NAC transcription factor family genes are differentially expressed in rice during infections with Rice dwarf virus, Rice black-streaked dwarf virus, Rice grassy stunt virus, Rice ragged stunt virus, and Rice transitory yellowing virus

OsNAC103, an NAC transcription factor negatively regulates plant height in rice

MAIN CONCLUSION

OsNAC103 negatively regulates rice plant height by influencing the cell cycle and crosstalk of phytohormones. Plant height is an important characteristic of rice farming and is directly related to agricultural yield. Although there has been great progress in research on plant growth regulation, numerous genes remain to be elucidated. NAC transcription factors are widespread in plants and have a vital function in plant growth. Here, we observed that the overexpression of OsNAC103 resulted in a dwarf phenotype, whereas RNA interference (RNAi) plants and osnac103 mutants showed no significant difference. Further investigation revealed that the cell length did not change, indicating that the dwarfing of plants was caused by a decrease in cell number due to cell cycle arrest. The content of the bioactive cytokinin N6-Δ2-isopentenyladenine (iP) decreased as a result of the cytokinin synthesis gene being downregulated and the enhanced degradation of cytokinin oxidase. OsNAC103 overexpression also inhibited cell cycle progression and regulated the activity of the cell cyclin OsCYCP2;1 to arrest the cell cycle. We propose that OsNAC103 may further influence rice development and gibberellin-cytokinin crosstalk by regulating the Oryza sativa homeobox 71 (OSH71). Collectively, these results offer novel perspectives on the role of OsNAC103 in controlling plant architecture.

RT-RPA-PfAgo System: A Rapid, Sensitive, and Specific Multiplex Detection Method for Rice-Infecting Viruses

The advancement in CRISPR-Cas biosensors has transmuted the detection of plant viruses owing to their rapid and higher sensitivity. However, false positives and restricted multiplexing capabilities are still the challenges faced by this technology, demanding the exploration of novel methodologies. In this study, a novel detection system was developed by integrating reverse transcriptome (RT) techniques with recombinase polymerase isothermal amplification (RPA) and Pyrococcus furiosus Argonaute (PfAgo). The RT-RPA-PfAgo system enabled the simultaneous detection of rice ragged stunt virus (RRSV), rice grassy stunt virus (RGSV), and rice black streaked dwarf virus (RBSDV). Identifying targets via guide DNA without being hindered by protospacer adjacent motif sequences is the inherent merit of PfAgo, with the additional advantage of it being simple, cost-effective, and exceptionally sensitive, with detection limits between 3.13 and 5.13 copies/µL, in addition to it effectively differentiating between the three distinct viruses. The field evaluations were also in accordance with RT-PCR methods. The RT-RPA-PfAgo system proved to be a robust, versatile, highly specific, and sensitive method with great potential for practicality in future plant virus diagnostics.

Investigation of the Relationship between Genetic and Breeding Characteristics of WBPH Behavior according to Resistant Materials in Rice

Rice accounts for most of the calories consumed by the world's population. However, the whitebacked planthopper (WBPH), Sogatella furcifera (Horvath), is an insect that can cause rice yield loss. WBPH sucks the stems of rice and negatively affects yield and grain quality. Therefore, numerous insecticides have been developed to control WBPH in rice fields. However, chemical pesticides cause serious problems such as environmental pollution and ecosystem disturbance. Here, we research the possibility of using previously reported rice extracts obtained using methanol, Chrysoeriol 7(C7) and Cochlioquinone-9 (cq-9), as potential insect repellents. WBPH was caged with C7 or cq-9 and monitored, and the WBPH behavior was recorded. The number of WBPHs approaching the periphery of the C7 and cq-9 was very low. In cages containing the C7 and cq-9, only 13 and 7 WBPHs out of 100, respectively, walked around the material. In addition, foliar spraying with C7 and cq-9 did not negatively affect the plant height. The expression level of genes related to resistance was maintained at a high level in the resistant lines when treated with WBPHs alone, but was at a similar level to those of the controls when treated with C7 or cq-9. Interfering with WBPH access did not adversely affect the plant phenotype. Recently, people's interest in the environment has increased, and the use of plant-derived materials is also increasing. There is a new trend towards using plant extracts as an environmentally friendly means of managing resistance to WBPH during the rice cultivation period, while also avoiding environmental pollution.

The Role of Plant Transcription Factors in the Fight against Plant Viruses

Plants are vulnerable to the challenges of unstable environments and pathogen infections due to their immobility. Among various stress conditions, viral infection is a major threat that causes significant crop loss. In response to viral infection, plants undergo complex molecular and physiological changes, which trigger defense and morphogenic pathways. Transcription factors (TFs), and their interactions with cofactors and cis-regulatory genomic elements, are essential for plant defense mechanisms. The transcriptional regulation by TFs is crucial in establishing plant defense and associated activities during viral infections. Therefore, identifying and characterizing the critical genes involved in the responses of plants against virus stress is essential for the development of transgenic plants that exhibit enhanced tolerance or resistance. This article reviews the current understanding of the transcriptional control of plant defenses, with a special focus on NAC, MYB, WRKY, bZIP, and AP2/ERF TFs. The review provides an update on the latest advances in understanding how plant TFs regulate defense genes expression during viral infection.

Transcription Factor ZmNAC20 Improves Drought Resistance by Promoting Stomatal Closure and Activating Expression of Stress-Responsive Genes in Maize

Drought is a major environmental threat that limits crop growth, development, and productivity worldwide. Improving drought resistance with genetic engineering methods is necessary to tackle global climate change. It is well known that NAC (NAM, ATAF and CUC) transcription factors play a critical role in coping with drought stress in plants. In this study, we identified an NAC transcription factor ZmNAC20, which regulates drought stress response in maize. ZmNAC20 expression was rapidly upregulated by drought and abscisic acid (ABA). Under drought conditions, the ZmNAC20-overexpressing plants had higher relative water content and survival rate than the wild-type maize inbred B104, suggesting that overexpression of ZmNAC20 improved drought resistance in maize. The detached leaves of ZmNAC20-overexpressing plants lost less water than those of wild-type B104 after dehydration. Overexpression of ZmNAC20 promoted stomatal closure in response to ABA. ZmNAC20 was localized in the nucleus and regulated the expression of many genes involved in drought stress response using RNA-Seq analysis. The study indicated that ZmNAC20 improved drought resistance by promoting stomatal closure and activating the expression of stress-responsible genes in maize. Our findings provide a valuable gene and new clues on improving crop drought resistance.

Genome and Transcriptome-Wide Analysis of OsWRKY and OsNAC Gene Families in Oryza sativa and Their Response to White-Backed Planthopper Infestation

Plants are threatened by a wide variety of herbivorous insect assaults, and display a variety of inherent and induced defenses that shield them against herbivore attacks. Looking at the massive damage caused by the white-backed planthopper (WBPH), Sogatella furcifera, we undertook a study to identify and functionally annotate OsWRKY and OsNAC transcription factors (TFs) in rice, especially their involvement in WBPH stress. OsWRKY and OsNAC TFs are involved in various developmental processes and responses to biotic and abiotic stresses. However, no comprehensive reports are available on the specific phycological functions of most of the OsWRKY and OsNAC genes in rice during WBPH infestation. The current study aimed to comprehensively explore the OsWRKY and OsNAC genes by analyzing their phylogenetic relationships, subcellular localizations, exon-intron arrangements, conserved motif identities, chromosomal allocations, interaction networks and differential gene expressions during stress conditions. Comparative phylogenetic trees of 101 OsWRKY with 72 AtWRKY genes, and 121 OsNAC with 110 AtNAC genes were constructed to study relationships among these TFs across species. Phylogenetic relationships classified OsWRKY and OsNAC into eight and nine clades, respectively. Most TFs in the same clade had similar genomic features that represented similar functions, and had a high degree of co-expression. Some OsWRKYs (Os09g0417800 (OsWRKY62), Os11g0117600 (OsWRKY50), Os11g0117400 (OsWRKY104) and OsNACs (Os05g0442700, Os12g0630800, Os01g0862800 and Os12g0156100)) showed significantly higher expressions under WBPH infestation, based on transcriptome datasets. This study provides valuable information and clues about predicting the potential roles of OsWRKYs and OsNACs in rice, by combining their genome-wide characterization, expression profiling, protein-protein interactions and gene expressions under WBPH stress. These findings may require additional investigation to understand their metabolic and expression processes, and to develop rice cultivars that are resistant to WBPH.

Inducible expression of truncated NAC62 provides tolerance against Alternaria brassicicola and imparts developmental changes in Indian mustard

Indian mustard (Brassica juncea) faces significant yield loss due to the 'Black Spot Disease,' caused by a fungus Alternaria brassicicola. In plants, NAC transcription factors (NAC TFs) are known for their roles in development and stress tolerance. One such NAC TF, NAC 62, was induced during A. brassicicola challenge in Sinapis alba, a non-host resistant plant against this fungus. Sequence analyses of BjuNAC62 from B. juncea showed that it belonged to the membrane-bound class of transcription factors. Gene expression study revealed differential protein processing of NAC62 between B. juncea and S. alba on pathogen challenge. Furthermore, NAC62 processing to 25 kDa protein was found to be unique to the resistant plant during pathogenesis. Conditional expression of BjuNAC62ΔC, which lacks its transmembrane domain, in B. juncea showed improved tolerance to A. brassicicola. BjuNAC62ΔC processing to 25 kDa product was also observed in tolerant transgenic plants. Additionally, transgenic plants showed induced expression of genes associated with defense-related phytohormone signaling pathways on pathogen challenge. Again, altered phenotypes suggest a possible developmental effect of BjuNAC62∆C in transgenic plants. The overall results suggest that the processing of BjuNAC62 might be playing a crucial role in resistance response against Black Spot disease by modulating defense-associated genes.

Transcriptome sequencing and differential expression analysis of natural and BTH-treated wound healing in potato tubers (Solanum tuberosum L.)

Background

Wound healing is a representative phenomenon of potato tubers subjected to mechanical injuries. Our previous results found that benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH) promoted the wound healing of potato tubers. However, the molecular mechanism related to inducible wound healing remains unknown.

Results

Transcriptomic evaluation of healing tissues from potato tubers at three stages, namely, 0 d (nonhealing), 5 d (wounded tubers healed for 5 d) and 5 d (BTH-treated tubers healed for 5 d) using RNA-Seq and differentially expressed genes (DEGs) analysis showed that more than 515 million high-quality reads were generated and a total of 7665 DEGs were enriched, and 16 of these DEGs were selected by qRT-PCR analysis to further confirm the RNA sequencing data. Gene ontology (GO) enrichment analysis indicated that the most highly DEGs were involved in metabolic and cellular processes, and KEGG enrichment analysis indicated that a large number of DEGs were associated with plant hormones, starch and sugar metabolism, fatty acid metabolism, phenylpropanoid biosynthesis and terpenoid skeleton biosynthesis. Furthermore, a few candidate transcription factors, including MYB, NAC and WRKY, and genes related to Ca²⁺-mediated signal transduction were also found to be differentially expressed during wound healing. Most of these enriched DEGs were upregulated after BTH treatment.

Conclusion

This comparative expression profile provided useful resources for studies of the molecular mechanism via these promising candidates involved in natural or elicitor-induced wound healing in potato tubers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08480-1.

Bacillus amyloliquefaciens SN16-1-Induced Resistance System of the Tomato against Rhizoctonia solani

Tomato (Solanum lycopersicum), as an important economical vegetable, is often infected with Rhizoctonia solani, which results in a substantial reduction in production. Therefore, the molecular mechanism of biocontrol microorganisms assisting tomato to resist pathogens is worth exploring. Here, we use Bacillus amyloliquefaciens SN16-1 as biocontrol bacteria, and employed RNA-Seq technology to study tomato gene and defense-signaling pathways expression. Gene Ontology (GO) analyses showed that an oxidation-reduction process, peptidase regulator activity, and oxidoreductase activity were predominant. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that phenylpropanoid biosynthesis, biosynthesis of unsaturated fatty acids, aldosterone synthesis and secretion, and phototransduction were significantly enriched. SN16-1 activated defenses in the tomato via systemic-acquired resistance (which depends on the salicylic acid signaling pathway), rather than classic induction of systemic resistance. The genes induced by SN16-1 included transcription factors, plant hormones (ethylene, auxin, abscisic acid, and gibberellin), receptor-like kinases, heat shock proteins, and defense proteins. SN16-1 rarely activated pathogenesis-related proteins, but most pathogenesis-related proteins were induced in the presence of the pathogens. In addition, the molecular mechanisms of the response of tomatoes to SN16-1 and R. solani RS520 were significantly different.

Cytochrome P450 Monooxygenases CYP6AY3 and CYP6CW1 Regulate Rice Black-Streaked Dwarf Virus Replication in Laodelphax striatellus (Fallén)

The small brown planthopper, Laodelphax striatellus (Fallén), is an important agricultural pest that causes significant losses by sucking and transmitting multiple plant viruses, such as rice black-streaked dwarf virus (RBSDV). Insecticides are commonly used to control planthoppers and cause the induction or overexpression of cytochrome P450 monooxygenases (P450s) from the CYP3 and CYP4 clades after insecticide application. However, little is known about the roles of insecticides and P450s in the regulation of viral replication in insects. In this study, RBSDV-infected L. striatellus were injected with imidacloprid, deltamethrin, pymetrozine, and buprofezin, respectively. The insecticide treatments caused a significant decrease in RBSDV abundance in L. striatellus. Treatment of piperonyl butoxide (PBO), an effective inhibitor of P450s, significantly increased the RBSDV abundance in L. striatellus. Fourteen P450 candidate genes in the CYP3 clade and 21 in the CYP4 clade were systematically identified in L. striatellus, and their expression patterns were analyzed under RBSDV infection, in different tissues, and at different developmental stages. Among the thirty-five P450 genes, the expression level of CYP6CW1 was the highest, while CYP6AY3 was the lowest after RBSDV infection. Knockdown of CYP6CW1 and CYP6AY3 significantly increased the virus abundance and promoted virus replication in L. striatellus. Overall, our data reveal that CYP6CW1 and CYP6AY3 play a critical role in the regulation of virus replication in L.striatellus.

Effects of graphene on morphology, microstructure and transcriptomic profiling of Pinus tabuliformis Carr. roots

Graphene has shown great potential for improving growth of many plants, but its effect on woody plants remains essentially unstudied. In this work, Pinus tabuliformis Carr. bare-rooted seedlings grown outdoors in pots were irrigated with a graphene solution over a concentration range of 0-50 mg/L for six months. Graphene was found to stimulate root growth, with a maximal effect at 25 mg/L. We then investigated root microstructure and carried out transcript profiling of root materials treated with 0 and 25 mg/L graphene. Graphene treatment resulted in plasma-wall separation and destruction of membrane integrity in root cells. More than 50 thousand of differentially expressed genes (DEGs) were obtained by RNA sequencing, among which 6477 could be annotated using other plant databases. The GO enrichment analysis and KEGG pathway analysis of the annotated DEGs indicated that abiotic stress responses, which resemble salt stress, were induced by graphene treatment in roots, while responses to biotic stimuli were inhibited. Numerous metabolic processes and hormone signal transduction pathways were altered by the treatment. The growth promotion effects of graphene may be mediated by encouraging proline synthesis, and suppression of the expression of the auxin response gene SMALL AUXIN UP-REGULATED RNA 41 (SAUR41), PYL genes which encode ABA receptors, and GSK3 homologs.

The NAC side of the fruit: tuning of fruit development and maturation

Fruits and seeds resulting from fertilization of flowers, represent an incredible evolutionary advantage in angiosperms and have seen them become a critical element in our food supply.Many studies have been conducted to reveal how fruit matures while protecting growing seeds and ensuring their dispersal. As result, several transcription factors involved in fruit maturation and senescence have been isolated both in model and crop plants. These regulators modulate several cellular processes that occur during fruit ripening such as chlorophyll breakdown, tissue softening, carbohydrates and pigments accumulation.The NAC superfamily of transcription factors is known to be involved in almost all these aspects of fruit development and maturation. In this review, we summarise the current knowledge regarding NACs that modulate fruit ripening in model species (Arabidopsis thaliana and Solanum lycopersicum) and in crops of commercial interest (Oryza sativa, Malus domestica, Fragaria genus, Citrus sinensis and Musa acuminata).

Degradome Analysis of Tomato and Nicotiana benthamiana Plants Infected with Potato Spindle Tuber Viroid

Viroids are infectious non-coding RNAs that infect plants. During infection, viroid RNAs are targeted by Dicer-like proteins, generating viroid-derived small RNAs (vd-sRNAs) that can guide the sequence specific cleavage of cognate host mRNAs via an RNA silencing mechanism. To assess the involvement of these pathways in pathogenesis associated with nuclear-replicating viroids, high-throughput sequencing of sRNAs and degradome analysis were carried out on tomato and Nicotiana benthamiana plants infected by potato spindle tuber viroid (PSTVd). Both hosts develop similar stunting and leaf curling symptoms when infected by PSTVd, thus allowing comparative analyses. About one hundred tomato mRNAs potentially targeted for degradation by vd-sRNAs were initially identified. However, data from biological replicates and comparisons between mock and infected samples reduced the number of bona fide targets-i.e., those identified with high confidence in two infected biological replicates but not in the mock controls-to only eight mRNAs that encode proteins involved in development, transcription or defense. Somewhat surprisingly, results of RT-qPCR assays revealed that the accumulation of only four of these mRNAs was inhibited in the PSTVd-infected tomato. When these analyses were extended to mock inoculated and PSTVd-infected N. benthamiana plants, a completely different set of potential mRNA targets was identified. The failure to identify homologous mRNA(s) targeted by PSTVd-sRNA suggests that different pathways could be involved in the elicitation of similar symptoms in these two species. Moreover, no significant modifications in the accumulation of miRNAs and in the cleavage of their targeted mRNAs were detected in the infected tomato plants with respect to the mock controls. Taken together, these data suggest that stunting and leaf curling symptoms induced by PSTVd are elicited by a complex plant response involving multiple mechanisms, with RNA silencing being only one of the possible components.

NAC Candidate Gene Marker for bgm-1 and Interaction With QTL for Resistance to Bean Golden Yellow Mosaic Virus in Common Bean

Genetic resistance is the primary means for control of Bean golden yellow mosaic virus (BGYMV) in common bean (Phaseolus vulgaris L.). Breeding for resistance is difficult because of sporadic and uneven infection across field nurseries. We sought to facilitate breeding for BGYMV resistance by improving marker-assisted selection (MAS) for the recessive bgm-1 gene and identifying and developing MAS for quantitative trait loci (QTL) conditioning resistance. Genetic linkage mapping in two recombinant inbred line populations and genome-wide association study (GWAS) in a large breeding population and two diversity panels revealed a candidate gene for bgm-1 and three QTL BGY4.1, BGY7.1, and BGY8.1 on independent chromosomes. A mutation (5 bp deletion) in a NAC (No Apical Meristem) domain transcriptional regulator superfamily protein gene Phvul.003G027100 on chromosome Pv03 corresponded with the recessive bgm-1 resistance allele. The five bp deletion in exon 2 starting at 20 bp (Pv03: 2,601,582) is expected to cause a stop codon at codon 23 (Pv03: 2,601,625), disrupting further translation of the gene. A T m -shift assay marker named PvNAC1 was developed to track bgm-1. PvNAC1 corresponded with bgm-1 across ∼1,000 lines which trace bgm-1 back to a single landrace "Garrapato" from Mexico. BGY8.1 has no effect on its own but exhibited a major effect when combined with bgm-1. BGY4.1 and BGY7.1 acted additively, and they enhanced the level of resistance when combined with bgm-1. T m -shift assay markers were generated for MAS of the QTL, but their effectiveness requires further validation.

Comparative RNA-Seq analysis unfolds a complex regulatory network imparting yellow mosaic disease resistance in mungbean [Vigna radiata (L.) R. Wilczek]

Yellow Mosaic Disease (YMD) in mungbean [Vigna radiata (L.) R. Wilczek] is one of the most damaging diseases in Asia. In the northern part of India, the YMD is caused by Mungbean Yellow Mosaic India Virus (MYMIV), while in southern India this is caused by Mungbean Yellow Mosaic Virus (MYMV). The molecular mechanism of YMD resistance in mungbean remains largely unknown. In this study, RNA-seq analysis was conducted between a resistant (PMR-1) and a susceptible (Pusa Vishal) mungbean genotype under infected and control conditions to understand the regulatory network operating between mungbean-YMV. Overall, 76.8 million raw reads could be generated in different treatment combinations, while mapping rate per library to the reference genome varied from 86.78% to 93.35%. The resistance to MYMIV showed a very complicated gene network, which begins with the production of general PAMPs (pathogen-associated molecular patterns), then activation of various signaling cascades like kinases, jasmonic acid (JA) and brassinosteroid (BR), and finally the expression of specific genes (like PR-proteins, virus resistance and R-gene proteins) leading to resistance response. The function of WRKY, NAC and MYB transcription factors in imparting the resistance against MYMIV could be established. The string analysis also revealed the role of proteins involved in kinase, viral movement and phytoene synthase activity in imparting YMD resistance. A set of novel stress-related EST-SSRs are also identified from the RNA-Seq data which may be used to find the linked genes/QTLs with the YMD resistance. Also, 11 defence-related transcripts could be validated through quantitative real-time PCR analysis. The identified gene networks have led to an insight about the defence mechanism operating against MYMIV infection in mungbean which will be of immense use to manage the YMD resistance in mungbean.

Sixty Years After the First Description: Genome Sequence and Biological Characterization of European Wheat Striate Mosaic Virus Infecting Cereal Crops

High-throughput sequencing technologies were used to identify plant viruses in cereal samples surveyed from 2012 to 2017. Fifteen genome sequences of a tenuivirus infecting wheat, oats, and spelt in Estonia, Norway, and Sweden were identified and characterized by their distances to other tenuivirus sequences. Like most tenuiviruses, the genome of this tenuivirus contains four genomic segments. The isolates found from different countries shared at least 92% nucleotide sequence identity at the genome level. The planthopper Javesella pellucida was identified as a vector of the virus. Laboratory transmission tests using this vector indicated that wheat, oats, barley, rye, and triticale, but none of the tested pasture grass species (Alopecurus pratensis, Dactylis glomerata, Festuca rubra, Lolium multiflorum, Phleum pratense, and Poa pratensis), are susceptible. Taking into account the vector and host range data, the tenuivirus we have found most probably represents European wheat striate mosaic virus first identified about 60 years ago. Interestingly, whereas we were not able to infect any of the tested cereal species mechanically, Nicotiana benthamiana was infected via mechanical inoculation in laboratory conditions, displaying symptoms of yellow spots and vein clearing evolving into necrosis, eventually leading to plant death. Surprisingly, one of the virus genome segments (RNA2) encoding both a putative host systemic movement enhancer protein and a putative vector transmission factor was not detected in N. benthamiana after several passages even though systemic infection was observed, raising fundamental questions about the role of this segment in the systemic spread in several hosts.

Symptoms and yield loss caused by rice stripe mosaic virus

Background

Rice stripe mosaic virus (RSMV) is a tentative new Cytorhabdovirus species in family Rhabdoviridae transmitted by the leafhopper Recilia dorsalis. Although the virus was first detected in southern China in 2015, few studies have investigated rice symptoms and yield losses caused by RSMV infection.

Methods

In this study, we observed and systematically compared symptoms of three virally infected, representative varieties of indica, hybrid and japonica rice and determined the yield parameters of the artificially inoculated plants.

Results

The three RSMV-infected cultivated rice varieties exhibited slight dwarfing, striped mosaicism, stiff, crinkled or even twisted leaves, an increased number of tillers, delayed heading, cluster-shaped shortening of panicles and mostly unfilled grains. Slight differences in symptom occurrence time were observed under different environmental conditions. For example, mosaic symptoms appeared earlier and crinkling symptoms appeared later, with both symptoms later receding in some infected plants. Yield losses due to RSMV also differed among varieties. The most serious yield reduction was experienced by indica rice (cv. Meixiangzhan), followed by hybrid indica rice (cv. Wuyou 1179) and then japonica (cv. Nipponbare). Single panicle weight, seed setting rate and 1000-kernel weight were reduced in the three infected varieties compared with healthy plants—by 85.42, 94.85 and 31.56% in Meixiangzhan; 52.43, 53.06 and 25.65% in Wuyou 1179 and 25.53, 49.32 and 23.86% in Nipponbare, respectively.

Conclusions

Our findings contribute basic data for field investigations, formulation of prevention and control strategies and further study of the pathogenesis of RSMV.

The NAC Protein from Tamarix hispida, ThNAC7, Confers Salt and Osmotic Stress Tolerance by Increasing Reactive Oxygen Species Scavenging Capability

Plant specific NAC (NAM, ATAF1/2 and CUC2) transcription factors (TFs) play important roles in response to abiotic stress. In this study, we identified and characterized a NAC protein, ThNAC7, from Tamarix hispida. ThNAC7 is a nuclear localized protein and has transcriptional activation activity. ThNAC7 expression was markedly induced by salt and osmotic stresses. Transiently transformed T. hispida seedlings overexpressing ThNAC7 (OE) or with RNA interference (RNAi) silenced ThNAC7 were generated to investigate abiotic stress tolerance via the gain- and loss- of function. Overexpressing ThNAC7 showed an increased reactive oxygen species (ROS) scavenging capabilities and proline content, which was accomplished by enhancing the activities of superoxide dismutase (SOD) and peroxidase (POD) in transiently transformed T. hispida and stably transformed Arabidopsis plants. Additionally, ThNAC7 activated these physiological changes by regulating the transcription level of P5CS, SOD and PODgenes. RNA-sequencing (RNA-seq) comparison between wild-type and ThNAC7-transformed Arabidopsis showed that more than 40 known salt tolerance genes might regulated by ThNAC7, including stress tolerance-related genes and TF genes. The results indicated that ThNAC7 induces the transcription level of genes associated with stress tolerance to enhance salt and osmotic stress tolerance via an increase in osmotic potential and enhanced ROS scavenging.

Rice NAC transcription factor ONAC066 functions as a positive regulator of drought and oxidative stress response

BACKGROUND

NAC (NAM, ATAF and CUC) transcriptional factors constitute a large family with more than 150 members in rice and several members of this family have been demonstrated to play crucial roles in rice abiotic stress response. In the present study, we report the function of a novel stress-responsive NAC gene, ONAC066, in rice drought and oxidative stress tolerance.

RESULTS

ONAC066 was localized in nuclei of cells when transiently expressed in Nicotiana benthamiana and is a transcription activator with the binding ability to NAC recognition sequence (NACRS) and AtJUB1 binding site (JBS). Expression of ONAC066 was significantly induced by PEG, NaCl, H₂O₂ and abscisic acid (ABA). Overexpression of ONAC066 in transgenic rice improved drought and oxidative stress tolerance and increased ABA sensitivity, accompanied with decreased rate of water loss, increased contents of proline and soluble sugars, decreased accumulation of reactive oxygen species (ROS) and upregulated expression of stress-related genes under drought stress condition. By contrast, RNAi-mediated suppression of ONAC066 attenuated drought and oxidative stress tolerance and decreased ABA sensitivity, accompanied with increased rate of water loss, decreased contents of proline and soluble sugars, elevated accumulation of ROS and downregulated expression of stress-related genes under drought stress condition. Furthermore, yeast one hybrid and chromatin immunoprecipitation-PCR analyses revealed that ONAC066 bound directly to a JBS-like cis-elements in OsDREB2A promoter and activated the transcription of OsDREB2A.

CONCLUSION

ONAC066 is a nucleus-localized transcription activator that can respond to multiple abiotic stress factors. Functional analyses using overexpression and RNAi-mediated suppression transgenic lines demonstrate that ONAC066 is a positive regulator of drought and oxidative stress tolerance in rice.

RNA-Seq analysis of gene expression changes triggered by Xanthomonas oryzae pv. oryzae in a susceptible rice genotype

BACKGROUND

Xanthomonas oryzae pv. oryzae (Xoo) is a destructive disease in most of the rice growing regions worldwide. Xoo injects the transcriptional activator-like (TAL) effector protein into the host cell to induce the susceptibility (S) gene(s) for spreading the disease. In the current study, a susceptible rice genotype, JG30, was inoculated with wild Xoo strain PXO99^A and its mutant PH without any TAL effector, to retrieve the differentially expressed genes (DEGs) having a role in susceptibility.

RESULTS

RNA-Seq data analysis showed that 1143 genes were significantly differentially expressed (p-value ≤0.05) at 12, 24, 36 and 48 h post inoculation (hpi). Expression patterns, evaluated by quantitative real-time PCR (qRT-PCR), of randomly selected eight genes were similar to the RNA-Seq data. KEGG pathway classified the DEGs into photosynthesis and biosynthesis of phenylpropanoid pathway. Gene ontology (GO) analysis categorized the DEGs into the biological pathway, cellular component, and molecular function. We identified 43 differentially expressed transcription factors (TFs) belonging to different families. Also, clusters of the DEGs representing kinase and peroxidase responsive genes were retrieved. MapMan pathway analysis representing the expression pattern of genes expressed highly in biotic stress and metabolic pathways after PXO99^A infection relative to PH.

CONCLUSIONS

DEGs were identified in susceptible rice genotype inoculated with PXO99^A relative to mutant strain PH. The identified 1143 DEGs were predicted to be included in the different biological processes, signaling mechanism and metabolic pathways. The Jasmonic acid (JA) responsive genes were identified to be downregulated in PXO99^A infected leaves. This study would be useful for the researchers to reveal the potential functions of genes involved in the rice susceptibility to PXO99^A infection.

Revealing shared differential co-expression profiles in rice infected by virus from reoviridae and sequiviridae group

Differential co-expression is a cutting-edge approach to analyze gene expression data and identify both shared and divergent expression patterns. The availability of high-throughput gene expression datasets and efficient computational approaches have unfolded the opportunity to a systems level understanding of functional genomics of different stresses with respect to plants. We performed the meta-analysis of the available microarray data for reoviridae and sequiviridae infection in rice with the aim to identify the shared gene co-expression profile. The microarray data were downloaded from ArrayExpress and analyzed through a modified Weighted Gene Co-expression Network Analysis (WGCNA) protocol. WGCNA clustered the genes based on the expression intensities across the samples followed by identification of modules, eigengenes, principal components, topology overlap, module membership and module preservation. The module preservation analysis identified 4 modules; salmon (638 genes), midnightblue (584 genes), lightcyan (686 genes) and red (562 genes), which are highly preserved in both the cases. The networks in case of reoviridae infection showed neatly packed clusters whereas, in sequiviridae, the clusters were loosely connected which is due to the differences in the correlation values. We also identified 83 common transcription factors targeting the hub genes from all the identified modules. This study provides a coherent view of the comparative aspect of the expression of common genes involved in different virus infections which may aid in the identification of novel targets and development of new intervention strategy against the virus.

Comparative proteomic analysis of maize (Zea mays L.) seedlings under rice black-streaked dwarf virus infection

BACKGROUND

Maize rough dwarf disease (MRDD) is a severe disease that has been occurring frequently in southern China and many other Asian countries. MRDD is caused by the infection of Rice black streaked dwarf virus (RBSDV) and leads to significant economic losses in maize production. To well understand the destructive effects of RBSDV infection on maize growth, comparative proteomic analyses of maize seedlings under RBSDV infection was performed using an integrated approach involving LC-MS/MS and Tandem Mass Tag (TMT) labeling.

RESULTS

In total, 7615 maize proteins, 6319 of which were quantified. A total of 116 differentially accumulated proteins (DAPs) were identified, including 35 up- and 81 down-regulated proteins under the RBSDV infection. Enrichment analysis showed that the DAPs were most strongly associated with cyanoamino acid metabolism, protein processing in ER, and ribosome-related pathways. Two sulfur metabolism-related proteins were significantly reduced, indicating that sulfur may participate in the resistance against RBSDV infection. Furthermore, 15 DAPs involved in six metabolic pathways were identified in maize under the RBSDV infection.

CONCLUSIONS

Our data revealed that the responses of maize to RBSDV infection were controlled by various metabolic pathways.

Dynamic phytohormone profiling of rice upon rice black-streaked dwarf virus invasion

Rice black-streaked dwarf virus (RBSDV) is the causal agent of rice black-streaked dwarf disease, a serious constraint to rice production. A great deal of effort has been made to elucidate the transcriptome and proteome changes of rice upon virus inoculation. However, the relationship between RBSDV invasion and rice endogenous phytohormone profiling is largely unclear. Here, we surveyed the dynamic content profiling of endogenous phytohormones, which were severely disturbed by RBSDV invasion. The levels of abscisic acid (ABA) and cytokinins (CTKs) increased, while indole-3-acetic acid (IAA), gibberellins (GAs), jasmonic acid (JA), and salicylic acid (SA) decreased, accompanied by changes in the transcripts of genes participating in phytohormone metabolism and signalling pathways. Moreover, exogenously supplied GA₃ could rescue the typical dwarfing symptom, and pre-application of SA largely decreased the occurrence of RBSDV disease in rice. The results partially suggest that RBSDV successfully invaded host rice by modulating the expression patterns of phytohormone metabolism to upset the balance of plant endogenous phytohormones.

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

NAC transcription factors are widespread in the plant kingdom and play essential roles in the transcriptional regulation of defense responses. In this study, we isolated a novel NAC transcription factor gene, TaNAC30, from a cDNA library constructed from wheat (Triticum aestivum) plants inoculated with the stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst). TaNAC30 contains a typical NAM domain and localizes to the nucleus. Yeast one-hybrid assays revealed that TaNAC30 exhibits transcriptional activity and that its C-terminus is necessary for the activation of transcription. Expression of TaNAC30 increased when host plants were infected with a virulent race (CYR31) of the rust fungus Pst. Silencing of TaNAC30 by virus-induced gene silencing inhibited colonization of the virulent Pst isolate CYR31. Moreover, detailed histological analyses showed that silencing of TaNAC30 enhanced resistance to Pst by inducing a significant increase in the accumulation of H₂ O₂ . Finally, we overexpressed TaNAC30 in fission yeast and determined that cell viability was severely reduced in TaNAC30-transformed cells grown on medium containing H₂ O₂ . These results suggest that TaNAC30 negatively regulates plant resistance in a compatible wheat-Pst interaction.

RNA-Seq transcriptome analysis of Amaranthus palmeri with differential tolerance to glufosinate herbicide

Amaranthus palmeri (Amaranthaceae) is a noxious weed in several agroecosystems and in some cases seriously threatens the sustainability of crop production in North America. Glyphosate-resistant Amaranthus species are widespread, prompting the use of alternatives to glyphosate such as glufosinate, in conjunction with glufosinate-resistant crop cultivars, to help control glyphosate-resistant weeds. An experiment was conducted to analyze the transcriptome of A. palmeri plants that survived exposure to 0.55 kg ha-1 glufosinate. Since there was no record of glufosinate use at the collection site, survival of plants within the population are likely due to genetic expression that pre-dates selection; in the formal parlance of weed science this is described as natural tolerance. Leaf tissues from glufosinate-treated and non-treated seedlings were harvested 24 h after treatment (HAT) for RNA-Seq analysis. Global gene expression was measured using Illumina DNA sequence reads from non-treated and treated surviving (presumably tolerant, T) and susceptible (S) plants. The same plants were used to determine the mechanisms conferring differential tolerance to glufosinate. The S plants accumulated twice as much ammonia as did the T plants, 24 HAT. The relative copy number of the glufosinate target gene GS2 did not differ between T and S plants, with 1 to 3 GS2 copies in both biotypes. A reference cDNA transcriptome consisting of 72,780 contigs was assembled, with 65,282 sequences putatively annotated. Sequences of GS2 from the transcriptome assembly did not have polymorphisms unique to the tolerant plants. Five hundred sixty-seven genes were differentially expressed between treated T and S plants. Of the upregulated genes in treated T plants, 210 were more highly induced than were the upregulated genes in the treated S plants. Glufosinate-tolerant plants had greater induction of ABC transporter, glutathione S-transferase (GST), NAC transcription factor, nitronate monooxygenase (NMO), chitin elicitor receptor kinase (CERK1), heat shock protein 83, ethylene transcription factor, heat stress transcription factor, NADH-ubiquinone oxidoreductase, ABA 8'-hydroxylase, and cytochrome P450 genes (CYP72A, CYP94A1). Seven candidate genes were selected for validation using quantitative real time-PCR. While GST was upregulated in treated tolerant plants in at least one population, CYP72A219 was consistently highly expressed in all treated tolerant biotypes. These genes are candidates for contributing tolerance to glufosinate. Taken together, these results show that differential induction of stress-protection genes in a population can enable some individuals to survive herbicide application. Elevated expression of detoxification-related genes can get fixed in a population with sustained selection pressure, leading to evolution of resistance. Alternatively, sustained selection pressure could select for mutation(s) in the GS2 gene with the same consequence.

Genome-wide analysis and expression patterns of the NAC transcription factor family in Medicago truncatula

NAC transcription factor (TF) family proteins are expressed in various developmental stages and following various stresses. NAC TFs are involved in mediating various physiological functions of plants and participate in various signaling pathways under biotic or abiotic stress. The present study provided a comprehensive functional analysis of members of the MtNAC TF family. Via screening of Medicago truncatula genome information, we identified 97 MtNAC TFs in M. truncatula and compared the phylogenetic analysis of 14 conserved groups with their Arabidopsis and rice counterparts. The NAC TFs were categorized into 14 groups based on their conserved motifs and gene structure. The predicted M. truncatula NAC genes were distributed among eight chromosomes, and in addition, we found that these genes showed mass gene duplication. Through expression profiling of RNA-seq data analysis, we determined that NAC family members were expressed significantly under different abiotic stresses. This indicates that the NAC TF shows different functions in M. truncatula. Together, this genome-wide analysis of the NAC gene family in M. truncatula, could be applied to improving stress tolerance in plants.

Transcriptomics Analysis of Apple Leaves in Response to Alternaria alternata Apple Pathotype Infection

Alternaria blotch disease of apple (Malus × domestica Borkh.), caused by the apple pathotype of Alternaria alternata, is one of the most serious fungal diseases to affect apples. To develop an understanding of how apples respond to A. alternata apple pathotype (AAAP) infection, we examined the host transcript accumulation over the period between 0 and 72 h post AAAP inoculation. Large-scale gene expression analysis was conducted of the compatible interaction between "Starking Delicious" apple cultivar and AAAP using RNA-Seq and digital gene expression (DGE) profiling methods. Our results show that a total of 9080 differentially expressed genes (DEGs) were detected (>two-fold and FDR < 0.001) by RNA-Seq. During the early phase of infection, 12 h post inoculation (HPI), AAAP exhibited limited fungal development and little change in the transcript accumulation status (950 DEGs). During the intermediate phase of infection, the period between 18 and 36 HPI, increased fungal development, active infection, and increased transcript accumulation were detected (4111 and 3838 DEGs detected at each time point, respectively). The majority of DEGs were detected by 72 HPI, suggesting that this is an important time point in the response of apples' AAAP infection. Subsequent gene ontology (GO) and pathway enrichment analyses showed that DEGs are predominately involved in biological processes and metabolic pathways; results showed that almost gene associated with photosynthesis, oxidation-reduction were down-regulated, while transcription factors (i.e., WRKY, MYB, NAC, and Hsf) and DEGs involved in cell wall modification, defense signaling, the synthesis of defense-related metabolites, including pathogenesis-related (PRs) genes and phenylpropanoid/cyanoamino acid /flavonoid biosynthesis, were activated during this process. Our study also suggested that the cell wall defensive vulnerability and the down-regulation of most PRs and HSP70s in "Starking Delicious" following AAAP infection might interpret its susceptible to AAAP.

Rice NAC transcription factor ONAC095 plays opposite roles in drought and cold stress tolerance

BACKGROUND

The NAC (NAM, ATAF and CUC) transcriptional factors constitute a large family with more than 150 members in rice and some of them have been demonstrated to play crucial roles in plant abiotic stress response. Here, we report the characterization of a rice stress-responsive NAC gene, ONAC095, and the exploration of its function in drought and cold stress tolerance.

RESULTS

Expression of ONAC095 was up-regulated by drought stress and abscisic acid (ABA) but down-regulated by cold stress. ONAC095 protein had transactivation activity and the C2 domain in C-terminal was found to be critical for transactivation activity. Transgenic rice lines with overexpression of ONAC095 (ONAC095-OE) and dominant chimeric repressor-mediated suppression of ONAC095 (ONAC095-SRDX) were generated. The ONAC095-OE plants showed comparable phenotype to wild type under drought and cold stress conditions. However, the ONAC095-SRDX plants displayed an improved drought tolerance but exhibited an attenuated cold tolerance. The ONAC095-SRDX plants had decreased water loss rate, increased proline and soluble sugar contents, and up-regulated expression of drought-responsive genes under drought condition, whereas the ONAC095-SRDX plants accumulated excess reactive oxygen species, increased malondialdehyde content and down-regulated expression of cold-responsive genes under cold condition. Furthermore, ONAC095-SRDX plants showed an increased ABA sensitivity, contained an elevated ABA level, and displayed altered expression of ABA biosynthetic and metabolic genes as well as some ABA signaling-related genes.

CONCLUSION

Functional analyses through dominant chimeric repressor-mediated suppression of ONAC095 demonstrate that ONAC095 plays opposite roles in drought and cold stress tolerance, acting as a negative regulator of drought response but as a positive regulator of cold response in rice.

Overexpression of a Stress-Responsive NAC Transcription Factor Gene ONAC022 Improves Drought and Salt Tolerance in Rice

The NAC transcription factors play critical roles in regulating stress responses in plants. However, the functions for many of the NAC family members in rice are yet to be identified. In the present study, a novel stress-responsive rice NAC gene, ONAC022, was identified. Expression of ONAC022 was induced by drought, high salinity, and abscisic acid (ABA). The ONAC022 protein was found to bind specifically to a canonical NAC recognition cis-element sequence and showed transactivation activity at its C-terminus in yeast. The ONAC022 protein was localized to nucleus when transiently expressed in Nicotiana benthamiana. Three independent transgenic rice lines with overexpression of ONAC022 were generated and used to explore the function of ONAC022 in drought and salt stress tolerance. Under drought stress condition in greenhouse, soil-grown ONAC022-overexpressing (N22oe) transgenic rice plants showed an increased drought tolerance, leading to higher survival ratios and better growth than wild-type (WT) plants. When grown hydroponically in Hogland solution supplemented with 150 mM NaCl, the N22oe plants displayed an enhanced salt tolerance and accumulated less Na(+) in roots and shoots as compared to WT plants. Under drought stress condition, the N22oe plants exhibited decreased rates of water loss and transpiration, reduced percentage of open stomata and increased contents of proline and soluble sugars. However, the N22oe lines showed increased sensitivity to exogenous ABA at seed germination and seedling growth stages but contained higher level of endogenous ABA. Expression of some ABA biosynthetic genes (OsNCEDs and OsPSY), signaling and regulatory genes (OsPP2C02, OsPP2C49, OsPP2C68, OsbZIP23, OsAP37, OsDREB2a, and OsMYB2), and late stress-responsive genes (OsRAB21, OsLEA3, and OsP5CS1) was upregulated in N22oe plants. Our data demonstrate that ONAC022 functions as a stress-responsive NAC with transcriptional activator activity and plays a positive role in drought and salt stress tolerance through modulating an ABA-mediated pathway.