TaOPR2 encodes a 12-oxo-phytodienoic acid reductase involved in the biosynthesis of jasmonic acid in wheat (Triticum aestivum L.)

Sugarcane ScOPR1 gene enhances plant disease resistance through the modulation of hormonal signaling pathways

KEY MESSAGE

Transgenic plants stably overexpressing ScOPR1 gene enhanced disease resistance by increasing the accumulation of JA, SA, and GST, as well as up-regulating the expression of genes related to signaling pathways. 12-Oxo-phytodienoate reductase (OPR) is an oxidoreductase that depends on flavin mononucleotide (FMN) and catalyzes the conversion of 12-oxophytodienoate (12-OPDA) into jasmonic acid (JA). It plays a key role in plant growth and development, and resistance to adverse stresses. In our previous study, we have obtained an OPR gene (ScOPR1, GenBank Accession Number: MG755745) from sugarcane. This gene showed positive responses to methyl jasmonate (MeJA), salicylic acid (SA), abscisic acid (ABA), and Sporisorium scitamineum, suggesting its potential for pathogen resistance. Here, in our study, we observed that Nicotiana benthamiana leaves transiently overexpressing ScOPR1 exhibited weaker disease symptoms, darker 3,3-diaminobenzidine (DAB) staining, higher accumulation of reactive oxygen species (ROS), and higher expression of hypersensitive response (HR) and SA pathway-related genes after inoculation with Ralstonia solanacearum and Fusarium solanacearum var. coeruleum. Furthermore, the transgenic N. benthamiana plants stably overexpressing the ScOPR1 gene showed enhanced resistance to pathogen infection by increasing the accumulation of JA, SA, and glutathione S-transferase (GST), as well as up-regulating genes related to HR, JA, SA, and ROS signaling pathways. Transcriptome analysis revealed that the specific differentially expressed genes (DEGs) in ScOPR1-OE were significantly enriched in hormone transduction signaling and plant-pathogen interaction pathways. Finally, a functional mechanism model of the ScOPR1 gene in response to pathogen infection was depicted. This study provides insights into the molecular mechanism of ScOPR1 and presents compelling evidence supporting its positive involvement in enhancing plant disease resistance.

Functional analysis of a rice 12-oxo-phytodienoic acid reductase gene (OsOPR1) involved in Cd stress tolerance

BACKGROUND

The accumulation of cadmium (Cd) in plants may compromise the growth and development of plants, thereby endangering human health through the food chain. Understanding how plants respond to Cd is important for breeding low-Cd rice cultivars.

METHODS

In this study, the functions of 12-oxo-phytodienoic acid reductase 1 (OsOPR1) were predicted through bioinformatics analysis. The expression levels of OsOPR1 under Cd stress were analyzed by using qRT-PCR. Then, the role that OsOPR1 gene plays in Cd tolerance was studied in Cd-sensitive yeast strain (ycf1), and the Cd concentration of transgenic yeast was analyzed using inductively coupled plasma mass spectrometry (ICP-MS).

RESULTS

Bioinformatics analysis revealed that OsOPR1 was a protein with an Old yellow enzyme-like FMN (OYE_like_FMN) domain, and the cis-acting elements which regulate hormone synthesis or responding abiotic stress were abundant in the promoter region, which suggested that OsOPR1 may exhibit multifaceted biological functions. The expression pattern analysis showed that the expression levels of OsOPR1 were induced by Cd stress both in roots and roots of rice plants. However, the induced expression of OsOPR1 by Cd was more significant in the roots compared to that in roots. In addition, the overexpression of OsOPR1 improved the Cd tolerance of yeast cells by affecting the expression of antioxidant enzyme related genes and reducing Cd content in yeast cells.

CONCLUSION

Overall, these results suggested that OsOPR1 is a Cd-responsive gene and may has a potential for breeding low-Cd or Cd-tolerant rice cultivars and for phytoremediation of Cd-contaminated in farmland.

Melatonin influences methyl jasmonate-induced protection of photosynthetic activity in wheat plants against heat stress by regulating ethylene-synthesis genes and antioxidant metabolism

Melatonin (MT) and methyl jasmonate (MeJA) play important roles in the adaptation of plants to different stress factors by modulating stress tolerance mechanisms. The present study reports the involvement of MT (100 µM) in MeJA (10 µM)-induced photosynthetic performance and heat stress acclimation through regulation of the antioxidant metabolism and ethylene production in wheat (Triticum aestivum L.) plants. Plants exposed to 40 °C for 6 h per day for 15 days and allowed to retrieve at 28 °C showed enhanced oxidative stress and antioxidant metabolism, increased 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS) activity and ethylene production, and decreased photosynthetic performance. In contrast, the exogenously applied MT and MeJA reduced oxidative stress through improved S-assimilation (+ 73.6% S content), antioxidant defense system (+ 70.9% SOD, + 115.8% APX and + 104.2% GR, and + 49.5% GSH), optimized ethylene level to 58.4% resulting in improved photosynthesis by 75%. The use of p-chlorophenyl alanine, a MT biosynthesis inhibitor along with MeJA in the presence of heat stress reduced the photosynthetic performance, ATP-S activity and GSH content, substantiated the requirement of MT in the MeJA-induced photosynthetic response of plants under heat stress. These findings suggest that MeJA evoked the plant's ability to withstand heat stress by regulating the S-assimilation, antioxidant defense system, and ethylene production, and improving photosynthetic performance was dependent on MT.

Cold stress triggers freezing tolerance in wheat (Triticum aestivum L.) via hormone regulation and transcription of related genes

Low temperatures limit the geographic distribution and yield of plants. Hormones play an important role in coordinating the growth and development of plants and their tolerance to low temperatures. However, the mechanisms by which hormones affect plant resistance to extreme cold stress in the natural environment are still unclear. In this study, two winter wheat varieties with different cold resistances, Dn1 and J22, were used to conduct targeted plant hormone metabolome analysis on the tillering nodes of winter wheat at 5 °C, -10 °C and -25 °C using an LC-ESI-MS/MS system. We screened 39 hormones from 88 plant hormone metabolites and constructed a partial regulatory network of auxin, jasmonic acid and cytokinin. GO analysis and enrichment of KEGG pathways in different metabolites showed that the 'plant hormone signal transduction' pathway was the most common. Our study showed that extreme low temperature increased the most levels of auxin, cytokinin and salicylic acid, and decreased levels of jasmonic acid and abscisic acid, and that levels of auxin, jasmonic acid and cytokinin in Dn1 were higher than those in J22. These changes in hormone levels were associated with changes in gene expression in synthesis, catabolism, transport and signal transduction pathways. These results differ from the previous hormone regulation mechanisms, which were mostly obtained at 4 °C. Our results provide a basis for further understanding the molecular mechanisms by which plant endogenous hormones regulate plant freezing stress tolerance.

Integrative Analysis of Metabolome and Transcriptome Reveals the Role of Strigolactones in Wounding-Induced Rice Metabolic Re-Programming

Plants have evolved mechanisms to adapt to wounding, a threat occurring separately or concomitantly with other stresses. During the last decades, many efforts have been made to elucidate the wounding signaling transduction. However, we know little about the metabolic re-programming under wounding, let alone whether and how strigolactones (SLs) participate in this progress. Here, we reported a metabolomic and transcriptomic analysis of SLs synthetic and signal mutants in rice before and after wounding. A series of metabolites differentially responded to wounding in the SLs mutants and wild-type rice, among which flavones were enriched. Besides, the SLs mutants accumulated more jasmonic acid (JA) and jasmonyl isoleucine (JA-lle) than the wild-type rice after wounding, suggesting an interplay of SLs and JAs during responding to wounding. Further transcriptome data showed that cell wall, ethylene, and flavones pathways might be affected by wounding and SLs. In addition, we identified candidate genes regulated by SLs and responding to wounding. In conclusion, our work provides new insights into wounding-induced metabolic re-programming and the SLs’ function.

Impact of Heat Stress on Expression of Wheat Genes Responsive to Hessian Fly Infestation

Heat stress compromises wheat (Triticum aestivium) resistance to Hessian fly (HF, Mayetiola destructor (Say)). This study aimed to investigate the impact of heat stress on transcript expression of wheat genes associated with resistance to HF infestation under normal and heat-stressed conditions. To this end, ‘Molly’, a wheat cultivar containing the resistance gene H13, was subjected to HF infestation, heat stress, and the combination of HF infestation and heat stress. Our RNA-Seq approach identified 21 wheat genes regulated by HF infestation under normal temperatures (18 °C) and 155 genes regulated by HF infestation when plants were exposed to 35 °C for 6 h. Three differentially expressed genes (DEGs) from the RNA-Seq analysis were selected to validate the gene function of these DEGs using the RT-qPCR approach, indicating that these DEGs may differentially contribute to the expression of wheat resistance during the early stage of wheat–HF interaction under various stresses. Moreover, the jasmonate ZIM domain (JAZ) gene was also significantly upregulated under these treatments. Our results suggest that the genes in heat-stressed wheat plants are more responsive to HF infestation than those in plants growing under normal temperature conditions, and these genes in HF-infested wheat plants are more responsive to heat stress than those in plants without infestation.

Genome-Wide Identification and Analysis of bZIP Gene Family and Resistance of TaABI5 (TabZIP96) under Freezing Stress in Wheat (Triticum aestivum)

The basic leucine zipper (bZIP) regulates plant growth and responds to stress as a key transcription factor of the Abscisic acid (ABA) signaling pathway. In this study, TabZIP genes were identified in wheat and the gene structure, physicochemical properties, cis-acting elements, and gene collinearity were analyzed. RNA-Seq and qRT-PCR analysis showed that ABA and abiotic stress induced most TabZIP genes expression. The ectopic expression of TaABI5 up-regulated the expression of several cold-responsive genes in Arabidopsis. Physiological indexes of seedlings of different lines under freezing stress showed that TaABI5 enhanced the freezing tolerance of plants. Subcellular localization showed that TaABI5 is localized in the nucleus. Furthermore, TaABI5 physically interacted with cold-resistant transcription factor TaICE1 in yeast two-hybrid system. In conclusion, this study identified and analyzed members of the TabZIP gene family in wheat. It proved for the first time that the gene TaABI5 affected the cold tolerance of transgenic plants and was convenient for us to understand the cold resistance molecular mechanism of TaABI5. These results will provide a new inspiration for further study on improving plant abiotic stress resistance.

Cerium-Promoted Ginsenosides Accumulation by Regulating Endogenous Methyl Jasmonate Biosynthesis in Hairy Roots of Panax ginseng

Among rare earth elements, cerium has the unique ability of regulating the growth of plant cells and the biosynthesis of metabolites at different stages of plant development. The signal pathways of Ce3+-mediated ginsenosides biosynthesis in ginseng hairy roots were investigated. At a low concentration, Ce3+ improved the elongation and biomass of hairy roots. The Ce3+-induced accumulation of ginsenosides showed a high correlation with the reactive oxygen species (ROS), as well as the biosynthesis of endogenous methyl jasmonate (MeJA) and ginsenoside key enzyme genes (PgSS, PgSE and PgDDS). At a Ce3+ concentration of 20 mg L-1, the total ginsenoside content was 1.7-fold, and the total ginsenosides yield was 2.7-fold that of the control. Malondialdehyde (MDA) content and the ROS production rate were significantly higher than those of the control. The activity of superoxide dismutase (SOD) was significantly activated within the Ce3+ concentration range of 10 to 30 mg L-1. The activity of catalase (CAT) and peroxidase (POD) strengthened with the increasing concentration of Ce3+ in the range of 20-40 mg L-1. The Ce3+ exposure induced transient production of superoxide anion (O2•-) and hydrogen peroxide (H2O2). Together with the increase in the intracellular MeJA level and enzyme activity for lipoxygenase (LOX), there was an increase in the gene expression level of MeJA biosynthesis including PgLOX, PgAOS and PgJMT. Our results also revealed that Ce3+ did not directly influence PgSS, PgSE and PgDDS activity. We speculated that Ce3+-induced ROS production could enhance the accumulation of ginsenosides in ginseng hairy roots via the direct stimulation of enzyme genes for MeJA biosynthesis. This study demonstrates a potential approach for understanding and improving ginsenoside biosynthesis that is regulated by Ce3+-mediated signal transduction.

Role of jasmonic acid in plants: the molecular point of view

Recent updates in JA biosynthesis, signaling pathways and the crosstalk between JA and others phytohormones in relation with plant responses to different stresses. In plants, the roles of phytohormone jasmonic acid (JA), amino acid conjugate (e.g., JA-Ile) and their derivative emerged in last decades as crucial signaling compounds implicated in stress defense and development in plants. JA has raised a great interest, and the number of researches on JA has increased rapidly highlighting the importance of this phytohormone in plant life. First, JA was considered as a stress hormone implicated in plant response to biotic stress (pathogens and herbivores) which confers resistance to biotrophic and hemibiotrophic pathogens contrarily to salicylic acid (SA) which is implicated in plant response to necrotrophic pathogens. JA is also implicated in plant responses to abiotic stress (such as soil salinity, wounding and UV). Moreover, some researchers have recently revealed that JA controls several physiological processes like root growth, growth of reproductive organs and, finally, plant senescence. JA is also involved in the biosynthesis of various metabolites (e.g., phytoalexins and terpenoids). In plants, JA signaling pathways are well studied in few plants essentially Arabidopsis thaliana, Nicotiana benthamiana, and Oryza sativa L. confirming the crucial role of this hormone in plants. In this review, we highlight the last foundlings about JA biosynthesis, JA signaling pathways and its implication in plant maturation and response to environmental constraints.

The OPR gene family in watermelon: Genome-wide identification and expression profiling under hormone treatments and root-knot nematode infection

The enzyme 12-oxo-phytodienoic acid reductase (OPR) is important in the jasmonic acid (JA) biosynthesis pathway and thus plays a vital role in plant defence. However, systematic and comprehensive analyses of OPR genes in watermelon and their roles in defence responses are extremely limited. The physicochemical properties, phylogenetic tree, gene structure and cis-acting elements of watermelon OPR genes were analysed using bioinformatics, and qRT-PCR and RNA-Seq were applied to assay expression of OPR genes in watermelon. A total of five OPR family genes were identified in watermelon, which were unevenly distributed across the four chromosomes. Phylogenetic analysis assigned OPR members from different plant species to five subfamilies (OPRI-OPRV). The motif compositions of OPR members were relatively conserved. Expression analysis using qRT-PCR revealed that ClOPR genes, except for ClOPR5, were highly expressed in the flower and fruit. RNA-seq analysis showed that the ClOPR genes had different expression patterns during flesh and rind development. Furthermore, the ClOPR genes, particularly ClOPR2 and ClOPR4, were significantly upregulated by exogenous JA, salicylic acid (SA) and ethylene (ET) treatments. In addition, red light induced expression of ClOPR2 and ClOPR4 in leaves and roots of root-knot nematode (RKN)-infected watermelon plants, suggesting their involvement in red light-induced defence against RKN. These results provide a theoretical basis for elucidating the diverse functions of OPR family genes in watermelon.

A WRKY transcription factor, TaWRKY40-D, promotes leaf senescence associated with jasmonic acid and abscisic acid pathways in wheat

Leaf senescence is a complex and precise regulatory process that is correlated with numerous internal and environmental factors. Leaf senescence is tightly related to the redistribution of nutrients, which significantly affects productivity and quality, especially in crops. Evidence shows that the mediation of transcriptional regulation by WRKY transcription factors is vital for the fine-tuning of leaf senescence. However, the underlying mechanisms of the involvement of WRKY in leaf senescence are still unclear in wheat. Using RNA sequencing data, we isolated a novel WRKY transcription factor, TaWRKY40-D, which localizes in the nucleus and is basically induced by the progression of leaf senescence. TaWRKY40-D is a promoter of natural and dark-induced leaf senescence in transgenic Arabidopsis thaliana and wheat. We also demonstrated a positive response of TaWRKY40-D in wheat upon jasmonic acid (JA) and abscisic acid (ABA) treatment. Consistent with this, the detached leaves of TaWRKY40-D VIGS (virus-induced gene silencing) wheat plants showed a stay-green phenotype, while TaWRKY40-D overexpressing Arabidopsis plants showed premature leaf senescence after JA and ABA treatment. Moreover, our results revealed that TaWRKY40-D positively regulates leaf senescence, possibly by altering the biosynthesis and signalling of JA and ABA pathway genes. Together, our results suggest a new regulator of JA- and ABA-related leaf senescence, as well as a new candidate gene that can be used for molecular breeding in wheat.

A WRKY transcription factor, TaWRKY42-B, facilitates initiation of leaf senescence by promoting jasmonic acid biosynthesis

BACKGROUND

Leaf senescence comprises numerous cooperative events, integrates environmental signals with age-dependent developmental cues, and coordinates the multifaceted deterioration and source-to-sink allocation of nutrients. In crops, leaf senescence has long been regarded as an essential developmental stage for productivity and quality, whereas functional characterization of candidate genes involved in the regulation of leaf senescence has, thus far, been limited in wheat.

RESULTS

In this study, we analyzed the expression profiles of 97 WRKY transcription factors (TFs) throughout the progression of leaf senescence in wheat and subsequently isolated a potential regulator of leaf senescence, TaWRKY42-B, for further functional investigation. By phenotypic and physiological analyses in TaWRKY42-B-overexpressing Arabidopsis plants and TaWRKY42-B-silenced wheat plants, we confirmed the positive role of TaWRKY42-B in the initiation of developmental and dark-induced leaf senescence. Furthermore, our results revealed that TaWRKY42-B promotes leaf senescence mainly by interacting with a JA biosynthesis gene, AtLOX3, and its ortholog, TaLOX3, which consequently contributes to the accumulation of JA content. In the present study, we also demonstrated that TaWRKY42-B was functionally conserved with AtWRKY53 in the initiation of age-dependent leaf senescence.

CONCLUSION

Our results revealed a novel positive regulator of leaf senescence, TaWRKY42-B, which mediates JA-related leaf senescence via activation of JA biosynthesis and has the potential to be a target gene for molecular breeding in wheat.

Genome-Wide Analysis of OPR Family Genes in Cotton Identified a Role for GhOPR9 in Verticillium dahliae Resistance

The 12-oxo-phytodienoic acid reductases (OPRs) have been proven to play a major role in plant development and growth. Although the classification and functions of OPRs have been well understood in Arabidopsis, tomato, rice, maize, and wheat, the information of OPR genes in cotton genome and their responses to biotic and abiotic stresses have not been reported. In this study, we found 10 and 9 OPR genes in Gossypium hirsutum and Gossypium barbadense, respectively. They were classified into three groups, based on the similar gene structure and conserved protein motifs. These OPR genes just located on chromosome 01, chromosome 05, and chromosome 06. In addition, the whole genome duplication (WGD) or segmental duplication events contributed to the evolution of the OPR gene family. The analyses of cis-acting regulatory elements of GhOPRs showed that the functions of OPR genes in cotton might be related to growth, development, hormone, and stresses. Expression patterns showed that GhOPRs were upregulated under salt treatment and repressed by polyethylene glycol 6000 (PEG6000). The expression patterns of GhOPRs were different in leaf, root, and stem under V. dahliae infection. GhOPR9 showed a higher expression level than other OPR genes in cotton root. The virus-induced gene silencing (VIGS) analysis suggested that knockdown of GhOPR9 could increase the susceptibility of cotton to V. dahliae infection. Furthermore, GhOPR9 also modulated the expressions of jasmonic acid (JA) pathway-regulated genes under the V. dahliae infection. Overall, our results provided the evolution and potential functions of the OPR genes in cotton. These findings suggested that GhOPR9 might play an important role in cotton resistance to V. dahliae.

Identification of chromosomes in Triticum aestivum possessing genes that confer tolerance to the synthetic auxin herbicide halauxifen-methyl

Natural tolerance in hexaploid bread wheat (Triticum aestivum L.) to synthetic auxin herbicides is primarily due to rapid metabolic detoxification, but genes encoding these herbicide-detoxifying enzymes have yet to be identified. Herbicide safeners are commonly applied in wheat to achieve herbicide tolerance by inducing the expression and activity of herbicide-detoxifying enzymes. While safeners have been utilized for decades, knowledge of mechanisms that induce gene expression is limited. Our objective was to identify wheat chromosomes possessing genes that endow natural or safener-induced tolerance to halauxifen-methyl (HM), a postemergence (POST) wheat-selective synthetic auxin herbicide, using alien substitution (the S genome of Aegilops searsii) and aneuploid lines. Two POST rates of HM were applied to seedlings with 1-2 leaves (Zadoks stages 11-12), and the highest HM rate was also applied with the safener cloquintocet-mexyl (CM). Wheat chromosomes possessing genes associated only with natural HM tolerance were identified because Ae. searsii is HM-sensitive but CM-responsive. Lines with substitutions for 5A and 5B displayed sensitivity to HM, and experiments with nullisomic-tetrasomic (NT) lines further indicated major genes associated with HM tolerance are present on 5A and 5B chromosomes. However, the genes on 5A appear to play a larger role because lines lacking 5A chromosomes displayed more sensitivity than lines lacking 5B. Overall, these results can be utilized to guide future transcriptome analyses to identify candidate genes that confer HM tolerance in wheat.

(E)-Nerolidol is a volatile signal that induces defenses against insects and pathogens in tea plants

Plants release large amounts of volatile organic compounds (VOCs) in response to attackers. Several VOCs can serve as volatile signals to elicit defense responses in undamaged tissues and neighboring plants, but many questions about the ecological functions of VOCs remain unanswered. Tea plants are impacted by two harmful invaders, the piercing herbivore Empoasca (Matsumurasca) onukii Matsuda and the pathogen Colletotrichum fructicola. To determine the VOC signals in tea, we confirmed CsOPR3 as a marker gene and set up a rapid screening method based on a 1.51 kb CsOPR3 promoter fused with a β-glucuronidase (GUS) reporter construct (OPR3p::GUS) in Arabidopsis. Using this screening system, a terpenoid volatile (E)-nerolidol was identified as a potent signal that elicits plant defenses. The early responses triggered by (E)-nerolidol included the activation of a mitogen-activated protein kinase and WRKY, an H2O2 burst, and the induction of jasmonic acid and abscisic acid signaling. The induced plants accumulated high levels of defense-related chemicals, which possessed broad-spectrum anti-herbivore or anti-pathogen properties, and ultimately triggered resistance against Empoasca onukii and Colletotrichum fructicola in tea. We propose that these findings can supply an environmentally friendly management strategy for controlling an insect pest and a disease of tea plants.

Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode

BACKGROUND

Catalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies.

RESULTS

Restriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F₁ population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16-60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9-1, Q18-66 and Q18-73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis.

CONCLUSIONS

This is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.

Additive and heterozygous (dis)advantage GWAS models reveal candidate genes involved in the genotypic variation of maize hybrids to Azospirillum brasilense

Maize genotypes can show different responsiveness to inoculation with Azospirillum brasilense and an intriguing issue is which genes of the plant are involved in the recognition and growth promotion by these Plant Growth-Promoting Bacteria (PGPB). We conducted Genome-Wide Association Studies (GWAS) using additive and heterozygous (dis)advantage models to find candidate genes for root and shoot traits under nitrogen (N) stress and N stress plus A. brasilense. A total of 52,215 Single Nucleotide Polymorphism (SNP) markers were used for GWAS analyses. For the six root traits with significant inoculation effect, the GWAS analyses revealed 25 significant SNPs for the N stress plus A. brasilense treatment, in which only two were overlapped with the 22 found for N stress only. Most were found by the heterozygous (dis)advantage model and were more related to exclusive gene ontology terms. Interestingly, the candidate genes around the significant SNPs found for the maize-A. brasilense association were involved in different functions previously described for PGPB in plants (e.g. signaling pathways of the plant's defense system and phytohormone biosynthesis). Our findings are a benchmark in the understanding of the genetic variation among maize hybrids for the association with A. brasilense and reveal the potential for further enhancement of maize through this association.

Genome-Wide Identification and Characterization of the OPR Gene Family in Wheat (Triticum aestivum L.)

The 12-oxo-phytodienoic acid reductases (OPRs), which belong to the old yellow enzyme (OYE) family, are flavin mononucleotide (FMN)-dependent oxidoreductases with critical functions in plants. Despite the clear characteristics of growth and development, as well as the defense responses in Arabidopsis, tomato, rice, and maize, the potential roles of OPRs in wheat are not fully understood. Here, forty-eight putative OPR genes were found and classified into five subfamilies, with 6 in sub. I, 4 in sub. II, 33 in sub. III, 3 in sub. IV, and 2 in sub. V. Similar gene structures and conserved protein motifs of TaOPRs in wheat were identified in the same subfamilies. An analysis of cis-acting elements in promoters revealed that the functions of OPRs in wheat were mostly related to growth, development, hormones, biotic, and abiotic stresses. A total of 14 wheat OPR genes were identified as tandem duplicated genes, while 37 OPR genes were segmentally duplicated genes. The expression patterns of TaOPRs were tissue- and stress-specific, and the expression of TaOPRs could be regulated or induced by phytohormones and various stresses. Therefore, there were multiple wheat OPR genes, classified into five subfamilies, with functional diversification and specific expression patterns, and to our knowledge, this was the first study to systematically investigate the wheat OPR gene family. The findings not only provide a scientific foundation for the comprehensive understanding of the wheat OPR gene family, but could also be helpful for screening more candidate genes and breeding new varieties of wheat, with a high yield and stress resistance.

Crop Pollen Development under Drought: From the Phenotype to the Mechanism

Drought stress induced pollen sterility is a harmful factor that reduces crop yield worldwide. During the reproductive process, the meiotic stage and the mitotic stage in anthers are both highly vulnerable to water deficiency. Drought at these stages causes pollen sterility by affecting the nature and structure of the anthers, including the degeneration of some meiocytes, disorientated microspores, an expanded middle layer and abnormal vacuolizated tapeta. The homeostasis of the internal environment is imbalanced in drought-treated anthers, involving the decreases of gibberellic acid (GA) and auxin, and the increases of abscisic acid (ABA), jasmonic acid (JA) and reactive oxygen species (ROS). Changes in carbohydrate availability, metabolism and distribution may be involved in the effects of drought stress at the reproductive stages. Here, we summarize the molecular regulatory mechanism of crop pollen development under drought stresses. The meiosis-related genes, sugar transporter genes, GA and ABA pathway genes and ROS-related genes may be altered in their expression in anthers to repair the drought-induced injures. It could also be that some drought-responsive genes, mainly expressed in the anther, regulate the expression of anther-related genes to improve both drought tolerance and anther development. A deepened understanding of the molecular regulatory mechanism of pollen development under stress will be beneficial for breeding drought-tolerant crops with high and stable yield under drought conditions.

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 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.

Transcriptome analysis reveals the effects of grafting on sugar and α-linolenic acid metabolisms in fruits of cucumber with two different rootstocks

Flavor quality in cucumber is affected by different rootstocks, but the molecular mechanism is largely unclean. To clarify the differences of sugar and aromatic compounds, cucumber (cucumis sativus) fruits from plants of self-grafted (SG) or grafted onto figleaf gourd (Cucurbita ficifolia; G1) or 'Weisheng No.1' rootstock (Cucurbita moschata ⅹCucurbita moschata hybrids; G2) were performed the transcriptome analysis. We obtained 1013 and 920 differentially expressed genes (DEGs) from G1 and G2 compared to SG respectively, in which 453 genes were co-expressed. Functional annotations showed many DEGs were involved in glycolysis/gluconeogenesis metabolism, fructose metabolism and α-Linolenic acid metabolisms, 20 DEGs were selected from the 3 pathways to validate sequencing accuracy by quantitative real-time PCR. The gene relative expression levels were concurrent with RNA-seq results and sugar and aromatic compounds content phenotypes. Moreover, some vital transcript factors and transport proteins were analyzed. These findings indicate that different rootstocks could induce significantly changes in the physiological profiling and transcripts of sugar- and aromatic flavor-related genes. This study provides a novel insight into the molecular mechanisms of fruit quality regulated by candidate genes.

Molecular and Ultrastructural Mechanisms Underlying Yellow Dwarf Symptom Formation in Wheat after Infection of Barley Yellow Dwarf Virus

Wheat (Tritium aestivum L.) production is essential for global food security. Infection of barley yellow dwarf virus-GAV (BYDV-GAV) results in wheat showing leaf yellowing and plant dwarfism symptom. To explore the molecular and ultrastructural mechanisms underlying yellow dwarf symptom formation in BYDV-GAV-infected wheat, we investigated the chloroplast ultrastructure via transmission electron microscopy (TEM), examined the contents of the virus, H₂O₂, and chlorophyll in Zhong8601, and studied the comparative transcriptome through microarray analyses in the susceptible wheat line Zhong8601 after virus infection. TEM images indicated that chloroplasts in BYDV-GAV-infected Zhong8601 leaf cells were fragmentized. Where thylakoids were not well developed, starch granules and plastoglobules were rare. Compared with mock-inoculated Zhong8601, chlorophyll content was markedly reduced, but the virus and H₂O₂ contents were significantly higher in BYDV-GAV-infected Zhong8601. The transcriptomic analyses revealed that chlorophyll biosynthesis and chloroplast related transcripts, encoding chlorophyll a/b binding protein, glucose-6-phosphate/phosphate translocator 2, and glutamyl-tRNA reductase 1, were down-regulated in BYDV-GAV-infected Zhong8601. Some phytohormone signaling-related transcripts, including abscisic acid (ABA) signaling factors (phospholipase D alpha 1 and calcineurin B-like protein 9) and nine ethylene response factors, were up-regulated. Additionally, reactive oxygen species (ROS)-related genes were transcriptionally regulated in BYDV-GAV infected Zhong8601, including three up-regulated transcripts encoding germin-like proteins (promoting ROS accumulation) and four down-regulated transcripts encoding peroxides (scavenging ROS). These results clearly suggest that the yellow dwarf symptom formation is mainly attributed to reduced chlorophyll content and fragmentized chloroplasts caused by down-regulation of the chlorophyll and chloroplast biosynthesis related genes, ROS excessive accumulation, and precisely transcriptional regulation of the above-mentioned ABA and ethylene signaling- and ROS-related genes in susceptible wheat infected by BYDV-GAV.

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.