Constitutive expression of the defense-related Rir1b gene in transgenic rice plants confers enhanced resistance to the rice blast fungus Magnaporthe grisea

Pleiotropic changes revealed by in situ recovery of the semi-dwarf gene sd1 in rice

The "Green Revolution" that dramatically reduced cultivar heights and sharply boosted rice production mid-century was achieved in large part through introgression of defective alleles of Semi-Dwarf 1 (SD1), which encodes a GA20ox oxidase involved in the final steps of the synthesis of bioactive gibberellin in rice. Here, we ask whether converting the defective sd1 version in a modern semi-dwarf cultivar back to wild-type SD1 in situ recovers ancestral plant traits, and more broadly, what it reveals about pleiotropic effects of this gene. We assess these effects of SD1 restoration in three independent recombinant lines recovered from F₂ progeny of a cross between 93-11 and PA64s. We then used RNA-seq to dissect gene network changes that accompanied SD1 restoration. We report that this in situ restoration of wild-type SD1 nearly doubles plant height, increases total grain yield per panicle, and elongates the second-leaf length. Comparison of expression profiles reveals changes in key nodes of the gibberellin pathway, such as OsKO1 and OsGA2ox3, and more broadly in genes related to metabolic networks, defense response, and catabolic processes. Two JA-induced genes, RIR1b and OsPR1b, are extremely down-regulated after SD1 restoration, suggesting that SD1 restoration alters the balance between GA and JA to plant growth, at the cost of degrading the defense response. This in situ approach at the SD1 locus also provides a model example that is applicable to other systems and will further understanding of gene networks underlying high-yield traits in crops.

Calcium Signaling Is Suppressed in Magnaporthe oryzae Conidia by Bacillus cereus HS24

Rice yield is greatly reduced owing to rice blast, a polycyclic fungal disease caused by the ascomycete Magnaporthe oryzae. Previously, Bacillus cereus HS24, isolated from a rice farm, showed a strong antimicrobial effect toward M. oryzae. To better exploit it as a biocontrol agent, HS24 was studied for the mechanism that it uses to suppress rice blast. Conidium germination in M. oryzae was significantly inhibited by HS24, whereby inhibition reached 97.8% at the concentration of 10⁷ CFU/ml. The transcription levels of Ca²⁺/calmodulin-dependent protein kinase II, PMC1, and CCH1, key genes involved in the M. oryzae Ca²⁺ signaling pathway, were significantly decreased in HS24-treated conidia at high concentration. The treatment of M. oryzae with the corresponding Ca²⁺ signaling pathway inhibitors KN-93, verapamil, and cyclopiazonic acid significantly reduced conidium germination. This inhibitory effect was found to be concentration dependent, similar to the HS24 treatment. We also found that HS24 was able to decrease the intracellular free Ca²⁺ concentration in M. oryzae conidia significantly. The addition of exogenous Ca²⁺ did not diminish the inhibitory effect of HS24 on the reduction of intracellular free Ca²⁺ concentration and the level of conidium germination. In conclusion, B. cereus HS24 at high concentration prevents extracellular Ca²⁺ from entering the conidia in M. oryzae, causes a significant reduction of intracellular free Ca²⁺ concentration, and results in the inhibition of conidium germination.

H2O2-Based Method for Rapid Detection of Transgene-Free Rice Plants from Segregating CRISPR/Cas9 Genome-Edited Progenies

Genome-editing techniques such as CRISPR/Cas9 have been widely used in crop functional genomics and improvement. To efficiently deliver the guide RNA and Cas9, most studies still rely on Agrobacterium-mediated transformation, which involves a selection marker gene. However, several limiting factors may impede the efficiency of screening transgene-free genome-edited plants, including the time needed to produce each life cycle, the response to selection reagents, and the labor costs of PCR-based genotyping. To overcome these disadvantages, we developed a simple and high-throughput method based on visual detection of antibiotics-derived H₂O₂ to verify transgene-free genome-edited plants. In transgenic rice containing hygromycin phosphotransferase (HPT), H₂O₂ content did not change in the presence of hygromycin B (HyB). In contrast, in transgenic-free rice plants with 10-h HyB treatment, levels of H₂O₂ and malondialdehyde, indicators of oxidative stress, were elevated. Detection of H₂O₂ by 3,3′-diaminobenzidine (DAB) staining suggested that H₂O₂ could be a marker to efficiently distinguish transgenic and non-transgenic plants. Analysis of 24 segregating progenies of an HPT-containing rice plant by RT-PCR and DAB staining verified that DAB staining is a feasible method for detecting transformants and non-transformants. Transgene-free genome-edited plants were faithfully validated by both PCR and the H₂O₂-based method. Moreover, HyB induced overproduction of H₂O₂ in leaves of Arabidopsis, maize, tobacco, and tomato, which suggests the potential application of the DAB method for detecting transgenic events containing HPT in a wide range of plant species. Thus, visual detection of DAB provides a simple, cheap, and reliable way to efficiently identify transgene-free genome-edited and HPT-containing transgenic rice.

The rice ethylene response factor OsERF83 positively regulates disease resistance to Magnaporthe oryzae

Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice (Oryza sativa) worldwide. Here, we report the identification and functional characterization of a novel ethylene response factor (ERF) gene, OsERF83, which was expressed in rice leaves in response to rice blast fungus infection. OsERF83 expression was also induced by treatments with methyl jasmonate, ethephon, and salicylic acid, indicating that multiple phytohormones could be involved in the regulation of OsERF83 expression under biotic stress. Subcellular localization and transactivation analyses demonstrated that OsERF83 is a nucleus-localized transcriptional activator. A gel-shift assay using recombinant OsERF83 protein indicated that, like other ERFs, it binds to the GCC box. Transgenic rice plants overexpressing OsERF83 exhibited significantly suppressed lesion formation after rice blast infection, indicating that OsERF83 positively regulates disease resistance in rice. Genes encoding several classes of pathogenesis-related (PR) proteins, including PR1, PR2, PR3, PR5, and PR10, were upregulated in the OsERF83ox plants. Taken together, our findings show that OsERF83 is a novel ERF transcription factor that confers blast resistance by regulating the expression of defense-related genes in rice.

Prospects of Understanding the Molecular Biology of Disease Resistance in Rice

Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host-pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.

OsNAC111, a blast disease-responsive transcription factor in rice, positively regulates the expression of defense-related genes

Plants respond to pathogen attack by transcriptionally regulating defense-related genes via various types of transcription factors. We identified a transcription factor in rice, OsNAC111, belonging to the TERN subgroup of the NAC family that was transcriptionally upregulated after rice blast fungus (Magnaporthe oryzae) inoculation. OsNAC111 was localized in the nucleus of rice cells and had transcriptional activation activity in yeast and rice cells. Transgenic rice plants overexpressing OsNAC111 showed increased resistance to the rice blast fungus. In OsNAC111-overexpressing plants, the expression of several defense-related genes, including pathogenesis-related (PR) genes, was constitutively high compared with the control. These genes all showed blast disease-responsive expression in leaves. Among them, two chitinase genes and one β-1,3-glucanase gene showed reduced expression in transgenic rice plants in which OsNAC111 function was suppressed by a chimeric repressor (OsNAC111-SRDX). OsNAC111 activated transcription from the promoters of the chitinase and β-1,3-glucanase genes in rice cells. In addition, brown pigmentation at the infection sites, a defense response of rice cells to the blast fungus, was lowered in OsNAC111-SRDX plants at the early infection stage. These results indicate that OsNAC111 positively regulates the expression of a specific set of PR genes in the disease response and contributes to disease resistance.

TaWIR1 contributes to post-penetration resistance to Magnaporthe oryzae, but not Blumeria graminis f. sp. tritici, in wheat

Members of the Wheat-Induced Resistance 1 (TaWIR1) gene family are highly induced in response to a wide range of pathogens. Homologues have been identified in barley, but not in Brachypodium, whereas, in rice, only distant WIR1 candidates are known. Phylogenetic analysis placed TaWIR1a and TaWIR1b within a distinct clade of wheat transcripts, whereas TaWIR1c clustered with HvWIR1 genes. Transcripts of all three TaWIR1 genes were strongly induced by a wheat-adapted isolate of Magnaporthe oryzae. Virus-induced gene silencing of the TaWIR1 gene family had no effect on the initial penetration of epidermal cells by M. oryzae. However, following the establishment of an infection site, the fungus was able to grow more extensively within the leaf tissue, relative to control leaves, indicating a role for the TaWIR1 gene family in the cell-to-cell movement of M. oryzae. In contrast, the silencing of TaWIR1 transcripts had no effect on epidermal cell penetration by a wheat-adapted isolate of Blumeria graminis, or on the subsequent growth of hyphae. Differential transcription of TaWIR1 genes was also seen in epidermal peels, relative to the remaining leaf tissue, following inoculation with M. oryzae.

Characteristic expression of rice pathogenesis-related proteins in rice leaves during interactions with Xanthomonas oryzae pv. oryzae

Pathogenesis-related (PR) proteins play an important role in the disease resistance response. To better understand the function of rice PR proteins, we examined the expressions of ten PR proteins in rice leaves at different developmental stages with or without the interaction between rice and Xanthomonas oryzae pv. oryzae (Xoo). The results showed that most of the PR proteins were expressed in rice leaves in normal growth conditions, suggesting that they play a role in rice growth. Six out of ten PR proteins (PR1, PR2, PR3, PR4b, PR8, and PR-pha) showed enhanced expression in Xa21-mediated resistance responses at late stages after inoculation with Xoo. The remaining four PR proteins (PR5, PR6, PR15, and PR16) did not show changes in expression in the resistance response. The expressions of PR proteins in the resistance reaction were further compared with those in the susceptible reaction and a mock treatment. Interestingly, several of the PR proteins were expressed at the highest levels in the susceptible reaction and at the lowest levels in the mock treatment. Among the other four PR proteins, PR5 and PR16 showed changes in the abundance only in the susceptible response, while PR6 and PR15 showed no detectable difference in expression. These data provide fundamental knowledge about the expression of PR proteins in the interaction between rice and Xoo.

Convergent evidence for a role of WIR1 proteins during the interaction of barley with the powdery mildew fungus Blumeria graminis

Pathogen attack triggers a multifaceted defence response in plants that includes the accumulation of pathogenesis-related proteins and their corresponding transcripts. One of these transcripts encodes for WIR1, a small glycine- and proline-rich protein of unknown function that appears to be specific to grass species. Here we describe members of the HvWIR1 multigene family of barley with respect to phylogenetic relationship, transcript regulation, co-localization with quantitative trait loci for resistance to the barley powdery mildew fungus Blumeria graminis (DC.) E.O. Speer f.sp. hordei, the association of single nucleotide polymorphisms or gene haplotypes with resistance, as well as phenotypic effects of gene silencing by RNAi. HvWIR1 is encoded by a multigene family of moderate complexity that splits up into two major clades, one of those being also represented by previously described cDNA sequences from wheat. All analysed WIR1 transcripts accumulated in response to powdery mildew attack in leaves and all mapped WIR1 genes were associated with quantitative trait loci for resistance to B. graminis. Moreover, single nucleotide polymorphisms or haplotypes of WIR1 members were associated with quantitative resistance of barley to B. graminis, and transient WIR1 gene silencing affected the interaction of epidermal cells with the pathogen. The presented data provide convergent evidence for a role of the HvWIR1a gene and possibly other family members, during the interaction of barley with B. graminis.

Nonhost and basal resistance: how to explain specificity?

Nonhost resistance to plant pathogens can be constitutive or induced by microbes. Successful pathogens suppress microbe-induced plant defences by delivering appropriate effectors, which are apparently not sufficiently effective on nonhost plant species, as can be concluded from the strong host specificity of many biotroph plant pathogens. Such effectors act on particular plant targets, such as promoters or motifs in expressed sequences. Despite much progress in the elucidation of the molecular aspects of nonhost resistance to plant pathogens, very little is known about the genes that determine whether effectors can or cannot suppress the basal defence. In hosts they can, in nonhosts they cannot. The targets determining the host status of plants can be identified in inheritance studies. Recent reports have indicated that nonhost resistance is inherited polygenically, and exhibits strong similarity and association with the basal resistance of plants to adapted pathogens.

Recent advances in rice biotechnology--towards genetically superior transgenic rice

Rice biotechnology has made rapid advances since the first transgenic rice plants were produced 15 years ago. Over the past decade, this progress has resulted in the development of high frequency, routine and reproducible genetic transformation protocols for rice. This technology has been applied to produce rice plants that withstand several abiotic stresses, as well as to gain tolerance against various pests and diseases. In addition, quality improving and increased nutritional value traits have also been introduced into rice. Most of these gains were not possible through conventional breeding technologies. Transgenic rice system has been used to understand the process of transformation itself, the integration pattern of transgene as well as to modulate gene expression. Field trials of transgenic rice, especially insect-resistant rice, have recently been performed and several other studies that are prerequisite for safe release of transgenic crops have been initiated. New molecular improvisations such as inducible expression of transgene and selectable marker-free technology will help in producing superior transgenic product. It is also a step towards alleviating public concerns relating to issues of transgenic technology and to gain regulatory approval. Knowledge gained from rice can also be applied to improve other cereals. The completion of the rice genome sequencing together with a rich collection of full-length cDNA resources has opened up a plethora of opportunities, paving the way to integrate data from the large-scale projects to solve specific biological problems.

Isolation and characterization of novel defense response genes involved in compatible and incompatible interactions between rice and Magnaporthe grisea

To identify early-induced defense genes involved in broad-spectrum resistance to rice blast, suppression subtractive hybridization was used to generate two cDNA libraries enriched for transcripts differentially expressed in Pi9(t)-resistant and -susceptible plants. After differential screening by membrane-based hybridization and subsequent confirmation by reverse Northern blot analysis, selected clones were sequenced and analyzed. Forty-seven unique cDNA clones were found and assigned to eight different groups according to the putative function of their homologous genes in the database. These genes may be involved in pathogen or stress response, signal transduction, transcription, cell transport, metabolism, energy or protein destination. Northern blot analysis showed that most of these genes were induced or suppressed after blast infection, and that half of them showed differential expression patterns between compatible and incompatible interactions. Interestingly, all but one of the identified genes are reported here for the first time to be involved in defense response to rice blast. In addition, hybridization of these clones with cDNAs synthesized from RNA samples from bacterial blight-infected leaves showed that few of them are induced or repressed in Xa21- or Xa7-resistant plants, suggesting a minimum overlap of defense responses mediated by different resistance genes to fungal and bacterial pathogens at an early stage of infection. Further characterization and functional analysis of these genes will enhance our understanding of the molecular mechanism of broad-spectrum resistance in rice.

Cytological and molecular analysis of the Hordeum vulgare-Puccinia triticina nonhost interaction

Cultivated barley, Hordeum vulgare L., is considered to be a nonhost or intermediate host species for the wheat leaf rust fungus Puccinia triticina. Here, we have investigated, at the microscopic and molecular levels, the reaction of barley cultivars to wheat leaf rust infection. In the nonhost resistant cultivar Cebada Capa, abortion of fungal growth occurred at both pre- and posthaustorial stages, suggesting that defense genes are expressed throughout the development of the inappropriate fungus during the nonhost resistance reaction. In the two barley lines L94 and Bowman, a low level of prehaustorial resistance to P. triticina was observed and susceptibility was comparable to that of wheat control plants. Suppression subtractive hybridization was used to identify genes that are differentially expressed during the nonhost resistance reaction in Cebada Capa as well as during the successful establishment of the inappropriate wheat leaf rust fungus in L94. Northern analysis indicated that two candidate genes, including a barley ortholog of the rice resistance gene Xa21, are putatively involved in nonhost and non-race-specific resistance reactions. In addition, a new gene that is specifically induced during the successful development of the inappropriate fungus P. triticina in barley has been identified.

A network of rice genes associated with stress response and seed development

We used a systematic approach to build a network of genes associated with developmental and stress responses in rice by identifying interaction domains for 200 proteins from stressed and developing tissues, by measuring the associated gene expression changes in different tissues exposed to a variety of environmental, biological, and chemical stress treatments, and by localizing the cognate genes to regions of stress-tolerance trait genetic loci. The integrated data set suggests that similar genes respond to environmental cues and stresses, and some may also regulate development. We demonstrate that the data can be used to correctly predict gene function in monocots and dicots. As a result, we have identified five genes that contribute to disease resistance in Arabidopsis.