of the wheat photo-thermo-sensitive genetic male sterile (PTGMS) line and generates useful male sterile resources for improving wheat hybrid breeding.

Genetic Mechanisms of Cold Signaling in Wheat (Triticum aestivum L.)

Cold stress is a major environmental factor affecting the growth, development, and productivity of various crop species. With the current trajectory of global climate change, low temperatures are becoming more frequent and can significantly decrease crop yield. Wheat (Triticum aestivum L.) is the first domesticated crop and is the most popular cereal crop in the world. Because of a lack of systematic research on cold signaling pathways and gene regulatory networks, the underlying molecular mechanisms of cold signal transduction in wheat are poorly understood. This study reviews recent progress in wheat, including the ICE-CBF-COR signaling pathway under cold stress and the effects of cold stress on hormonal pathways, reactive oxygen species (ROS), and epigenetic processes and elements. This review also highlights possible strategies for improving cold tolerance in wheat.

Genome-Wide Analysis of the Soybean TIFY Family and Identification of GmTIFY10e and GmTIFY10g Response to Salt Stress

TIFY proteins play crucial roles in plant abiotic and biotic stress responses. Our transcriptome data revealed several TIFY family genes with significantly upregulated expression under drought, salt, and ABA treatments. However, the functions of the GmTIFY family genes are still unknown in abiotic stresses. We identified 38 GmTIFY genes and found that TIFY10 homologous genes have the most duplication events, higher selection pressure, and more obvious response to abiotic stresses compared with other homologous genes. Expression pattern analysis showed that GmTIFY10e and GmTIFY10g genes were significantly induced by salt stress. Under salt stress, GmTIFY10e and GmTIFY10g transgenic Arabidopsis plants showed higher root lengths and fresh weights and had significantly better growth than the wild type (WT). In addition, overexpression of GmTIFY10e and GmTIFY10g genes in soybean improved salt tolerance by increasing the PRO, POD, and CAT contents and decreasing the MDA content; on the contrary, RNA interference plants showed sensitivity to salt stress. Overexpression of GmTIFY10e and GmTIFY10g in Arabidopsis and soybean could improve the salt tolerance of plants, while the RNAi of GmTIFY10e and GmTIFY10g significantly increased sensitivity to salt stress in soybean. Further analysis demonstrated that GmTIFY10e and GmTIFY10g genes changed the expression levels of genes related to the ABA signal pathway, including GmSnRK2, GmPP2C, GmMYC2, GmCAT1, and GmPOD. This study provides a basis for comprehensive analysis of the role of soybean TIFY genes in stress response in the future.

Investigation of the JASMONATE ZIM-DOMAIN Gene Family Reveals the Canonical JA-Signaling Pathway in Pineapple

JASMONATE ZIM-DOMAIN (JAZ) proteins are negative regulators of the jasmonate (JA)-signaling pathway and play pivotal roles in plant resistance to biotic and abiotic stresses. Genome-wide identification of JAZ genes has been performed in many plant species. However, systematic information about pineapple (Ananas comosus L. Merr.) JAZ genes (AcJAZs) is still not available. In this study, we identified 14 AcJAZ genes and classified them into five groups along with the Arabidopsis and rice orthologs. The AcJAZ genes have 3–10 exons, and the putative AcJAZ proteins have between two and eight conserved regions, including the TIFY motif and Jas domain. The cis-acting element analysis revealed that the putative promoter regions of AcJAZs contain between three and eight abiotic stress-responsive cis-acting elements. The gene-expression analysis suggested that AcJAZs were expressed differentially during plant development and subjected to regulation by the cold, heat, salt, and osmotic stresses as well as by phytohormones. Moreover, the BiFC analysis of protein interactions among the central JA-signaling regulators showed that AcJAZ4, AcMYC2, AcNINJA, and AcJAM1 could interact with AcJAZ5 and AcJAZ13 in vivo, indicating a canonical JA-signaling pathway in pineapple. These results increase our understanding of the functions of AcJAZs and the responses of the core players in the JA-signaling pathway to abiotic stresses.

Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment

BACKGROUND

Jasmonate-ZIM domain (JAZ) repressors negatively regulate signal transduction of jasmonates, which regulate plant development and immunity. However, no comprehensive analysis of the JAZ gene family members has been done in the common fig (Ficus carica L.) during fruit development and hormonal treatment.

RESULTS

In this study, 10 non-redundant fig JAZ family genes (FcJAZs) distributed on 7 chromosomes were identified in the fig genome. Phylogenetic and structural analysis showed that FcJAZ genes can be grouped into 5 classes. All the classes contained relatively complete TIFY and Jas domains. Yeast two hybrid (Y2H) results showed that all FcJAZs proteins may interact with the identified transcription factor, FcMYC2. Tissue-specific expression analysis showed that FcJAZs were highly expressed in the female flowers and roots. Expression patterns of FcJAZs during the fruit development were analyzed by RNA-Seq and qRT-PCR. The findings showed that, most FcJAZs were significantly downregulated from stage 3 to 5 in the female flower, whereas downregulation of these genes was observed in the fruit peel from stage 4 to 5. Weighted-gene co-expression network analysis (WGCNA) showed the expression pattern of FcJAZs was correlated with hormone signal transduction and plant-pathogen interaction. Putative cis-elements analysis of FcJAZs and expression patterns of FcJAZs which respond to hormone treatments revealed that FcJAZs may regulate fig fruit development by modulating the effect of ethylene or gibberellin.

CONCLUSIONS

This study provides a comprehensive analysis of the FcJAZ family members and provides information on FcJAZs contributions and their role in regulating the common fig fruit development.

Genome-wide characterization of the sorghum JAZ gene family and their responses to phytohormone treatments and aphid infestation

Jasmonate ZIM-domain (JAZ) proteins are the key repressors of the jasmonic acid (JA) signal transduction pathway and play a crucial role in stress-related defense, phytohormone crosstalk and modulation of the growth-defense tradeoff. In this study, the sorghum genome was analyzed through genome-wide comparison and domain scan analysis, which led to the identification of 18 sorghum JAZ (SbJAZ) genes. All SbJAZ proteins possess the conserved TIFY and Jas domains and they formed a phylogenetic tree with five clusters related to the orthologs of other plant species. Similarly, evolutionary analysis indicated the duplication events as a major force of expansion of the SbJAZ genes and there was strong neutral and purifying selection going on. In silico analysis of the promoter region of the SbJAZ genes indicates that SbJAZ5, SbJAZ6, SbJAZ13, SbJAZ16 and SbJAZ17 are rich in stress-related cis-elements. In addition, expression profiling of the SbJAZ genes in response to phytohormones treatment (JA, ET, ABA, GA) and sugarcane aphid (SCA) was performed in two recombinant inbred lines (RILs) of sorghum, resistant (RIL 521) and susceptible (RIL 609) to SCA. Taken together, data generated from phytohormone expression and in silico analysis suggests the putative role of SbJAZ9 in JA-ABA crosstalk and SbJAZ16 in JA-ABA and JA-GA crosstalk to regulate certain physiological processes. Notably, upregulation of SbJAZ1, SbJAZ5, SbJAZ13 and SbJAZ16 in resistant RIL during JA treatment and SCA infestation suggests putative functions in stress-related defense and to balance the plant defense to promote growth. Overall, this report provides valuable insight into the organization and functional characterization of the sorghum JAZ gene family.

Key Genes in the JAZ Signaling Pathway Are Up-Regulated Faster and More Abundantly in Caterpillar-Resistant Maize

Jasmonic acid (JA) and its derivatives, collectively known as jasmonates (JAs), are important signaling hormones for plant responses against chewing herbivores. In JA signaling networks, jasmonate ZIM-domain (JAZ) proteins are transcriptional repressors that regulate JA-modulated downstream herbivore defenses. JAZ repressors are widely presented in land plants, however, there is only limited information about the regulation/function of JAZ proteins in maize. In this study, we performed a comprehensive expression analysis of ZmJAZ genes with other selected genes in the jasmonate pathway in response to feeding by fall armyworm (Spodoptera frugiperda, FAW), mechanical wounding, and exogenous hormone treatments in two maize genotypes differing in FAW resistance. Results showed that transcript levels of JAZ genes and several key genes in JA-signaling and biosynthesis pathways were rapidly and abundantly expressed in both genotypes in response to these various treatments. However, there were key differences between the two genotypes in the expression of ZmJAZ1 and ZmCOI1a, these two genes were expressed significantly rapidly and abundantly in the resistant line which was tightly regulated by endogenous JA level upon feeding. For instance, transcript levels of ZmJAZ1 increase dramatically within 30 min of FAW-fed Mp708 but not Tx601, correlating with the JA accumulation. The results also demonstrated that wounding or JA treatment alone was not as effective as FAW feeding; this suggests that insect-derived factors are required for optimal defense responses.

Genome-Wide Identification and Expression Analysis of JAZ Family Involved in Hormone and Abiotic Stress in Sweet Potato and Its Two Diploid Relatives

Jasmonate ZIM-domain (JAZ) proteins are key repressors of a jasmonic acid signaling pathway. They play essential roles in the regulation of plant growth and development, as well as environmental stress responses. However, this gene family has not been explored in sweet potato. In this study, we identified 14, 15, and 14 JAZs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90), and its two diploid relatives Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30), respectively. These JAZs were divided into five subgroups according to their phylogenetic relationships with Arabidopsis. The protein physiological properties, chromosome localization, phylogenetic relationship, gene structure, promoter cis-elements, protein interaction network, and expression pattern of these 43 JAZs were systematically investigated. The results suggested that there was a differentiation between homologous JAZs, and each JAZ gene played different vital roles in growth and development, hormone crosstalk, and abiotic stress response between sweet potato and its two diploid relatives. Our work provided comprehensive comparison and understanding of the JAZ genes in sweet potato and its two diploid relatives, supplied a theoretical foundation for their functional study, and further facilitated the molecular breeding of sweet potato.

Transcriptome-Wide Identification and Characterization of the JAZ Gene Family in Mentha canadensis L

Jasmonate ZIM-domain (JAZ) proteins are the crucial transcriptional repressors in the jasmonic acid (JA) signaling process, and they play pervasive roles in plant development, defense, and plant specialized metabolism. Although numerous JAZ gene families have been discovered across several plants, our knowledge about the JAZ gene family remains limited in the economically and medicinally important Chinese herb Mentha canadensis L. Here, seven non-redundant JAZ genes named McJAZ1–McJAZ7 were identified from our reported M. canadensis transcriptome data. Structural, amino acid composition, and phylogenetic analysis showed that seven McJAZ proteins contained the typical zinc-finger inflorescence meristem (ZIM) domain and JA-associated (Jas) domain as conserved as those in other plants, and they were clustered into four groups (A-D) and distributed into five subgroups (A1, A2, B1, B2, and D). Quantitative real-time PCR (qRT-PCR) analysis showed that seven McJAZ genes displayed differential expression patterns in M. canadensis tissues, and preferentially expressed in flowers. Furthermore, the McJAZ genes expression was differentially induced after Methyl jasmonate (MeJA) treatment, and their transcripts were variable and up- or down-regulated under abscisic acid (ABA), drought, and salt treatments. Subcellular localization analysis revealed that McJAZ proteins are localized in the nucleus or cytoplasm. Yeast two-hybrid (Y2H) assays demonstrated that McJAZ1-5 interacted with McCOI1a, a homolog of Arabidopsis JA receptor AtCOI1, in a coronatine-dependent manner, and most of McJAZ proteins could also form homo- or heterodimers. This present study provides valuable basis for functional analysis and exploitation of the potential candidate McJAZ genes for developing efficient strategies for genetic improvement of M. canadensis.

Comprehensive analysis of formin gene family highlights candidate genes related to pollen cytoskeleton and male fertility in wheat (Triticum aestivum L.)

Background

Formin, a highly conserved multi-domain protein, interacts with microfilaments and microtubules. Although specifically expressed formin genes in anthers are potentially significant in research on male sterility and hybrid wheat breeding, similar reports in wheat, especially in thermo-sensitive genic male sterile (TGMS) wheat, remain elusive.

Results

Herein, we systematically characterized the formin genes in TGMS wheat line BS366 named TaFormins (TaFHs) and predicted their functions in inducing stress response. In total, 25 TaFH genes were uncovered, majorly localized in 2A, 2B, and 2D chromosomes. According to the neighbor-joining (NJ) method, all TaFH proteins from wheat and other plants clustered in 6 sub-groups (A-F). The modeled 3D structures of TaFH1-A/B, TaFH2-A/B, TaFH3-A/B and TaFH3-B/D were validated. And different numbers of stress and hormone-responsive regulatory elements in their 1500 base pair promoter regions were contained in the TaFH genes copies. TaFHs had specific temporal and spatial expression characteristics, whereby TaFH1, TaFH4, and TaFH5 were expressed highly in the stamen of BS366. Besides, the accumulation of TaFHs was remarkably lower in a low-temperature sterile condition (Nanyang) than fertile condition (Beijing), particularly at the early stamen development stage. The pollen cytoskeleton of BS366 was abnormal in the three stages under sterile and fertile environments. Furthermore, under different stress levels, TaFHs expression could be induced by drought, salt, abscisic acid (ABA), salicylic acid (SA), methyl jasmonate (MeJA), indole-3-acetic acid (IAA), polyethylene glycol (PEG), and low temperature. Some miRNAs, including miR167, miR1120, and miR172, interacts with TaFH genes; thus, we constructed an interaction network between microRNAs, TaFHs, phytohormone responses, and distribution of cytoskeleton to reveal the regulatory association between upstream genes of TaFH family members and sterile.

Conclusions

Collectively, this comprehensive analysis provides novel insights into TaFHs and miRNA resources for wheat breeding. These findings are, therefore, valuable in understanding the mechanism of TGMS fertility conversion in wheat.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07878-7.

Genome-wide identification, phylogenetic analysis, and expression analysis of the SPL gene family in orchardgrass (Dactylis glomerata L.)

SPL (SQUAMOSA promoter binding protein-like) is a plant-specific transcription factor family that contains the conserved SBP domain, which plays a vital role in the vegetative-to-reproductive phase transition, flowering development and regulation, tillering/branching, and stress responses. Although the SPL family has been identified and characterized in various plant species, limited information about it has been obtained in orchardgrass, which is a critical forage crop worldwide. In this study, 17 putative DgSPL genes were identified among seven chromosomes, and seven groups that share similar gene structures and conserved motifs were determined by phylogenetic analysis. Of these, eight genes have potential target sites for miR156. cis-Element and gene ontology annotation analysis indicated DgSPLs may be involved in regulating development and abiotic stress responses. The expression patterns of eight DgSPL genes at five developmental stages, in five tissues, and under three stress conditions were determined by RNA-seq and qRT-PCR. These assays indicated DgSPLs are involved in vegetative-to-reproductive phase transition, floral development, and stress responses. The transient expression analysis in tobacco and heterologous expression assays in yeast indicated that miR156-targeted DG1G01828.1 and DG0G01071.1 are nucleus-localized proteins, that may respond to drought, salt, and heat stress. Our study represents the first systematic analysis of the SPL family in orchardgrass. This research provides a comprehensive assessment of the DgSPL family, which lays the foundation for further examination of the role of miR156/DgSPL in regulating development and stress responses in forages grasses.

New Insights Into Structure and Function of TIFY Genes in Zea mays and Solanum lycopersicum: A Genome-Wide Comprehensive Analysis

The TIFY gene family, a key plant-specific transcription factor (TF) family, is involved in diverse biological processes including plant defense and growth regulation. Despite TIFY proteins being reported in some plant species, a genome-wide comparative and comprehensive analysis of TIFY genes in plant species can reveal more details. In the current study, the members of the TIFY gene family were significantly increased by the identification of 18 and six new members using maize and tomato reference genomes, respectively. Thus, a genome-wide comparative analysis of the TIFY gene family between 48 tomato (Solanum lycopersicum, a dicot plant) genes and 26 maize (Zea mays, a monocot plant) genes was performed in terms of sequence structure, phylogenetics, expression, regulatory systems, and protein interaction. The identified TIFYs were clustered into four subfamilies, namely, TIFY-S, JAZ, ZML, and PPD. The PPD subfamily was only detected in tomato. Within the context of the biological process, TIFY family genes in both studied plant species are predicted to be involved in various important processes, such as reproduction, metabolic processes, responses to stresses, and cell signaling. The Ka/Ks ratios of the duplicated paralogous gene pairs indicate that all of the duplicated pairs in the TIFY gene family of tomato have been influenced by an intense purifying selection, whereas in the maize genome, there are three duplicated blocks containing Ka/Ks > 1, which are implicated in evolution with positive selection. The amino acid residues present in the active site pocket of TIFY proteins partially differ in each subfamily, although the Mg or Ca ions exist heterogeneously in the centers of the active sites of all the predicted TIFY protein models. Based on the expression profiles of TIFY genes in both plant species, JAZ subfamily proteins are more associated with the response to abiotic and biotic stresses than other subfamilies. In conclusion, globally scrutinizing and comparing the maize and tomato TIFY genes showed that TIFY genes play a critical role in cell reproduction, plant growth, and responses to stress conditions, and the conserved regulatory mechanisms may control their expression.

Genome-Wide Identification of Wheat WRKY Gene Family Reveals That TaWRKY75-A Is Referred to Drought and Salt Resistances

It is well known that WRKY transcription factors play essential roles in plants' response to diverse stress responses, especially to drought and salt stresses. However, a full comprehensive analysis of this family in wheat is still missing. Here we used in silico analysis and identified 124 WRKY genes, including 294 homeologous copies from a high-quality reference genome of wheat (Triticum aestivum). We also found that the TaWRKY gene family did not undergo gene duplication rather than gene loss during the evolutionary process. The TaWRKY family members displayed different expression profiles under several abiotic stresses, indicating their unique functions in the mediation of particular responses. Furthermore, TaWRKY75-A was highly induced after polyethylene glycol and salt treatments. The ectopic expression of TaWRKY75-A in Arabidopsis enhanced drought and salt tolerance. A comparative transcriptome analysis demonstrated that TaWRKY75-A integrated jasmonic acid biosynthetic pathway and other potential metabolic pathways to increase drought and salt resistances in transgenic Arabidopsis. Our study provides valuable insights into the WRKY family in wheat and will generate a useful genetic resource for improving wheat breeding.

Genome-wide identification and expression analysis of jasmonate ZIM domain gene family in tuber mustard (Brassica juncea var. tumida)

Tuber mustard, which is the raw material of Fuling pickle, is a crop with great economic value. However, during growth and development, tuber mustard is frequently attacked by the pathogen Plasmodiophora brassicae and frequently experiences salinity stress. Jasmonic acid (JA) is a hormone related to plant resistance to biotic and abiotic stress. Jasmonate ZIM domain proteins (JAZs) are crucial components of the JA signaling pathway and play important roles in plant responses to biotic and abiotic stress. To date, no information is available about the characteristics of the JAZ family genes in tuber mustard. Here, 38 BjJAZ genes were identified in the whole genome of tuber mustard. The BjJAZ genes are located on 17 of 18 chromosomes in the tuber mustard genome. The gene structures and protein motifs of the BjJAZ genes are conserved between tuber mustard and Arabidopsis. The results of qRT-PCR analysis showed that BjuA030800 was specifically expressed in root, and BjuA007483 was specifically expressed in leaf. In addition, 13 BjJAZ genes were transiently induced by P. brassicae at 12 h, and 7 BjJAZ genes were induced by salt stress from 12 to 24 h. These results provide valuable information for further studies on the role of BjJAZ genes in the regulation of plant growth and development and in the response to biotic and abiotic stress.

The TIFY Gene Family in Wheat and its Progenitors: Genome-wide Identification, Evolution and Expression Analysis

Background:

The TIFY gene family is a group of plant-specific proteins involved in the jasmonate (JA) metabolic process, which plays a vital role in plant growth and development as well as stress response. Although it has been extensively studied in many species, the significance of this family is not well studied in wheat.

Objective:

To comprehensively understand the genome organization and evolution of TIFY family in wheat, a genome-wide identification was performed in wheat and its two progenitors using updated genome information provided here.

Results:

In total, 63, 13 and 17 TIFY proteins were identified in wheat, Triticum urartu and Aegilops tauschii respectively. Phylogenetic analysis clustered them into 18 groups with 14 groups possessing A, B and D copies in wheat, demonstrating the completion of the genome as well as the two rounds of allopolyploidization events. Gene structure, conserved protein motif and cis-regulatory element divergence of A, B, D homoeologous copies were also investigated to gain insight into the evolutionary conservation and divergence of homoeologous genes. Furthermore, the expression profiles of the genes were detected using the available RNA-seq and the expression of 4 drought-responsive candidates was further validated through qRT-PCR analysis. Finally, the co-expression network was constructed and a total of 22 nodes with 121 edges of gene pairs were found.

Conclusion:

This study systematically reported the characteristics of the wheat TIFY family, which ultimately provided important targets for further functional analysis and also facilitated the elucidation of the evolution mechanism of TIFY genes in wheat and more.

Transcriptome analysis of responses in Brachypodium distachyon overexpressing the BdbZIP26 transcription factor

BACKGROUND

Biotic and abiotic stresses are the major cause of reduced growth, persistence, and yield in agriculture. Over the past decade, RNA-Sequencing and the use of transgenics with altered expression of stress related genes have been utilized to gain a better understanding of the molecular mechanisms leading to salt tolerance in a variety of species. Identification of transcription factors that, when overexpressed in plants, improve multiple stress tolerance may be valuable for crop improvement, but sometimes overexpression leads to deleterious effects during normal plant growth.

RESULTS

Brachypodium constitutively expressing the BdbZIP26:GFP gene showed reduced stature compared to wild type plants (WT). RNA-Seq analysis comparing WT and bZIP26 transgenic plants revealed 7772 differentially expressed genes (DEGs). Of these DEGs, 987 of the DEGs were differentially expressed in all three transgenic lines. Many of these DEGs are similar to those often observed in response to abiotic and biotic stress, including signaling proteins such as kinases/phosphatases, calcium/calmodulin related proteins, oxidases/reductases, hormone production and signaling, transcription factors, as well as disease responsive proteins. Interestingly, there were many DEGs associated with protein turnover including ubiquitin-related proteins, F-Box and U-box related proteins, membrane proteins, and ribosomal synthesis proteins. Transgenic and control plants were exposed to salinity stress. Many of the DEGs between the WT and transgenic lines under control conditions were also found to be differentially expressed in WT in response to salinity stress. This suggests that the over-expression of the transcription factor is placing the plant in a state of stress, which may contribute to the plants diminished stature.

CONCLUSION

The constitutive expression of BdbZIP26:GFP had an overall negative effect on plant growth and resulted in stunted plants compared to WT plants under control conditions, and a similar response to WT plants under salt stress conditions. The results of gene expression analysis suggest that the transgenic plants are in a constant state of stress, and that they are trying to allocate resources to survive.

Genome-Wide Analysis Reveals Stress and Hormone Responsive Patterns of JAZ Family Genes in Camellia Sinensis

JAZ (Jasmonate ZIM-domain) proteins play pervasive roles in plant development and defense reaction. However, limited information is known about the JAZ family in Camellia sinensis. In this study, 12 non-redundant JAZ genes were identified from the tea plant genome database. Phylogenetic analysis showed that the 12 JAZ proteins belong to three groups. The cis-elements in promoters of CsJAZ genes and CsJAZ proteins interaction networks were also analyzed. Quantitative RT–PCR analysis showed that 7 CsJAZ genes were preferentially expressed in roots. Furthermore, the CsJAZ expressions were differentially induced by cold, heat, polyethylene glycol (PEG), methyl jasmonate (MeJA), and gibberellin (GA) stimuli. The Pearson correlations analysis based on expression levels showed that the CsJAZ gene pairs were differentially expressed under different stresses, indicating that CsJAZs might exhibit synergistic effects in response to various stresses. Subcellular localization assay demonstrated that CsJAZ3, CsJAZ10, and CsJAZ11 fused proteins were localized in the cell nucleus. Additionally, the overexpression of CsJAZ3, CsJAZ10, and CsJAZ11 in E. coli enhanced the growth of recombinant cells under abiotic stresses. In summary, this study will facilitate the understanding of the CsJAZ family in Camellia sinensis and provide new insights into the molecular mechanism of tea plant response to abiotic stresses and hormonal stimuli.

Genome-wide and expression pattern analysis of JAZ family involved in stress responses and postharvest processing treatments in Camellia sinensis

The JASMONATE-ZIM DOMAIN (JAZ) family genes are key repressors in the jasmonic acid signal transduction pathway. Recently, the JAZ gene family has been systematically characterized in many plants. However, this gene family has not been explored in the tea plant. In this study, 13 CsJAZ genes were identified in the tea plant genome. Phylogenetic analysis showed that the JAZ proteins from tea and other plants clustered into 11 sub-groups. The CsJAZ gene transcriptional regulatory network predictive and expression pattern analyses suggest that these genes play vital roles in abiotic stress responses, phytohormone crosstalk and growth and development of the tea plant. In addition, the CsJAZ gene expression profiles were associated with tea postharvest processing. Our work provides a comprehensive understanding of the CsJAZ family and will help elucidate their contributions to tea quality during tea postharvest processing.

Genomic identification and characterization of MYC family genes in wheat (Triticum aestivum L.)

Background

MYC transcriptional factors are members of the bHLH (basic helix-loop-helix) superfamily, and play important roles in plant growth and development. Recent studies have revealed that some MYCs are involved in the crosstalk between Jasmonic acid regulatory pathway and light signaling in Arabidopsis, but such kinds of studies are rare in wheat, especially in photo-thermo-sensitive genic male sterile (PTGMS) wheat line.

Results

27 non-redundant MYC gene copies, which belonged to 11 TaMYC genes, were identified in the whole genome of wheat (Chinese Spring). These gene copies were distributed on 13 different chromosomes, respectively. Based on the results of phylogenetic analysis, 27 TaMYC gene copies were clustered into group I, group III, and group IV. The identified TaMYC genes copies contained different numbers of light, stress, and hormone-responsive regulatory elements in their 1500 base pair promoter regions. Besides, we found that TaMYC3 was expressed highly in stem, TaMYC5 and TaMYC9 were expressed specially in glume, and the rest of TaMYC genes were expressed in all tissues (root, stem, leaf, pistil, stamen, and glume) of the PTGMS line BS366. Moreover, we found that TaMYC3, TaMYC7, TaMYC9, and TaMYC10 were highly sensitive to methyl jasmonate (MeJA), and other TaMYC genes responded at different levels. Furthermore, we confirmed the expression profiles of TaMYC family members under different light quality and plant hormone stimuli, and abiotic stresses. Finally, we predicted the wheat microRNAs that could interact with TaMYC family members, and built up a network to show their integrative relationships.

Conclusions

This study analyzed the size and composition of the MYC gene family in wheat, and investigated stress-responsive and light quality induced expression profiles of each TaMYC gene in the PTGMS wheat line BS366. In conclusion, we obtained lots of important information of TaMYC family, and the results of this study was supposed to contribute novel insights and gene and microRNA resources for wheat breeding, especially for the improvement of PTGMS wheat lines.

Evolutionary Analysis of JAZ Proteins in Plants: An Approach in Search of the Ancestral Sequence

Jasmonates are phytohormones that regulate development, metabolism and immunity. Signal transduction is critical to activate jasmonate responses, but the evolution of some key regulators such as jasmonate-ZIM domain (JAZ) repressors is not clear. Here, we identified 1065 JAZ sequence proteins in 66 lower and higher plants and analyzed their evolution by bioinformatics methods. We found that the TIFY and Jas domains are highly conserved along the evolutionary scale. Furthermore, the canonical degron sequence LPIAR(R/K) of the Jas domain is conserved in lower and higher plants. It is noteworthy that degron sequences showed a large number of alternatives from gymnosperms to dicots. In addition, ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motifs are displayed in all plant lineages from liverworts to angiosperms. However, the cryptic MYC2-interacting domain (CMID) domain appeared in angiosperms for the first time. The phylogenetic analysis performed using the Maximum Likelihood method indicated that JAZ ortholog proteins are grouped according to their similarity and plant lineage. Moreover, ancestral JAZ sequences were constructed by PhyloBot software and showed specific changes in the TIFY and Jas domains during evolution from liverworts to dicots. Finally, we propose a model for the evolution of the ancestral sequences of the main eight JAZ protein subgroups. These findings contribute to the understanding of the JAZ family origin and expansion in land plants.

Tobacco transcription repressors NtJAZ: Potential involvement in abiotic stress response and glandular trichome induction

Members of the Jasmonate ZIM domain (JAZ) proteins act as transcriptional repressors in the jasmonate (JA) hormonal response. To characterize the potential roles of JAZ gene family in plant development and abiotic stress response, fifteen JAZs were identified based on the genome of Nicotiana tabacum. Structural analysis confirmed the presence of single Jas and TIFY motif. Tissue expression pattern analysis indicated that NtJAZ-2, -3, -5, and -10 were highly expressed in roots and NtJAZ-11 was expressed only in the cotyledons. The transcript level of NtJAZ-3, -5, -9, and -10 in the stem epidermis was higher than that in the stem without epidermis. Dynamic expression of NtJAZs exposed to abiotic stress and phytohormone indicated that the expression of most NtJAZs was activated by salicylic acid, methyl jasmonate, gibberellic acid, cold, salt, and heat stresses. With abscisic acid treatment, NtJAZ-1, -2, and -3 were not activated; NtJAZ-4, -5, and -6 were up-regulated; and the remaining NtJAZ genes were inhibited. With drought stress, the expression of NtJAZ-1, -2, -3, -4, -5, -6, -7, and -8 was up-regulated, whereas the transcript of the remaining genes was inhibited. Moreover, high concentration MeJA (more than 1 mM MeJA) had an effect on secreting trichome induction, but inhabited the plant growth. Nine NtJAZs may play important role in secreting trichome induction. These results indicate that the JAZ proteins are convergence points for various phytohormone signal networks, which are involved in abiotic stress responses.

Genome-Wide Identification and Characterization of JAZ Protein Family in Two Petunia Progenitors

Jasmonate ZIM-domain (JAZ) family proteins are the key repressors in the jasmonate signaling pathway and play crucial roles in plant development, defenses, and responses to stresses. However, our knowledge about the JAZ protein family in petunia is limited. This research respectively identified 12 and 16 JAZ proteins in two Petunia progenitors, Petunia axillaris and Petunia inflata. Phylogenetic analysis showed that the 28 proteins could be divided into four groups (Groups A–D) and further classified into six subgroups (A1, A2, B1, B3, C, and D1); members in the same subgroup shared some similarities in motif composition and sequence structure. The Ka/Ks ratios of seven paralogous pairs were less than one, suggesting the petunia JAZ family might have principally undergone purifying selection. Quantitative real-time PCR (qRT-PCR) analysis revealed that PaJAZ genes presented differential expression patterns during the development of flower bud and anther in petunia, and the expression of PaJAZ5, 9, 12 genes was generally up-regulated after MeJA treatment. Subcellular localization assays demonstrated that proteins PaJAZ5, 9, 12 were localized in nucleus. Yeast two hybrid (Y2H) elucidated most PaJAZ proteins (PaJAZ1-7, 9, 12) might interact with transcription factor MYC2. This study provides insights for further investigation of functional analysis in petunia JAZ family proteins.

JAZ proteins modulate seed germination through interaction with ABI5 in bread wheat and Arabidopsis

Appropriate regulation of crop seed germination is of significance for agriculture production. In this study, we show that TaJAZ1, most closely related to Arabidopsis JAZ3, negatively modulates abscisic acid (ABA)-inhibited seed germination and ABA-responsive gene expression in bread wheat. Biochemical interaction assays demonstrate that the C-terminal part containing the Jas domain of TaJAZ1 physically interacts with TaABI5. Similarly, Arabidopsis jasmonate-ZIM domain (JAZ) proteins also negatively modulate ABA responses. Further we find that a subset of JAZ proteins could interact with ABI5 using the luciferase complementation imaging assays. Choosing JAZ3 as a representative, we demonstrate that JAZ3 interacts with ABI5 in vivo and represses the transcriptional activation activity of ABI5. ABA application could abolish the enrichment of JAZ proteins in the ABA-responsive gene promoter. Furthermore, we find that ABA application could induce the expression of jasmonate (JA) biosynthetic genes and then increase the JA concentrations partially dependent on the function of ABI5, consequently leading to the degradation of JAZ proteins. This study sheds new light on the crosstalk between JA and ABA in modulating seed germination in bread wheat and Arabidopsis.

Overexpression of TaJAZ1 increases powdery mildew resistance through promoting reactive oxygen species accumulation in bread wheat

Powdery mildew, caused by the biotrophic fungal pathogen Blumeria graminis f. sp. tritici, is a major limitation for wheat yield. However, the molecular mechanisms underlying wheat resistance against powdery mildew remain largely unclear. In this study, we report the role of JASMONATE-ZIM domain protein TaJAZ1 in regulating bread wheat resistance against powdery mildew. We generated transgenic bread wheat lines over-expressing the truncated TaJAZ1 without the Jas motif, which showed increased TaPR1/2 gene expression and reactive oxygen species accumulation, leading to enhanced resistance against powdery mildew. Simultaneously, we identified a Jasmonic acid (JA)-induced bHLH transcription factor TaMYC4 in bread wheat. We demonstrated that TaJAZ1 directly interacts with TaMYC4 to repress its transcriptional activity. Meanwhile, we show that the ZIM domain of TaJAZ1 interacts with the C terminus of TaNINJA, whereas the N-terminal EAR motif of TaNINJA interacts with the transcriptional co-repressor TaTPL. Collectively, our work pinpoints TaJAZ1 as a favorable gene to enhance bread wheat resistance toward powdery mildew, and provides a molecular framework for JA signaling in bread wheat.

Genome-wide identification and abiotic stress-responsive pattern of heat shock transcription factor family in Triticum aestivum L

Background

Enhancement of crop productivity under various abiotic stresses is a major objective of agronomic research. Wheat (Triticum aestivum L.) as one of the world’s staple crops is highly sensitive to heat stress, which can adversely affect both yield and quality. Plant heat shock factors (Hsfs) play a crucial role in abiotic and biotic stress response and conferring stress tolerance. Thus, multifunctional Hsfs may be potentially targets in generating novel strains that have the ability to survive environments that feature a combination of stresses.

Result

In this study, using the released genome sequence of wheat and the novel Hsf protein HMM (Hidden Markov Model) model constructed with the Hsf protein sequence of model monocot (Oryza sativa) and dicot (Arabidopsis thaliana) plants, genome-wide TaHsfs identification was performed. Eighty-two non-redundant and full-length TaHsfs were randomly located on 21 chromosomes. The structural characteristics and phylogenetic analysis with Arabidopsis thaliana, Oryza sativa and Zea mays were used to classify these genes into three major classes and further into 13 subclasses. A novel subclass, TaHsfC3 was found which had not been documented in wheat or other plants, and did not show any orthologous genes in A. thaliana, O. sativa, or Z. mays Hsf families. The observation of a high proportion of homeologous TaHsf gene groups suggests that the allopolyploid process, which occurred after the fusion of genomes, contributed to the expansion of the TaHsf family. Furthermore, TaHsfs expression profiling by RNA-seq revealed that the TaHsfs could be responsive not only to abiotic stresses but also to phytohormones. Additionally, the TaHsf family genes exhibited class-, subclass- and organ-specific expression patterns in response to various treatments.

Conclusions

A comprehensive analysis of Hsf genes was performed in wheat, which is useful for better understanding one of the most complex Hsf gene families. Variations in the expression patterns under different abiotic stress and phytohormone treatments provide clues for further analysis of the TaHsfs functions and corresponding signal transduction pathways in wheat.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5617-1) contains supplementary material, which is available to authorized users.

The moss jasmonate ZIM-domain protein PnJAZ1 confers salinity tolerance via crosstalk with the abscisic acid signalling pathway

Abscisic acid (ABA) and jasmonates (JAs) are the primary plant hormones involved in mediating salt tolerance. In addition, these two plant hormones exert a synergistic effect to inhibit seed germination. However, the molecular mechanism of the interaction between ABA signalling and JA signalling is still not well documented. Here, a moss jasmonate ZIM-domain gene (PnJAZ1), which encodes a nucleus-localized protein with conserved ZIM and Jas domains, was cloned from Pohlia nutans. PnJAZ1 expression was rapidly induced by various abiotic stresses. The PnJAZ1 protein physically interacted with MYC2 and was degraded by exogenous 12-oxo-phytodienoic acid (OPDA) treatment, implying that the JAZ protein-mediated signalling pathway is conserved in plants. Transgenic Arabidopsis and Physcomitrella plants overexpressing PnJAZ1 showed increased tolerance to salt stress and decreased ABA sensitivity during seed germination and early development. The overexpression of PnJAZ1 inhibited the expression of ABA pathway genes related to seed germination and seedling growth. Moreover, the transgenic Arabidopsis lines exhibited enhanced tolerance to auxin (IAA) and glucose, mimicking the phenotypes of abi4 or abi5 mutants. These results suggest that PnJAZ1 acts as a repressor, mediates JA-ABA synergistic crosstalk and enhances plant growth under salt stress.

Transcriptome sequencing of Antarctic moss under salt stress emphasizes the important roles of the ROS-scavenging system

Mosses are predominant terrestrial vegetation in Antarctica. Their distributions appear to be controlled more by water and salinity. The Antarctic moss Pohlia nutans can tolerate high salt stress. Here, high-throughput sequencing was employed to study the transcriptional characteristics of P. nutans under salt stress. Differentially expressed genes (DEGs) analysis showed that 1340 genes were significantly upregulated and 831 genes were markedly downregulated. The expression of representative DEGs including abscisic acid (ABA) and Jasmonates (JAs) pathway-related genes, antioxidant enzyme genes, and flavonoid biosynthesis-related genes were analyzed by real-time PCR and most were upregulated after salt stress. Furthermore, malondialdehyde (MDA) content was significantly increased after salt treatment. The levels of hydroxyl free radical (∙OH) first rose then quickly decreased. In addition, the activities of antioxidant enzymes, such as catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), and the flavonoid content were enhanced after salt stress. Exogenous application of ABA, Methyl jasmonate (MeJA) or proanthocyanidins (PA) improved the performance of P. nutans in response to high salt stress. Furthermore, real-time PCR showed that ABA or MeJA treatment upregulated the gene expression of antioxidant and flavonoid biosynthesis-related enzymes. These results suggest that the responses of P. nutans under salt stress are involved in activating phytohormone signaling pathways which trigger two main antioxidant defense systems (i.e., antioxidant enzymes and flavonoids) for protecting cell and scavenging reactive oxygen species.

Overexpression of Arabidopsis OPR3 in Hexaploid Wheat (Triticum aestivum L.) Alters Plant Development and Freezing Tolerance

Jasmonates are plant hormones that are involved in the regulation of different aspects of plant life, wherein their functions and molecular mechanisms of action in wheat are still poorly studied. With the aim of gaining more insights into the role of jasmonic acid (JA) in wheat growth, development, and responses to environmental stresses, we have generated transgenic bread wheat plants overexpressing Arabidopsis 12-OXOPHYTODIENOATE REDUCTASE 3 (AtOPR3), one of the key genes of the JA biosynthesis pathway. Analysis of transgenic plants showed that AtOPR3 overexpression affects wheat development, including germination, growth, flowering time, senescence, and alters tolerance to environmental stresses. Transgenic wheat plants with high AtOPR3 expression levels have increased basal levels of JA, and up-regulated expression of ALLENE OXIDE SYNTHASE, a jasmonate biosynthesis pathway gene that is known to be regulated by a positive feedback loop that maintains and boosts JA levels. Transgenic wheat plants with high AtOPR3 expression levels are characterized by delayed germination, slower growth, late flowering and senescence, and improved tolerance to short-term freezing. The work demonstrates that genetic modification of the jasmonate pathway is a suitable tool for the modulation of developmental traits and stress responses in wheat.

Genome-Wide Identification and Analysis of HAK/KUP/KT Potassium Transporters Gene Family in Wheat (Triticum aestivum L.)

In plants, the HAK (high-affinity K⁺)/KUP (K⁺ uptake)/KT (K⁺ transporter) family represents a large group of potassium transporters that play important roles in plant growth and environmental adaptation. Although HAK/KUP/KT genes have been extensively investigated in many plant species, they remain uncharacterized in wheat, especially those involved in the response to environmental stresses. In this study, 56 wheat HAK/KUP/KT (hereafter called TaHAKs) genes were identified by a genome-wide search using recently released wheat genomic data. Phylogenetic analysis grouped these genes into four clusters (Ι, II, III, IV), containing 22, 19, 7 and 8 genes, respectively. Chromosomal distribution, gene structure, and conserved motif analyses of the 56 TaHAK genes were subsequently performed. In silico RNA-seq data analysis revealed that TaHAKs from clusters II and III are constitutively expressed in various wheat tissues, while most genes from clusters I and IV have very low expression levels in the examined tissues at different developmental stages. qRT-PCR analysis showed that expression levels of TaHAK genes in wheat seedlings were significantly up- or downregulated when seedlings were exposed to K⁺ deficiency, high salinity, or dehydration. Furthermore, we functionally characterized TaHAK1b-2BL and showed that it facilitates K⁺ transport in yeast. Collectively, these results provide valuable information for further functional studies of TaHAKs, and contribute to a better understanding of the molecular basis of wheat development and stress tolerance.

Genome-wide identification and analysis of the COI gene family in wheat (Triticum aestivum L.)

Background

COI (CORONATINE INSENSITIVE), an F-box component of the Skp1-Cullin-F-box protein (SCF^COI1) ubiquitin E3 ligase, plays important roles in the regulation of plant growth and development. Recent studies have shown that COIs are involved in pollen fertility. In this study, we identified and characterized COI genes in the wheat genome and analyzed expression patterns under abiotic stress.

Results

A total of 18 COI candidate sequences for 8 members of COI gene family were isolated in wheat (Triticum aestivum L.). Phylogenetic and structural analyses showed that these COI genes could be divided into seven distinct subfamilies. The COI genes showed high expression in stamens and glumes. The qRT-PCR results revealed that wheat COIs were involved in several abiotic stress responses and anther/glume dehiscence in the photoperiod-temperature sensitive genic male sterile (PTGMS) wheat line BS366.

Conclusions

The structural characteristics and expression patterns of the COI gene family in wheat as well as the stress-responsive and differential tissue-specific expression profiles of each TaCOI gene were examined in PTGMS wheat line BS366. In addition, we examined SA- and MeJA-induced gene expression in the wheat anther and glume to investigate the role of COI in the JA signaling pathway, involved in the regulation of abnormal anther dehiscence in the PTGMS wheat line. The results of this study contribute novel and detailed information about the TaCOI gene family in wheat and could be used as a benchmark for future studies of the molecular mechanisms of PTGMS in other crops.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5116-9) contains supplementary material, which is available to authorized users.

Characterization of wheat (Triticum aestivum) TIFY family and role of Triticum Durum TdTIFY11a in salt stress tolerance

The TIFY proteins constitute a plant-specific super-family and they are involved in regulating many plant processes, such as development, defences and stress responses. The Jasmonate-ZIM-Domain (JAZ) proteins, the best-characterized sub-group of the TIFY family are key regulator of the jasmonic acid (JA) signalling pathway. Jasmonates regulate several aspects of plant development, and play a primary role in defence mechanisms as well as in plant responses to abiotic stresses. The TIFY family is well studied in dicots but poorly investigated in monocots. The present study reports an extensive genomic identification of TIFY proteins from Triticum aestivum. We identified 49 TIFY genes, which were annotated according to three sub-genomes (AABBDD) of T. aestivum. Following their clustering with Oryza sativa and Brachypodium distachyon, the 49 genes were grouped in 18 different TIFY homeologous subsets. Expression analyses of 6 representative TIFY genes on Tunisian durum wheat seedlings revealed their differential regulation by various stress treatment, including JA, ABA and salt stress. TIFY11a was specifically induced after salt treatment. Transgenic lines over-expressing TdTIFY11a showed higher germination and growth rates under high salinity conditions, compared to wild type plants. In summary, our results outline a relevant role of wheat TIFY proteins in promoting germination under salt stress.

Jasmonate signalling pathway in strawberry: Genome-wide identification, molecular characterization and expression of JAZs and MYCs during fruit development and ripening

Jasmonates (JAs) are signalling molecules involved in stress responses, development and secondary metabolism biosynthesis, although their roles in fleshy-fruit development and ripening processes are not well known. In strawberry fruit, it has been proposed that JAs could regulate the early development through the activation of the JAs biosynthesis. Moreover, it has been reported that JA treatment increases anthocyanin content in strawberry fruit involving the bioactive jasmonate biosynthesis. Nevertheless, JA signalling pathway, of which main components are the COI1-JAZ co-receptor and the MYC transcription factors (TFs), has not been characterized in strawberry until now. Here we identified and characterized the woodland strawberry (Fragaria vesca) JAZ and MYC genes as well as studied their expression during development and ripening stages in commercial strawberry (Fragaria × ananassa) fruit. We described twelve putative JAZ proteins and two MYC TFs, which showed high conservation with respect to their orthologs in Arabidopsis thaliana and in other fleshy-fruit species such as Malus × domestica, Vitis vinifera and Solanum lycopersicum as revealed by gene synteny and phylogenetic analyses. Noteworthy, their expression levels exhibited a significant decrease from fruit development to ripening stages in F. × ananassa, along with others of the JA signalling-related genes such as FaNINJA and FaJAMs, encoding for negative regulators of JA responses. Moreover, we found that main JA signalling-related genes such as FaMYC2, and FaJAZ1 are promptly induced by JA treatment at early times in F. × ananassa fruit. These results suggest the conservation of the canonical JA signalling pathway in strawberry and a possible role of this pathway in early strawberry fruit development, which also correlates negatively with the beginning of the ripening process.

The Jasmonate ZIM-domain protein gene SlJAZ2 regulates plant morphology and accelerates flower initiation in Solanum lycopersicum plants

JAZ (Jasmonate ZIM-domain) proteins are important repressors in JA signaling pathway. JAZs were proved taking part in various development processes and resistance to biotic and abiotic stresses in Arabiodopsis. However, in tomato, the functional study of JAZs is rare, especially on plant growth and development. Here, a typical tomato JAZ gene, SlJAZ2 was isolated. Tomato plants overexpressing SlJAZ2 exhibited quicker leaf initiation, reduced plant height and internode length, decreasing trichomes, earlier lateral bud emergence and advanced flowering transition. Further experiments showed that the pith cells in transgenic plant stem were much smaller than wild-type and the genes related to cell elongation and gibberellin biosynthesis were down-regulated. Genes mediating trichome formation were also inhibited in plant stem epidermis. In addition, the flower initiation of transgenic plants were earlier and genes controlling flowering time were up-regulated significantly after SlJAZ2 was overexpressed. Our research demonstrates that SlJAZ2 accelerates the transition from vegetative growth to reproductive growth.

Uncovering Male Fertility Transition Responsive miRNA in a Wheat Photo-Thermosensitive Genic Male Sterile Line by Deep Sequencing and Degradome Analysis

MicroRNAs (miRNAs) are endogenous small RNAs which play important negative regulatory roles at both the transcriptional and post-transcriptional levels in plants. Wheat is the most commonly cultivated plant species worldwide. In this study, RNA-seq analysis was used to examine the expression profiles of miRNA in the spikelets of photo-thermosenisitive genic male sterile (PTGMS) wheat line BS366 during male fertility transition. Through mapping on their corresponding precursors, 917-7,762 novel miRNAs were found in six libraries. Six novel miRNAs were selected for examination of their secondary structures and confirmation by stem-loop RT-PCR. In a differential expression analysis, 20, 22, and 58 known miRNAs exhibited significant differential expression between developmental stages 1 (secondary sporogenous cells had formed), 2 (all cells layers were present and mitosis had ceased), and 3 (meiotic division stage), respectively, of fertile and sterile plants. Some of these differential expressed miRNAs, such as tae-miR156, tae-miR164, tae-miR171, and tae-miR172, were shown to be associated with their targets. These targets were previously reported to be related to pollen development and/or male sterility, indicating that these miRNAs and their targets may be involved in the regulation of male fertility transition in the PTGMS wheat line BS366. Furthermore, target genes of miRNA cleavage sites were validated by degradome sequencing. In this study, a possible signal model for the miRNA-mediated signaling pathway during the process of male fertility transition in the PTGMS wheat line BS366 was developed. This study provides a new perspective for understanding the roles of miRNAs in male fertility in PTGMS lines of wheat.