A novel wheat NAC transcription factor, TaNAC30, negatively regulates resistance of wheat to stripe rust

Integrative systems biology of wheat susceptibility to Fusarium graminearum uncovers a conserved gene regulatory network and identifies master regulators targeted by fungal core effectors

BACKGROUND

Plant diseases are driven by an intricate set of defense mechanisms counterbalanced by the expression of host susceptibility factors promoted through the action of pathogen effectors. In spite of their central role in the establishment of the pathology, the primary components of plant susceptibility are still poorly understood and challenging to trace especially in plant-fungal interactions such as in Fusarium head blight (FHB) of bread wheat. Designing a system-level transcriptomics approach, we leveraged the analysis of wheat responses from a susceptible cultivar facing Fusarium graminearum strains of different aggressiveness and examined their constancy in four other wheat cultivars also developing FHB.

RESULTS

In this study, we describe unexpected differential expression of a conserved set of transcription factors and an original subset of master regulators were evidenced using a regulation network approach. The dual-integration with the expression data of pathogen effector genes combined with database mining, demonstrated robust connections with the plant molecular regulators and identified relevant candidate genes involved in plant susceptibility, mostly able to suppress plant defense mechanisms. Furthermore, taking advantage of wheat cultivars of contrasting susceptibility levels, a refined list of 142 conserved susceptibility gene candidates was proposed to be necessary host's determinants for the establishment of a compatible interaction.

CONCLUSIONS

Our findings emphasized major FHB determinants potentially controlling a set of conserved responses associated with susceptibility in bread wheat. They provide new clues for improving FHB control in wheat and also could conceivably leverage further original researches dealing with a broader spectrum of plant pathogens.

Are TaNAC Transcription Factors Involved in Promoting Wheat Yield by cis-Regulation of TaCKX Gene Family?

NAC transcription factors (TFs) are one of the largest TF families in plants, and TaNACs have been known to participate in the regulation of the transcription of many yield-regulating genes in bread wheat. The TaCKX gene family members (GFMs) have already been shown to regulate yield-related traits, including grain mass and number, leaf senescence, and root growth. The genes encode cytokinin (CK) degrading enzymes (CKXs) and are specifically expressed in different parts of developing wheat plants. The aim of the study was to identify and characterize TaNACs involved in the cis-regulation of TaCKX GFMs. After analysis of the initial transcription factor data in 1.5 Kb cis-regulatory sequences of a total of 35 homologues of TaCKX GFMs, we selected five of them, namely TaCKX1-3A, TaCKX22.1-3B, TaCKX5-3D, TaCKX9-1B, and TaCKX10, and identified five TaNAC genes: TaNACJ-1, TaNAC13a, TaNAC94, TaNACBr-1, and TaNAC6D, which are potentially involved in the cis-regulation of selected TaCKX genes, respectively. Protein feature analysis revealed that all of the selected TaNACs have a conserved NAC domain and showed a stable tertiary structure model. The expression profile of the selected TaNACs was studied in 5 day-old seedling roots, 5-6 cm inflorescences, 0, 4, 7, and 14 days-after-pollination (DAP) spikes, and the accompanying flag leaves. The expression pattern showed that all of the selected TaNACs were preferentially expressed in seedling roots, 7 and 14 DAP spikes, and flag leaves compared to 5-6 cm inflorescence and 0 and 4 DAP spikes and flag leaves in Kontesa and Ostka spring wheat cultivars (cvs.). In conclusion, the results of this study highlight the potential role of the selected TaNACs in the regulation of grain productivity, leaf senescence, root growth, and response to various stresses.

Comprehensive genomic characterisation of the NAC transcription factor family and its response to drought stress in Eucommia ulmoides

The NAC transcription factor family enhances plant adaptation to environmental challenges by participating in signalling pathways triggered by abiotic stressors and hormonal cues. We identified 69 NAC genes in the Eucommia ulmoides genome and renamed them according to their chromosomal distribution. These EuNAC proteins were clustered into 13 sub-families and distributed on 16 chromosomes and 2 scaffolds. The gene structures suggested that the number of exons varied from two to eight among these EuNACs, with a multitude of them containing three exons. Duplicated events resulted in a large gene family; 12 and four pairs of EuNACs were the result of segmental and tandem duplicates, respectively. The drought-stress response pattern of 12 putative EuNACs was observed under drought treatment, revealing that these EuNACs could play crucial roles in mitigating the effects of drought stress responses and serve as promising candidate genes for genetic engineering aimed at enhancing the drought stress tolerance of E. ulmoides. This study provides insight into the evolution, diversity, and characterisation of NAC genes in E. ulmoides and will be helpful for future characterisation of putative EuNACs associated with water deficit.

The transcription factor VaNAC72-regulated expression of the VaCP17 gene from Chinese wild Vitis amurensis enhances cold tolerance in transgenic grape (V. vinifera)

Papain-like cysteine proteases (PLCP) play diverse roles in plant biology. In our previous studies, a VaCP17 gene from the cold-tolerant Vitis amurensis accession 'Shuangyou' was isolated and its role in cold tolerance was preliminarily verified in Arabidopsis. Here, we confirmed the function of VaCP17 in cold tolerance by stably overexpressing VaCP17 in the cold-sensitive Vitis vinifera cultivar 'Thompson Seedless' and transiently silencing VaCP17 in 'Shuangyou' leaves. The results showed that overexpression of VaCP17 improved the cold tolerance in 'Thompson Seedless' as manifested by reduced electrolyte leakage and malondialdehyde accumulation, chlorophyll homeostasis, increased antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) activitiy, and rapid up-regulation of stress-related genes (VvKIN2, VvRD29B, and VvNCED1) compared with wild-type line. Conversely, RNA interfere-mediated knockdown of VaCP17 in 'Shuangyou' leaves resulted in opposite physiological and biochemical responses and exacerbated leaves wilting compared with control. Subsequently, by yeast one-hybrid, dual-luciferase assays, and transient overexpression of VaNAC72 in 'Shuangyou' leaves, a VaCP17-interacting protein VaNAC72 was confirmed to promote the expression of VaCP17 under cold stress, which depends on abscisic acid, methyl jasmonate, and salicylic acid signaling. By yeast two-hybrids, bimolecular fluorescence complementation and luciferase complementation assays, it was found that VaNAC72 could form homodimers or heterodimers with VaCBF2. Furthermore, co-expression analysis confirmed that VaNAC72 works synergistically with VaCBF2 or VaCP17 to up-regulate the expression of VaCP17. In conclusion, the study revealed that the VaNAC72-VaCP17 module positively regulated cold tolerance in grapevine, and this knowledge is useful for further revealing the cold-tolerance mechanism of V. amurensis and grape molecular breeding.

Cis-Regulation by NACs: A Promising Frontier in Wheat Crop Improvement

Crop traits are controlled by multiple genes; however, the complex spatio-temporal transcriptional behavior of genes cannot be fully understood without comprehending the role of transcription factors (TFs) and the underlying mechanisms of the binding interactions of their cis-regulatory elements. NAC belongs to one of the largest families of plant-specific TFs and has been associated with the regulation of many traits. This review provides insight into the cis-regulation of genes by wheat NACs (TaNACs) for the improvement in yield-related traits, including phytohormonal homeostasis, leaf senescence, seed traits improvement, root modulation, and biotic and abiotic stresses in wheat and other cereals. We also discussed the current potential, knowledge gaps, and prospects of TaNACs.

Comprehensive Analysis of NAC Genes Reveals Differential Expression Patterns in Response to Pst DC3000 and Their Overlapping Expression Pattern during PTI and ETI in Tomato

NAC (NAM/ATAF/CUC) transcription factors belong to a unique gene family in plants, which play vital roles in regulating diverse biological processes, including growth, development, senescence, and in response to biotic and abiotic stresses. Tomato (Solanum lycopersicum), as the most highly valued vegetable and fruit crop worldwide, is constantly attacked by Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), causing huge losses in production. Thus, it is essential to conduct a comprehensive identification of the SlNAC genes involved in response to Pst DC3000 in tomato. In this study, a complete overview of this gene family in tomato is presented, including genome localization, protein domain architectures, physical and chemical features, and nuclear location score. Phylogenetic analysis identified 20 SlNAC genes as putative stress-responsive genes, named SSlNAC 1–20. Expression profiles analysis revealed that 18 of these 20 SSlNAC genes were significantly induced in defense response to Pst DC3000 stress. Furthermore, the RNA-seq data were mined and analyzed, and the results revealed the expression pattern of the 20 SSlNAC genes in response to Pst DC3000 during the PTI and ETI. Among them, SSlNAC3, SSlNAC4, SSlNAC7, SSlNAC8, SSlNAC12, SSlNAC17, and SSlNAC19 were up-regulated against Pst DC3000 during PTI and ETI, which suggested that these genes may participate in both the PTI and ETI pathway during the interaction between tomato and Pst DC3000. In addition, SSlNAC genes induced by exogenous hormones, including indole-3-acetic acid (IAA), abscisic acid (ABA), salicylic acid (SA), and methyl jasmonic acid (MeJA), were also recovered. These results implied that SSlNAC genes may participate in the Pst DC3000 stress response by multiple regulatory pathways of the phytohormones. In all, this study provides important clues for further functional analysis and of the regulatory mechanism of SSlNAC genes under Pst DC3000 stress.

Harnessing genetic resistance to rusts in wheat and integrated rust management methods to develop more durable resistant cultivars

Wheat is one of the most important staple foods on earth. Leaf rust, stem rust and stripe rust, caused by Puccini triticina, Puccinia f. sp. graminis and Puccinia f. sp. striiformis, respectively, continue to threaten wheat production worldwide. Utilization of resistant cultivars is the most effective and chemical-free strategy to control rust diseases. Convectional and molecular biology techniques identified more than 200 resistance genes and their associated markers from common wheat and wheat wild relatives, which can be used by breeders in resistance breeding programmes. However, there is continuous emergence of new races of rust pathogens with novel degrees of virulence, thus rendering wheat resistance genes ineffective. An integration of genomic selection, genome editing, molecular breeding and marker-assisted selection, and phenotypic evaluations is required in developing high quality wheat varieties with resistance to multiple pathogens. Although host genotype resistance and application of fungicides are the most generally utilized approaches for controlling wheat rusts, effective agronomic methods are required to reduce disease management costs and increase wheat production sustainability. This review gives a critical overview of the current knowledge of rust resistance, particularly race-specific and non-race specific resistance, the role of pathogenesis-related proteins, non-coding RNAs, and transcription factors in rust resistance, and the molecular basis of interactions between wheat and rust pathogens. It will also discuss the new advances on how integrated rust management methods can assist in developing more durable resistant cultivars in these pathosystems.

Genome-Wide Identification of the NAC Transcription Factors in Gossypium hirsutum and Analysis of Their Responses to Verticillium wilt

The NAC transcription factors (NACs) are among the largest plant-specific gene regulators and play essential roles in the transcriptional regulation of both biotic and abiotic stress responses. Verticillium wilt of cotton caused by Verticillium dahliae (V. dahliae) is a destructive soil-borne disease that severely decreases cotton yield and quality. Although NACs constitute a large family in upland cotton (G. hirsutum L.), there is little systematic investigation of the NACs’ responsive to V. dahliae that has been reported. To further explore the key NACs in response to V. dahliae resistance and obtain a better comprehension of the molecular basis of the V. dahliae stress response in cotton, a genome-wide survey was performed in this study. To investigate the roles of GhNACs under V. dahliae induction in upland cotton, mRNA libraries were constructed from mocked and infected roots of upland cotton cultivars with the V. dahliae-sensitive cultivar “Jimian 11” (J11) and V. dahliae-tolerant cultivar “Zhongzhimian 2” (Z2). A total of 271 GhNACs were identified. Genome analysis showed GhNACs phylogenetically classified into 12 subfamilies and distributed across 26 chromosomes and 20 scaffolds. A comparative transcriptome analysis revealed 54 GhNACs were differentially expressed under V. dahliae stress, suggesting a potential role of these GhNACs in disease response. Additionally, one NAC090 homolog, GhNAC204, could be a positive regulator of cotton resistance to V. dahliae infection. These results give insight into the GhNAC gene family, identify GhNACs’ responsiveness to V. dahliae infection, and provide potential molecular targets for future studies for improving V. dahliae resistance in cotton.

Genome-Wide Survey and Functional Verification of the NAC Transcription Factor Family in Wild Emmer Wheat

The NAC transcription factor (TF) family is one of the largest TF families in plants, which has been widely reported in rice, maize and common wheat. However, the significance of the NAC TF family in wild emmer wheat (Triticum turgidum ssp. dicoccoides) is not yet well understood. In this study, a genome-wide investigation of NAC genes was conducted in the wild emmer genome and 249 NAC family members (TdNACs) were identified. The results showed that all of these genes contained NAM/NAC-conserved domains and most of them were predicted to be located on the nucleus. Phylogenetic analysis showed that these 249 TdNACs can be classified into seven clades, which are likely to be involved in the regulation of grain protein content, starch synthesis and response to biotic and abiotic stresses. Expression pattern analysis revealed that TdNACs were highly expressed in different wheat tissues such as grain, root, leaves and shoots. We found that TdNAC8470 was phylogenetically close to NAC genes that regulate either grain protein or starch accumulation. Overexpression of TdNAC8470 in rice showed increased grain starch concentration but decreased grain Fe, Zn and Mn contents compared with wild-type plants. Protein interaction analysis indicated that TdNAC8470 might interact with granule-bound starch synthase 1 (TdGBSS1) to regulate grain starch accumulation. Our work provides a comprehensive understanding of the NAC TFs family in wild emmer wheat and establishes the way for future functional analysis and genetic improvement of increasing grain starch content in wheat.

Current understanding of atypical resistance against fungal pathogens in wheat

Pathogens and pests are a major challenge to global food security. Around one hundred different pests and pathogens challenge wheat, one of the most important food crops in the world. Traditional worldwide use of a few key resistance genes in wheat cultivars has necessitated a diversification of the toolbox of resistance genes in wheat varieties over the coming decades to meet the global production demands. Recent advances in gene discovery and functional characterization of genetic resistance mechanisms in wheat reveal great diversity in the types and effectiveness of the underlying resistance genes. This article summarizes the recent developments in the discovery of non-traditional "atypical" resistance genes in wheat against diverse fungal pathogens.

Potential Targets for CRISPR/Cas Knockdowns to Enhance Genetic Resistance Against Some Diseases in Wheat (Triticum aestivum L.)

Wheat is one of the most important food crops worldwide. Even though wheat yields have increased considerably in recent years, future wheat production is predicted to face enormous challenges due to global climate change and new versions of diseases. CRISPR/Cas technology is a clean gene technology and can be efficiently used to target genes prone to biotic stress in wheat genome. Herein, the published research papers reporting the genetic factors corresponding to stripe rust, leaf rust, stem rust, powdery mildew, fusarium head blight and some insect pests were critically reviewed to identify negative genetic factors (Susceptible genes) in bread wheat. Out of all reported genetic factors related to these disease, 33 genetic factors (S genes) were found as negative regulators implying that their down-regulation, deletion or silencing improved disease tolerance/resistance. The results of the published studies provided the concept of proof that these 33 genetic factors are potential targets for CRISPR/Cas knockdowns to improve genetic tolerance/resistance against these diseases in wheat. The sequences of the 33 genes were retrieved and re-mapped on the latest wheat reference genome IWGSC RefSeq v2.1. Phylogenetic analysis revealed that pathogens causing the same type of disease had some common conserved motifs and were closely related. Considering the significance of these disease on wheat yield, the S genes identified in this study are suggested to be disrupted using CRISPR/Cas system in wheat. The knockdown mutants of these S genes will add to genetic resources for improving biotic stress resistance in wheat crop.

Comparative transcriptome analysis of resistant and susceptible wheat in response to Rhizoctonia cerealis

BACKGROUND

Sheath blight is an important disease caused by Rhizoctonia cerealis that affects wheat yields worldwide. No wheat varieties have been identified with high resistance or immunity to sheath blight. Understanding the sheath blight resistance mechanism is essential for controlling this disease. In this study, we investigated the response of wheat to Rhizoctonia cerealis infection by analyzing the cytological changes and transcriptomes of common wheat 7182 with moderate sensitivity to sheath blight and H83 with moderate resistance.

RESULTS

The cytological observation showed that the growth of Rhizoctonia cerealis on the surface and its expansion inside the leaf sheath tissue were more rapid in the susceptible material. According to the transcriptome sequencing results, a total of 88685 genes were identified in both materials, including 20156 differentially expressed genes (DEGs) of which 12087 was upregulated genes and 8069 was downregulated genes. At 36 h post-inoculation, compared with the uninfected control, 11498 DEGs were identified in resistant materials, with 5064 downregulated genes and 6434 upregulated genes, and 13058 genes were detected in susceptible materials, with 6759 downregulated genes and 6299 upregulated genes. At 72 h post-inoculation, compared with the uninfected control, 6578 DEGs were detected in resistant materials, with 2991 downregulated genes and 3587 upregulated genes, and 7324 genes were detected in susceptible materials, with 4119 downregulated genes and 3205 upregulated genes. Functional annotation and enrichment analysis showed that the main pathways enriched for the DEGs included biosynthesis of secondary metabolites, carbon metabolism, plant hormone signal transduction, and plant-pathogen interaction. In particular, phenylpropane biosynthesis pathway is specifically activated in resistant variety H83 after infection. Many DEGs also belonged to the MYB, AP2, NAC, and WRKY transcription factor families.

CONCLUSIONS

Thus, we suggest that the normal functioning of plant signaling pathways and differences in the expression of key genes and transcription factors in some important metabolic pathways may be important for defending wheat against sheath blight. These findings may facilitate further exploration of the sheath blight resistance mechanism in wheat and the cloning of related genes.

Genome-Wide Identification and Characterization of NAC Family in Hibiscus hamabo Sieb. et Zucc. under Various Abiotic Stresses

NAC transcription factor is one of the largest plant gene families, participating in the regulation of plant biological and abiotic stresses. In this study, 182 NAC proteins (HhNACs) were identified based on genomic datasets of Hibiscus hamabo Sieb. et Zucc (H. hamabo). These proteins were divided into 19 subfamilies based on their phylogenetic relationship, motif pattern, and gene structure analysis. Expression analysis with RNA-seq revealed that most HhNACs were expressed in response to drought and salt stress. Research of quantitative real-time PCR analysis of nine selected HhNACs supported the transcriptome data’s dependability and suggested that HhNAC54 was significantly upregulated under multiple abiotic stresses. Overexpression of HhNAC54 in Arabidopsis thaliana (A. thaliana) significantly increased its tolerance to salt. This study provides a basis for a comprehensive analysis of NAC transcription factor and insight into the abiotic stress response mechanism in H. hamabo.

Prediction of effector proteins and their implications in pathogenicity of phytopathogenic filamentous fungi: A review

Plant pathogenic fungi encode and secrete effector proteins to promote pathogenesis. In recent years, the important role of effector proteins in fungi and plant host interactions has become increasingly prominent. In this review, the functional characterization and molecular mechanisms by which fungal effector proteins modulate biological processes and suppress the defense of plant hosts are discussed, with an emphasis on cell localization during fungal infection. This paper also provides a comprehensive review of bioinformatic and experimental methods that are currently available for the identification of fungal effector proteins. We additionally summarize the secretion pathways and the methods for verifying the presence effector proteins in plant host cells. For future research, comparative genomic studies of different pathogens with varying life cycles will allow comprehensive and systematic identification of effector proteins. Additionally, functional analysis of effector protein interactions with a wider range of hosts (especially non-model crops) will provide more detailed repertoires of fungal effectors. Identifying effector proteins and verifying their functions will improve our understanding of their role in causing disease and in turn guide future strategies for combatting fungal infections.

A NAC Transcription Factor TuNAC69 Contributes to ANK-NLR-WRKY NLR-Mediated Stripe Rust Resistance in the Diploid Wheat Triticum urartu

Stripe rust is one of the most devastating diseases in wheat. Nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain receptors (NLRs) recognize pathogenic effectors and trigger plant immunity. We previously identified a unique NLR protein YrU1 in the diploid wheat Triticum urartu, which contains an N-terminal ANK domain and a C-terminal WRKY domain and confers disease resistance to stripe rust fungus Puccinia striiformis f. sp. Tritici (Pst). However, how YrU1 functions in disease resistance is not clear. In this study, through the RNA-seq analysis, we found that the expression of a NAC member TuNAC69 was significantly up-regulated after inoculation with Pst in the presence of YrU1. TuNAC69 was mainly localized in the nucleus and showed transcriptional activation in yeast. Knockdown TuNAC69 in diploid wheat Triticum urartu PI428309 that contains YrU1 by virus-induced gene silencing reduced the resistance to stripe rust. In addition, overexpression of TuNAC69 in Arabidopsis enhanced the resistance to powdery mildew Golovinomyces cichoracearum. In summary, our study indicates that TuNAC69 participates in the immune response mediated by NLR protein YrU1, and likely plays an important role in disease resistance to other pathogens.

The Roles of CCCH Zinc-Finger Proteins in Plant Abiotic Stress Tolerance

Zinc-finger proteins, a superfamily of proteins with a typical structural domain that coordinates a zinc ion and binds nucleic acids, participate in the regulation of growth, development, and stress adaptation in plants. Most zinc fingers are C2H2-type or CCCC-type, named after the configuration of cysteine (C) and histidine (H); the less-common CCCH zinc-finger proteins are important in the regulation of plant stress responses. In this review, we introduce the domain structures, classification, and subcellular localization of CCCH zinc-finger proteins in plants and discuss their functions in transcriptional and post-transcriptional regulation via interactions with DNA, RNA, and other proteins. We describe the functions of CCCH zinc-finger proteins in plant development and tolerance to abiotic stresses such as salt, drought, flooding, cold temperatures and oxidative stress. Finally, we summarize the signal transduction pathways and regulatory networks of CCCH zinc-finger proteins in their responses to abiotic stress. CCCH zinc-finger proteins regulate the adaptation of plants to abiotic stress in various ways, but the specific molecular mechanisms need to be further explored, along with other mechanisms such as cytoplasm-to-nucleus shuttling and post-transcriptional regulation. Unraveling the molecular mechanisms by which CCCH zinc-finger proteins improve stress tolerance will facilitate the breeding and genetic engineering of crops with improved traits.

Transcriptome analysis of sesame-Macrophomina phaseolina interactions revealing the distinct genetic components for early defense responses

Sesame (Sesamum indicum L.) is an oilseed crop challenged by many biotic stresses. Charcoal rot caused by Macrophomina phaseolina (MP) is one of the most devastating diseases of sesame. Till date, molecular mechanisms of resistance to charcoal rot in sesame is not yet reported. In this study, two sesame variety GT-10 (resistant) and RT-373 (susceptible) were identified with contrasting disease incidence when infected with MP. To get the molecular insight, root samples were collected at 0, 24, 48- and 72-h post inoculation (hpi) with the pathogen and generated RNAseq data was analyzed. A total of 1153 and 1226 differentially expressed genes (DEGS) were identified in GT-10 and RT-373, respectively. During the inoculation with MP, resistant genotype showed high number DEGs at early time point of 24 hpi and when compared to late expression in susceptible genotype at 48 hpi. Distinct clusters were represented for each time period represented by cytochrome P450 83B1-like, single anchor, hypothetical protein C4D60, kirola like and heat shock proteins in the resistant genotype contributing for resistance. Analysis of differentially expressed genes, catalogued the genes involved in synthesis of pathogenesis-related (PR) proteins, MYB, WRKY, leucine zipper protein, bHLH, bZIP and NAC transcription factors, ABC transporters (B, C and G subfamily), glutathione metabolism, secondary metabolites, fatty acid biosynthesis and phytohormones like auxin, abscisic acid, ethylene and gibberellic acid. Additionally, in the resistant response we have found three unique GO terms including ATP binding, ribonucleotide binding and nucleic acid binding in molecular function category. The molecular clues generated through this work will provide an important resource of genes contributing for disease resistance and could prioritize genes for functional validation in the important oil crop.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01039-6.

Genome Identification and Expression Analysis of GRAS Family Related to Development, Hormone and Pathogen Stress in Brachypodium distachyon

GRAS transcription factors are widely present in the plant kingdom and play important roles in regulating multiple plant physiological processes. Brachypodium distachyon is a model for grasses for researching plant-pathogen interactions. However, little is known about the BdGRAS family genes involved in plant response to biotic stress. In this study, we identified 63 genes of the GRAS family in B. distachyon. The phylogenetic analysis showed that BdGRAS genes were divided into ten subfamilies and unevenly distributed on five chromosomes. qRT-PCR results showed that the BdGRAS family genes were involved in the growth and development of B. distachyon. Moreover, the expression of the HAM subfamily genes of BdGRAS changed during the interaction between B. distachyon and Magnaporthe oryzae. Interestingly, BdGRAS31 in the HAM subfamily was regulated by miR171 after inoculation with M. oryzae. These results provide insight into the potential functions of the BdGRAS family in disease resistance.

Melatonin promotes potassium deficiency tolerance by regulating HAK1 transporter and its upstream transcription factor NAC71 in wheat

Melatonin (MT) is involved in various physiological processes and stress responses in animals and plants. However, little is known about the molecular mechanisms by which MT regulates potassium deficiency (DK) tolerance in crops. In this study, an appropriate concentration (50 μmol/L) was found to enhance the tolerance of wheat plants against DK. RNA-seq analysis showed that a total of 6253 and 5873 differentially expressed genes (DEGs) were separately identified in root and leaf tissues of the DK + MT-treated wheat plants. They functionally involved biological processes of secondary metabolite, signal transduction, and transport or catabolism. Of these, an upregulated high-affinity K transporter 1 (TaHAK1) gene was next characterized. TaHAK1 overexpression markedly enhanced the K absorption, while its transient silencing exhibited the opposite effect, suggesting its important role in MT-mediated DK tolerance. Moreover, yeast one-hybrid (Y1H) was used to screen the upstream regulators of TaHAK1 gene and the transcription factor TaNAC71 was identified. The binding between TaNAC71 and TaHAK1 promoter was evidenced by using Y1H, LUC, and EMSA assays. Transient overexpression of TaNAC71 in wheat protoplasts activated the TaHAK1 expression, whereas its transient silencing inhibited the TaHAK1 expression and aggravated the sensitivity to DK. Exogenous MT application greatly upregulated the expression of TaHAK1 in both transient overexpression and silencing systems. Our findings revealed some molecular mechanisms underlying MT-mediated DK tolerance and helped broaden its practical application in agriculture.

The mechanism of sesame resistance against Macrophomina phaseolina was revealed via a comparison of transcriptomes of resistant and susceptible sesame genotypes

BACKGROUND

Sesame (Sesamum indicum) charcoal rot, a destructive fungal disease caused by Macrophomina phaseolina (Tassi) Goid (MP), is a great threat to the yield and quality of sesame. However, there is a lack of information about the gene-for-gene relationship between sesame and MP, and the molecular mechanism behind the interaction is not yet clear. The aim of this study was to interpret the molecular mechanism of sesame resistance against MP in disease-resistant (DR) and disease-susceptible (DS) genotypes based on transcriptomics. This is the first report of the interaction between sesame and MP using this method.

RESULTS

A set of core genes that response to MP were revealed by comparative transcriptomics and they were preferentially associated with GO terms such as ribosome-related processes, fruit ripening and regulation of jasmonic acid mediated signalling pathway. It is also exhibited that translational mechanism and transcriptional mechanism could co-activate in DR so that it can initiate the immunity to MP more rapidly. According to weighted gene co-expression network analysis (WGCNA) of differentially expressed gene sets between two genotypes, we found that leucine-rich repeat receptor-like kinase (LRR-RLK) proteins may assume an important job in sesame resistance against MP. Notably, compared with DS, most key genes were induced in DR such as pattern recognition receptors (PRRs) and resistance genes, indicating that DR initiated stronger pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Finally, the study showed that JA/ET and SA signalling pathways all play an important role in sesame resistance to MP.

CONCLUSIONS

The defence response to MP of sesame, a complex bioprocess involving many phytohormones and disease resistance-related genes, was illustrated at the transcriptional level in our investigation. The findings shed more light on further understanding of different responses to MP in resistant and susceptible sesame.

NAC Transcription Factors as Positive or Negative Regulators during Ongoing Battle between Pathogens and Our Food Crops

The NAC (NAM, ATAF1/2, and CUC2) family of proteins is one of the largest plant-specific transcription factor (TF) families and its members play varied roles in plant growth, development, and stress responses. In recent years, NAC TFs have been demonstrated to participate in crop-pathogen interactions, as positive or negative regulators of the downstream defense-related genes. NAC TFs link signaling pathways between plant hormones, including salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA), or other signals, such as reactive oxygen species (ROS), to regulate the resistance against pathogens. Remarkably, NAC TFs can also contribute to hypersensitive response and stomatal immunity or can be hijacked as virulence targets of pathogen effectors. Here, we review recent progress in understanding the structure, biological functions and signaling networks of NAC TFs in response to pathogens in several main food crops, such as rice, wheat, barley, and tomato, and explore the directions needed to further elucidate the function and mechanisms of these key signaling molecules.

TaNAC35 acts as a negative regulator for leaf rust resistance in a compatible interaction between common wheat and Puccinia triticina

NAC (NAM, AFAT1/2, and CUC2) transcription factors play important roles in plant growth and in resistance to abiotic and biotic stresses. Here, we show that the TaNAC35 gene negatively regulates leaf rust resistance in the wheat line Thatcher + Lr14b (TcLr14b) when challenged with a virulent isolate of Puccinia triticina (Pt). The TaNAC35 gene was cloned from this line, and blastp results showed that its open reading frame (ORF) was 96.16% identical to the NAC35-like sequence reported from Aegilops tauschii, and that it encoded a protein with 387 amino acids (aa) including a conserved NAM domain with 145 aa at the N-terminal alongside the transcriptional activation domain with 220 aa in the C-terminal. Yeast-one-hybrid analysis proved that the C-terminal of the TaNAC35 protein was responsible for transcriptional activation. A 250-bp fragment from the 3'-end of this target gene was introduced to a BSMV-VIGS vector and used to infect the wheat line Thatcher + Lr14b (TcLr14b). The BSMV-VIGS/TaNAC35-infected plant material showed enhanced resistance (infection type "1") to Pt pathotype THTT, which was fully virulent (infection type "4") on BSMV-VIGS only infected TcLr14b plants. Histological studies showed that inhibition of TaNAC35 reduced the formation of haustorial mother cells (HMC) and mycelial growth, implying that the TaNAC35 gene plays a negative role in the response of TcLr14b to Pt pathotype THTT. These results provide molecular insight into the interaction between Pt and its wheat host, and identify a potential target for engineering resistance in wheat to this damaging pathogen.

Role of Genetics, Genomics, and Breeding Approaches to Combat Stripe Rust of Wheat

Puccinia striiformis (Pst) is a devastating biotrophic fungal pathogen that causes wheat stripe rust. It usually loves cool and moist places and can cause 100% crop yield losses in a single field when ideal conditions for disease incidence prevails. Billions of dollars are lost due to fungicide application to reduce stripe rust damage worldwide. Pst is a macrocyclic, heteroecious fungus that requires primary (wheat or grasses) as well as secondary host (Berberis or Mahonia spp.) for completion of life cycle. In this review, we have summarized the knowledge about pathogen life cycle, genes responsible for stripe rust resistance, and susceptibility in wheat. In the end, we discussed the importance of conventional and modern breeding tools for the development of Pst-resistant wheat varieties. According to our findings, genetic engineering and genome editing are less explored tools for the development of Pst-resistant wheat varieties; hence, we highlighted the putative use of advanced genome-modifying tools, i.e., base editing and prime editing, for the development of Pst-resistant wheat.

Wheat Transcription Factor TaSNAC11-4B Positively Regulates Leaf Senescence through Promoting ROS Production in Transgenic Arabidopsis

Senescence is the final stage of leaf development which is accompanied by highly coordinated and complicated reprogramming of gene expression. Genetic manipulation of leaf senescence in major crops including wheat has been shown to be able to increase stress tolerance and grain yield. NAC(No apical meristem (NAM), ATAF1/2, and cup-shaped cotyledon (CUC)) transcription factors (TFs) play important roles in regulating gene expression changes during leaf senescence and in response to abiotic stresses. Here, we report the characterization of TaSNAC11-4B (Uniprot: A0A1D5XI64), a wheat NAC family member that acts as a functional homolog of AtNAP, a key regulator of leaf senescence in Arabidopsis. The expression of TaSNAC11-4B was up-regulated with the progression of leaf senescence, in response to abscisic acid (ABA) and drought treatments in wheat. Ectopic expression of TaSNAC11-4B in Arabidopsis promoted ROS accumulation and significantly accelerated age-dependent as well as drought- and ABA-induced leaf senescence. Results from transcriptional activity assays indicated that the TaSNAC11-4B protein displayed transcriptional activation activities that are dependent on its C terminus. Furthermore, qRT-PCR and dual-Luciferase assay results suggested that TaSNAC11-4B could positively regulate the expression of AtrbohD and AtrbohF, which encode catalytic subunits of the ROS-producing NADPH oxidase. Further analysis of TaSNAC11-4B in wheat senescence and the potential application of this gene in manipulating leaf senescence with the purpose of yield increase and stress tolerance is discussed.

Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut

BACKGROUND

Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. However, little is known about NAC genes in peanut.

RESULTS

We performed a genome-wide characterization of NAC genes from the diploid wild peanut species Arachis duranensis and Arachis ipaensis, which included analyses of chromosomal locations, gene structures, conserved motifs, expression patterns, and cis-acting elements within their promoter regions. In total, 81 and 79 NAC genes were identified from A. duranensis and A. ipaensis genomes. Phylogenetic analysis of peanut NACs along with their Arabidopsis and rice counterparts categorized these proteins into 18 distinct subgroups. Fifty-one orthologous gene pairs were identified, and 46 orthologues were found to be highly syntenic on the chromosomes of both A. duranensis and A. ipaensis. Comparative RNA sequencing (RNA-seq)-based analysis revealed that the expression of 43 NAC genes was up- or downregulated under salt stress and under drought stress. Among these genes, the expression of 17 genes in cultivated peanut (Arachis hypogaea) was up- or downregulated under both stresses. Moreover, quantitative reverse transcription PCR (RT-qPCR)-based analysis revealed that the expression of most of the randomly selected NAC genes tended to be consistent with the comparative RNA-seq results.

CONCLUSION

Our results facilitated the functional characterization of peanut NAC genes, and the genes involved in salt and drought stress responses identified in this study could be potential genes for peanut improvement.

A wheat R2R3 MYB gene TaMpc1-D4 negatively regulates drought tolerance in transgenic Arabidopsis and wheat

MYB transcription factors (TFs) are one of the largest TF families, and R2R3-type MYB TFs participate in the multiply abiotic stress responses in wheat. In this study, an R2R3-type MYB gene Myb protein colourless 1 located on chromosome D (named TaMpc1-D4), was cloned from wheat. TaMpc1-D4-GFP protein was localized in the nucleus. Overexpression of TaMpc1-D4 reduced drought tolerance in transgenic Arabidopsis lines, which was supported by the lower germination rate, the shorter root length, a higher level of O₂^- and malonaldehyde (MDA), the decreased proline content, and limited activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT). Furthermore, P5CS1, RD29A, RD29B, DREB2A, ABF3, CBF1, CBF2, CBF3, ERF1, POD1, SOD (Cu/Zn), and CAT1 genes related to the stress and antioxidant system were remarkably down-regulated in TaMpc1-D4 transgenic Arabidopsis lines under drought stress. Silencing TaMpc1-D4 expression in wheat enhanced the relative water content (RWC), the proline content, and the activities of antioxidant enzymes, and activated stress-related and antioxidant-related genes (DREB1, DREB3, ERF3, ERF4b, ABF, P5CS, POD, SOD (Fe), and CAT). Taken together, these results indicated that TaMpc1-D4 negatively modulated drought tolerance by regulating the capacity of the enzyme system and the expression of stress-related and antioxidant-related genes.

Genome-wide identification and characterization of SRO gene family in wheat: Molecular evolution and expression profiles during different stresses

SRO (SIMILAR TO RCD ONE), a type of plant-specific small protein family, play important roles in plant growth and development, as well as in response to biotic/abiotic stresses. Although characterization of SROs have been performed in model plants, little is known about their function in wheat, especially under stress conditions. In this study, 30 SRO genes were identified from the wheat genome (TaSRO). They were phylogenetically separated into two groups with distinct structures. The cis-regulatory elements in the promoter region of TaSROs were analyzed and numerous elements functionally associated with stress responding and hormones were interpreted, implying the reason for induction expression patterns of TaSROs during abiotic and biotic stresses in wheat. Whole-genome replication events in the SRO gene family of wheat and seven other species (Arabidopsis thaliana, rice, maize, barley, soybean, upland cotton, and cucumber) were analyzed, resulting in 1, 12, 9, 23, 6, 5, and 3 of gene pairs, respectively. The tissue-specific expression pattern profiling revealed that most TaSROs are highly expressed in one or more tissues and may play an important role in wheat growth and development. In addition, qRT-PCR results further confirmed that these TaSRO genes are involved in wheat stress response. In summary, our study laid a theoretical basis for molecular function deciphering of TaSROs, especially in plant hormones and biotic/abiotic stress responses.

NAC transcription factor involves in regulating bacterial wilt resistance in potato

Bacterial wilt (BW) is a serious disease that affects potato (Solanum tuberosum L.) production. Although resistance to this disease has been reported, the underlying mechanism is unknown. In this study, we identified a NAC family transcription factor (StNACb4) from potato and characterised its structure, function, expression, its localisation at the tissue and its role in BW resistance. To this end, the transgenic Nicotiana benthamiana Domin lines were generated in which the expression of NACb4 was constitutively upregulated or suppressed using RNAi. Different tobacco mutants were stained after inoculating with Ralstonia solanacearum to observe the cell death and callose deposition. The results indicated that StNACb4 could be upregulated under the induction of R. solanacearum, and salicylic acid, abscisic acid and methyl jasmonate could also induce the expression of StNACb4. Tissue localisation analysis indicated that its expression was tissue specific, and it was mainly in the phloem of the vascular system of stems and leaves. NbNACb4 gene silencing can enhance the sensitivity of tobacco to R. solanacearum; on the contrary, StNACb4 gene overexpression can enhance the tolerance of tobacco to R. solanacearum. Meanwhile, StNACb4 gene overexpression can induce cell death and callose deposition in tobacco. The upregulated expression of StNACb4 can also activate the StPR10 gene expression. Our results provide important new insights into the regulatory mechanisms of bacterial wilt resistance in potato.

Genome-Wide Analysis of the Role of NAC Family in Flower Development and Abiotic Stress Responses in Cleistogenes songorica

Plant-specific NAC (NAM, ATAF, CUC) transcription factor (TF) family plays important roles in biological processes such as plant growth and response to stress. Nevertheless, no information is known about NAC TFs in Cleistogenes songorica, a prominent xerophyte desert grass in northwestern China. In this study, 162 NAC genes were found from the Cleistogenes songorica genome, among which 156 C. songoricaNAC (CsNAC) genes (96.3%) were mapped onto 20 chromosomes. The phylogenetic tree constructed by CsNAC and rice NAC TFs can be separated into 14 subfamilies. Syntenic and Ka/Ks analyses showed that CsNACs were primarily expanded by genomewide replication events, and purifying selection was the primary force driving the evolution of CsNAC family genes. The CsNAC gene expression profiles showed that 36 CsNAC genes showed differential expression between cleistogamous (CL) and chasmogamous (CH) flowers. One hundred and two CsNAC genes showed differential expression under heat, cold, drought, salt and ABA treatment. Twenty-three CsNAC genes were commonly differentially expressed both under stress responses and during dimorphic floret development. Gene Ontology (GO) annotation, coexpression network and qRT-PCR tests revealed that these CsNAC genes may simultaneously regulate dimorphic floret development and the response to stress. Our results may help to characterize the NAC transcription factors in C. songorica and provide new insights into the functional research and application of the NAC family in crop improvement, especially in dimorphic floret plants.

Transcription Factors in Plant Stress Responses: Challenges and Potential for Sugarcane Improvement

Increasing vulnerability of crops to a wide range of abiotic and biotic stresses can have a marked influence on the growth and yield of major crops, especially sugarcane (Saccharum spp.). In response to various stresses, plants have evolved a variety of complex defense systems of signal perception and transduction networks. Transcription factors (TFs) that are activated by different pathways of signal transduction and can directly or indirectly combine with cis-acting elements to modulate the transcription efficiency of target genes, which play key regulators for crop genetic improvement. Over the past decade, significant progresses have been made in deciphering the role of plant TFs as key regulators of environmental responses in particular important cereal crops; however, a limited amount of studies have focused on sugarcane. This review summarizes the potential functions of major TF families, such as WRKY, NAC, MYB and AP2/ERF, in regulating gene expression in the response of plants to abiotic and biotic stresses, which provides important clues for the engineering of stress-tolerant cultivars in sugarcane.

Genome-wide analysis of ethylene-response factor family in adzuki bean and functional determination of VaERF3 under saline-alkaline stress

Ethylene-response factor (ERF) proteins are members of a transcription factor family involved in plant growth and environmental stress responses, but the biological functions of ERF members in adzuki bean (Vigna angularis var. angularis) remain unknown. In addition, it is unclear whether these proteins have a role in regulating responses to abiotic stressors. Here, we identified 47 ERF genes by analyzing the adzuki bean genome. Whole-transcriptome analyses of plants under saline-alkaline stress suggested that the expression of 13 ERF genes was induced in response to saline-alkaline stress. Analysis of the cis-acting elements showed that the promoters of these saline-alkaline stress-inducible ERF genes contained LTRs, DREs, MYBs, ABREs, MYCs, CGTCA-, and TGACG-motifs, which are involved in abiotic stress responses. The expression of VaERF3 was induced by NaHCO₃, polyethylene glycol 6000, NaCl, and ABA (abscisic acid), as determined by qRT-PCR. Overexpression of VaERF3 in transgenic Arabidopsis resulted in higher levels of proline accumulation and lower malondialdehyde and reactive oxygen species contents in plants grown under saline-alkaline stress conditions. Moreover, VaERF3 encoded a nuclear-localized transcriptional activator that promoted the expression of stress-responsive genes. Collectively, these results are of great significance in elucidating the mechanisms of saline-alkaline stress responses in adzuki bean.

A wheat NAC interacts with an orphan protein and enhances resistance to Fusarium head blight disease

Taxonomically-restricted orphan genes play an important role in environmental adaptation, as recently demonstrated by the fact that the Pooideae-specific orphan TaFROG (Triticum aestivum Fusarium Resistance Orphan Gene) enhanced wheat resistance to the economically devastating Fusarium head blight (FHB) disease. Like most orphan genes, little is known about the cellular function of the encoded protein TaFROG, other than it interacts with the central stress regulator TaSnRK1α. Here, we functionally characterized a wheat (T. aestivum) NAC-like transcription factor TaNACL-D1 that interacts with TaFROG and investigated its' role in FHB using studies to assess motif analyses, yeast transactivation, protein-protein interaction, gene expression and the disease response of wheat lines overexpressing TaNACL-D1. TaNACL-D1 is a Poaceae-divergent NAC transcription factor that encodes a Triticeae-specific protein C-terminal region with transcriptional activity and a nuclear localisation signal. The TaNACL-D1/TaFROG interaction was detected in yeast and confirmed in planta, within the nucleus. Analysis of multi-protein interactions indicated that TaFROG could form simultaneously distinct protein complexes with TaNACL-D1 and TaSnRK1α in planta. TaNACL-D1 and TaFROG are co-expressed as an early response to both the causal fungal agent of FHB, Fusarium graminearum and its virulence factor deoxynivalenol (DON). Wheat lines overexpressing TaNACL-D1 were more resistant to FHB disease than wild type plants. Thus, we conclude that the orphan protein TaFROG interacts with TaNACL-D1, a NAC transcription factor that forms part of the disease response evolved within the Triticeae.

Genome-Wide Characterization and Expression Profiling of Squamosa Promoter Binding Protein-like (SBP) Transcription Factors in Wheat (Triticum aestivum L.)

Transcription factors (TFs) play fundamental roles in the developmental processes of all living organisms. Squamosa Promoter Binding Protein-like (SBP/SBP-Box) is a major family of plant-specific TFs, which plays important roles in multiple processes involving plant growth and development. While some work has been done, there is a lot more that is yet to be discovered in the hexaploid wheat SBP (TaSBP) family. With the completion of whole genome sequencing, genome-wide analysis of SBPs in common hexaploid wheat is now possible. In this study, we used protein–protein Basic Local Alignment Search Tool (BLASTp) to hunt the newly released reference genome sequence of hexaploid wheat (Chinese spring). Seventy-four TaSBP proteins (belonging to 56 genes) were identified and clustered into five groups. Gene structure and motif analysis indicated that most TaSBPs have relatively conserved exon–intron arrangements and motif composition. Analysis of transcriptional data showed that many TaSBP genes responded to some biological and abiotic stresses with different expression patterns. Moreover, three TaSBP genes were generally expressed in the majority of tissues throughout the wheat growth and also responded to many environmental biotic and abiotic stresses. Collectively, the detailed analyses presented here will help in understanding the roles of the TaSBP and also provide a reference for the further study of its biological function in wheat.

Novel Maize NAC Transcriptional Repressor ZmNAC071 Confers Enhanced Sensitivity to ABA and Osmotic Stress by Downregulating Stress-Responsive Genes in Transgenic Arabidopsis

NAC TFs play crucial roles in response to abiotic stresses in plants. Here, ZmNAC071 was identified as a nuclear located transcriptional repressor. Overexpression of ZmNAC071 in Arabidopsis enhanced sensitivity of transgenic plants to ABA and osmotic stress. The expression levels of SODs, PODs, P5CSs, and AtMYB61 were inhibited by ZmNAC071, which results in reduced ROS scavenging and proline content, increased ROS level, and water loss. Besides, the expression levels of some ABA or abiotic stress-related genes, like ABIs, RD29A, DREBs, and LEAs were also significantly inhibited by ZmNAC071. Yeast one-hybrid assay demonstrated that ZmNAC071 specifically bound to the cis-acting elements containing CGT[G/A] core sequences in the promoter of stress-related genes, suggesting that ZmNAC071 may participate in the regulation of transcription of these genes through recognizing the core sequences CGT[G/A]. These results will facilitate further studies concerning the cis-elements and downstream genes targeted by ZmNAC071 in maize.

TaNAC6s are involved in the basal and broad-spectrum resistance to powdery mildew in wheat

NACs are important transcriptional factors involved in growth and development as well as responses to abiotic and biotic stresses in plants. In this study, TaNAC6 was identified as a differentially expressed gene between two lines with broad-spectrum resistance to powdery mildew, NAU9918 and OE_Stpk-V, and their corresponding susceptible isogenic lines, SM-1 and Yangmai158, after Bgt inoculation by transcriptome analysis. Then, three homoeologous genes of TaNAC6 were cloned and named as TaNAC6-A, TaNAC6-B and TaNAC6-D, respectively. Each member of TaNAC6s was subcellular localized to the nucleus and displayed the transcriptional activation activity. However, the responses of them to pathogens and phytohormones were different. Transient overexpression of each TaNAC6 reduced the haustorium index of Yangmai158, and stable transformation of TaNAC6-A enhanced its resistance against Bgt, implying that TaNAC6s play important roles in basal resistance. Silencing of TaNAC6s compromised the resistance of OE_Stpk-V and NAU9918 suggesting that TaNAC6s play positive roles in the broad-spectrum resistance against Bgt. TaNAC6s might be induced by JA and then feedback regulate the JA pathway leading to improved resistance to Bgt. The role of TaNAC6s and their orthologous genes HvNAC6 and ATAF1 in the powdery mildew resistance implied these NAC6 genes share a common signal pathway across species.