Indeterminate Domain Proteins Regulate Rice Defense to Sheath Blight Disease

Enhanced Rice Resistance to Sheath Blight through Nitrate Transporter 1.1B Mutation without Yield Loss under NH4+ Fertilization

Nitrogen fertilization can promote rice yield but decrease resistance to sheath blight (ShB). In this study, the nitrate transporter 1.1b (nrt1.1b) mutant that exhibited less susceptibility to ShB but without compromising yield under NH4+ fertilization was screened. NRT1.1B's regulation of ShB resistance was independent of the total nitrogen concentration in rice under NH4+ conditions. In nrt1.1b mutant plants, the NH4+ application modulated auxin signaling, chlorophyll content, and phosphate signaling to promote ShB resistance. Furthermore, the findings indicated that NRT1.1B negatively regulated ShB resistance by positively modulating the expression of H+-ATPase gene OSA3 and phosphate transport gene PT8. The mutation of OSA3 and PT8 promoted ShB resistance by increasing the apoplastic pH in rice. Our study identified the ShB resistance mutant nrt1.1b, which maintained normal nitrogen use efficiency without compromising yield.

SHORT ROOT and INDETERMINATE DOMAIN family members govern PIN-FORMED expression to regulate minor vein differentiation in rice

C3 and C4 grasses directly and indirectly provide the vast majority of calories to the human diet, yet our understanding of the molecular mechanisms driving photosynthetic productivity in grasses is largely unexplored. Ground meristem cells divide to form mesophyll or vascular initial cells early in leaf development in C3 and C4 grasses. Here we define a genetic circuit composed of SHORT ROOT (SHR), INDETERMINATE DOMAIN (IDD), and PIN-FORMED (PIN) family members that specifies vascular identify and ground cell proliferation in leaves of both C3 and C4 grasses. Ectopic expression and loss-of-function mutant studies of SHR paralogs in the C3 plant Oryza sativa (rice) and the C4 plant Setaria viridis (green millet) revealed the roles of these genes in both minor vein formation and ground cell differentiation. Genetic and in vitro studies further suggested that SHR regulates this process through its interactions with IDD12 and 13. We also revealed direct interactions of these IDD proteins with a putative regulatory element within the auxin transporter gene PIN5c. Collectively, these findings indicate that a SHR-IDD regulatory circuit mediates auxin transport by negatively regulating PIN expression to modulate minor vein patterning in the grasses.

Progress in rice sheath blight resistance research

Rice sheath blight (ShB) disease poses a major threat to rice yield throughout the world. However, the defense mechanisms against ShB in rice remain largely unknown. ShB resistance is a typical quantitative trait controlled by multiple genes. With the rapid development of molecular methods, many quantitative trait loci (QTLs) related to agronomic traits, biotic and abiotic stresses, and yield have been identified by genome-wide association studies. The interactions between plants and pathogens are controlled by various plant hormone signaling pathways, and the pathways synergistically or antagonistically interact with each other, regulating plant growth and development as well as the defense response. This review summarizes the regulatory effects of hormones including auxin, ethylene, salicylic acid, jasmonic acid, brassinosteroids, gibberellin, abscisic acid, strigolactone, and cytokinin on ShB and the crosstalk between the various hormones. Furthermore, the effects of sugar and nitrogen on rice ShB resistance, as well as information on genes related to ShB resistance in rice and their effects on ShB are also discussed. In summary, this review is a comprehensive description of the QTLs, hormones, nutrition, and other defense-related genes related to ShB in rice. The prospects of targeting the resistance mechanism as a strategy for controlling ShB in rice are also discussed.

Calcineurin B-like interacting protein kinase 31 confers resistance to sheath blight via modulation of ROS homeostasis in rice

Sheath blight (ShB) severely threatens rice cultivation and production; however, the molecular mechanism of rice defence against ShB remains unclear. Screening of transposon Ds insertion mutants identified that Calcineurin B-like protein-interacting protein kinase 31 (CIPK31) mutants were more susceptible to ShB, while CIPK31 overexpressors (OX) were less susceptible. Sequence analysis indicated two haplotypes of CIPK31: Hap_1, with significantly higher CIPK31 expression, was less sensitive to ShB than the Hap_2 lines. Further analyses showed that the NAF domain of CIPK31 interacted with the EF-hand motif of respiratory burst oxidase homologue (RBOHA) to inhibit RBOHA-induced H₂ O₂ production, and RBOHA RNAi plants were more susceptible to ShB. These data suggested that the CIPK31-mediated increase in resistance is not associated with RBOHA. Interestingly, the study also found that CIPK31 interacted with catalase C (CatC); cipk31 mutants accumulated less H₂ O₂ while CIPK31 OX accumulated more H₂ O₂ compared to the wild-type control. Further analysis showed the interaction of the catalase domain of CatC with the NAF domain of CIPK31 by which CIPK31 inhibits CatC activity to accumulate more H₂ O₂ .

Genome-Wide Identification of the Highly Conserved INDETERMINATE DOMAIN (IDD) Zinc Finger Gene Family in Moso Bamboo (Phyllostachys edulis)

INDETERMINATE DOMAIN (IDD) proteins, a family of transcription factors unique to plants, function in multiple developmental processes. Although the IDD gene family has been identified in many plants, little is known about it in moso bamboo. In this present study, we identified 32 PheIDD family genes in moso bamboo and randomly sequenced the full-length open reading frames (ORFs) of ten PheIDDs. All PheIDDs shared a highly conserved IDD domain that contained two canonical C2H2-ZFs, two C2HC-ZFs, and a nuclear localization signal. Collinearity analysis showed that segmental duplication events played an important role in expansion of the PheIDD gene family. Synteny analysis indicated that 30 PheIDD genes were orthologous to those of rice (Oryza sativa). Thirty PheIDDs were expressed at low levels, and most PheIDDs exhibited characteristic organ-specific expression patterns. Despite their diverse expression patterns in response to exogenous plant hormones, 8 and 22 PheIDDs responded rapidly to IAA and 6-BA treatments, respectively. The expression levels of 23 PheIDDs were closely related to the outgrowth of aboveground branches and 20 PheIDDs were closely related to the awakening of underground dormant buds. In addition, we found that the PheIDD21 gene generated two products by alternative splicing. Both isoforms interacted with PheDELLA and PheSCL3. Furthermore, both isoforms could bind to the cis-elements of three genes (PH02Gene17121, PH02Gene35441, PH02Gene11386). Taken together, our work provides valuable information for studying the molecular breeding mechanism of lateral organ development in moso bamboo.

Cytological observation and transcriptome analysis reveal dynamic changes of Rhizoctonia solani colonization on leaf sheath and different genes recruited between the resistant and susceptible genotypes in rice

Sheath blight, caused by Rhizoctonia solani, is a big threat to the global rice production. To characterize the early development of R. solani on rice leaf and leaf sheath, two genotypes, GD66 (a resistant genotype) and Lemont (a susceptible genotype), were observed using four cytological techniques: the whole-mount eosin B-staining confocal laser scanning microscopy (WE-CLSM), stereoscopy, fluorescence microscopy, and plastic semi-thin sectioning after in vitro inoculation. WE-CLSM observation showed that, at 12 h post-inoculation (hpi), the amount of hyphae increased dramatically on leaf and sheath surface, the infection cushions occurred and maintained at a huge number from about 18 to 36 hpi, and then the infection cushions disappeared gradually from about 42 to 72 hpi. Interestingly, R. solani could not only colonize on the abaxial surfaces of leaf sheath but also invade the paraxial side of the leaf sheath, which shows a different behavior from that of leaf. RNA sequencing detected 6,234 differentially expressed genes (DEGs) for Lemont and 7,784 DEGs for GD66 at 24 hpi, and 2,523 DEGs for Lemont and 2,719 DEGs for GD66 at 48 hpi, suggesting that GD66 is recruiting more genes in fighting against the pathogen. Among DEGs, resistant genes, such as OsRLCK5, Xa21, and Pid2, displayed higher expression in the resistant genotype than the susceptible genotype at both 24 and 48 hpi, which were validated by quantitative reverse transcription-PCR. Our results indicated that the resistance phenotype of GD66 was the consequence of recruiting a series of resistance genes involved in different regulatory pathways. WE-CLSM is a powerful technique for uncovering the mechanism of R. solani invading rice and for detecting rice sheath blight-resistant germplasm.

Malectin Domain Protein Kinase (MDPK) Promotes Rice Resistance to Sheath Blight via IDD12, IDD13, and IDD14

Sheath blight (ShB) caused by Rhizoctonia solani is a major disease of rice, seriously affecting yield; however, the molecular defense mechanism against ShB remains unclear. A previous transcriptome analysis of rice identified that R. solani inoculation significantly induced MDPK. Genetic studies using MDPK RNAi and overexpressing plants identified that MDPK positively regulates ShB resistance. This MDPK protein was found localized in the endoplasmic reticulum (ER) and Golgi apparatus. Yeast one-hybrid assay, electrophoresis mobility shift assay (EMSA), and chromatin immunoprecipitation (ChIP) showed that the intermediate domain proteins IDD12, IDD13, and IDD14 bind to the MDPK promoter. Moreover, IDD14 was found to interact with IDD12 and IDD13 to form a transcription complex to activate MDPK expression. The three IDDs demonstrated an additive effect on MDPK activation. Further genetic studies showed that the IDD13 and IDD14 single mutants were more susceptible to ShB but not IDD12, while IDD12, IDD13, and IDD14 overexpressing plants were less susceptible than the wild-type plants. The IDD12, IDD13, and IDD14 mutants also proved the additive effect of the three IDDs on MDPK expression, which regulates ShB resistance in rice. Notably, MDPK overexpression maintained normal yield levels in rice. Thus, our study proves that IDD12, IDD13, and IDD14 activate MDPK to enhance ShB resistance in rice. These results improve our knowledge of rice defense mechanisms and provide a valuable marker for resistance breeding.

Ammonium transporter 1 increases rice resistance to sheath blight by promoting nitrogen assimilation and ethylene signalling

Sheath blight (ShB) significantly threatens rice yield production. However, the underlying mechanism of ShB defence in rice remains largely unknown. Here, we identified a highly ShB-susceptible mutant Ds-m which contained a mutation at the ammonium transporter 1;1 (AMT1;1) D³⁵⁸ N. AMT1;1 D³⁵⁸ N interacts with AMT1;1, AMT1;2 and AMT1;3 to inhibit the ammonium transport activity. The AMT1 RNAi was more susceptible and similar to the AMT1;1 D³⁵⁸ N mutant; however, plants with higher NH₄⁺ uptake activity were less susceptible to ShB. Glutamine synthetase 1;1 (GS1;1) mutant gs1;1 and overexpressors (GS1;1 OXs) were more and less susceptible to ShB respectively. Furthermore, AMT1;1 overexpressor (AMT1;1 OX)/gs1;1 and gs1;1 exhibited a similar response to ShB, suggesting that ammonium assimilation rather than accumulation controls the ShB defence. Genetic and physiological assays further demonstrated that plants with higher amino acid or chlorophyll content promoted rice resistance to ShB. Interestingly, the expression of ethylene-related genes was higher in AMT1;1 OX and lower in RNAi mutants than in wild-type. Also, ethylene signalling positively regulated rice resistance to ShB and NH₄⁺ uptake, suggesting that ethylene signalling acts downstream of AMT and also NH₄⁺ uptake is under feedback control. Taken together, our data demonstrated that the AMT1 promotes rice resistance to ShB via the regulation of diverse metabolic and signalling pathways.

Rhizoctonia solani Kühn Pathophysiology: Status and Prospects of Sheath Blight Disease Management in Rice

Sheath blight caused by necrotrophic fungus Rhizoctonia solani Kühn is one of the most serious diseases of rice. Use of high yielding semi dwarf cultivars with dense planting and high dose of nitrogenous fertilizers accentuates the incidence of sheath blight in rice. Its diverse host range and ability to remain dormant under unfavorable conditions make the pathogen more difficult to manage. As there are no sources of complete resistance, management through chemical control has been the most adopted method for sheath blight management. In this review, we provide an up-to-date comprehensive description of host-pathogen interactions, various control measures such as cultural, chemical, and biological as well as utilizing host plant resistance. The section on utilizing host plant resistance includes identification of resistant sources, mapping QTLs and their validation, identification of candidate gene(s) and their introgression through marker-assisted selection. Advances and prospects of sheath blight management through biotechnological approaches such as overexpression of genes and gene silencing for transgenic development against R. solani are also discussed.

OsbHLH057 targets the AATCA cis-element to regulate disease resistance and drought tolerance in rice

The AATCA motif was identified to respond pathogens infection in the promoter of defense-related gene Os2H16. OsbHLH057 bound to the motif to positively regulate rice disease resistance and drought tolerance. Sheath blight (ShB), caused by the necrotrophic fungus Rhizoctonia solani, is a devastating disease in rice (Oryza sativa L.). The transcriptional regulation of host defense-related genes in response to R. solani infection is poorly understood. In this study, we identified a cis-element, AATCA, in the promoter of Os2H16, a previously identified multifaceted defense-related gene in rice that responded to fungal attack. Using a DNA pull-down assay coupled with mass spectrometry, a basic helix-loop-helix (bHLH) transcription factor OsbHLH057 was determined to interact with the AATCA cis-element. OsbHLH057 was rapidly induced by R. solani, Xanthomonas oryzae pv. oryzae (Xoo), and osmotic stress. Furthermore, overexpressing OsbHLH057 enhanced rice disease resistance and drought tolerance, while knocking out OsbHLH057 made rice more susceptible to pathogens and drought. Overall, our results uncovered an OsbHLH057 and AATCA module that synergistically regulates the expression of Os2H16 in response to R. solani, Xoo, and drought in conjunction with the previously identified stress-related OsASR2 and GT-1 module.

Sheath blight resistance in rice is negatively regulated by WRKY53 via SWEET2a activation

Sheath blight (ShB) is one of the most common diseases in rice that significantly affects yield production. However, the underlying mechanisms of rice defense remain largely unknown. Our previous transcriptome analysis identified that infection with Rhizoctonia solani significantly induced the expression level of SWEET2a, a member of the SWEET sugar transporter. The sweet2a genome-editing mutants were less susceptible to ShB. Further yeast-one hybrid, ChIP, and transient assays demonstrated that WRKY53 binds to the SWEET2a promoter to activate its expression. WRKY53 is a key brassinosteroid (BR) signaling transcription factor. Similar to the BR receptor gene BRI1 and biosynthetic gene D2 mutants, the WRKY53 mutant and overexpressor were less and more susceptible to ShB compared to wild-type, respectively. Inoculation with R. solani induced expression of BRI1, D2, and WRKY53, but inhibited MPK6 (a BR-signaling regulator) activity. Also, MPK6 is known to phosphorylate WRKY53 to enhance its transcription activation activity. Transient assay results indicated that co-expression of MPK6 and WRKY53 enhanced WRKY53 trans-activation activity to SWEET2a. Furthermore, expression of WRKY53 SD (the active phosphorylated forms of WRKY53) but not WRKY53 SA (the inactive phosphorylated forms of WRKY53), enhanced WRKY53-mediated activation of SWEET2a compared to expression of WRKY53 alone. Taken together, our analyses showed that R. solani infection may activate BR signaling to induce SWEET2a expression via WRKY53 through negative regulation of ShB resistance in rice.

Protein Phosphatase 2A Catalytic Subunit PP2A-1 Enhances Rice Resistance to Sheath Blight Disease

Rice (Oryza sativa) production is damaged to a great extent by sheath blight disease (ShB). However, the defense mechanism in rice against this disease is largely unknown. Previous transcriptome analysis identified a significantly induced eukaryotic protein phosphatase 2A catalytic subunit 1 (PP2A-1) after the inoculation of Rhizoctonia solani. Five genes encoding PP2A exist in rice genome, and these five genes are ubiquitously expressed in different tissues and stages. Inoculation of R. solani showed that the genome edited pp2a-1 mutants using the CRISPR/Cas9 were more susceptible to ShB than the wild-type control, but other PP2A gene mutants exhibited similar response to ShB compared to wild-type plants. In parallel, PP2A-1 expression level was higher in the activation tagging line, and PP2A-1 overexpression inhibited plant height and promoted the resistance to ShB. PP2A-1-GFP was localized in the cytoplasm and nucleus. In addition, R. solani-dependent induction kinetics of pathogen-related genes PBZ1 and PR1b was lower in pp2a-1 mutants but higher in PP2A-1 activation line compared to those in the wild-type. In conclusion, our analysis shows that PP2A-1 is a member of protein phosphatase, which regulates rice resistance to ShB. This result broadens the understanding of the defense mechanism against ShB and provides a potential target for rice breeding for disease resistance.

Loose Plant Architecture 1-Interacting Kinesin-like Protein KLP Promotes Rice Resistance to Sheath Blight Disease

BACKGROUND

Sheath blight disease (ShB) is a destructive disease affecting rice production. Previously, we have reported that Loose Plant Architecture 1 (LPA1) promotes resistance to ShB. However, the mechanisms by which LPA1 confers resistance against this disease have not been extensively investigated. Notably, interactors that regulate LPA-1 activity remain elusive.

FINDINGS

In this study, we identified the interaction of kinesin-like protein (KLP) with LPA1 in the nucleus of rice cells by yeast two-hybrid, bimolecular fluorescent complimentary (BiFC), and co-immunoprecipitation (co-IP) assays. To investigate the role of KLP in promoting resistance to ShB, wild-type, klp mutant, and KLP overexpressor (KLP OX) rice plants were inoculated with Rhizoctonia solani AG1-IA. The results indicated that, compared with the wild-type control, klp mutants were more susceptible while KLP OX plants were less susceptible to ShB. Since LPA1 transcriptionally activates PIN-FORMED 1a (PIN1a), we examined the expression of 8 related PIN genes. The results showed that only the expression of PIN1a and PIN3b coincided with KLP expression levels. In addition, a chromatin immunoprecipitation (ChIP) assay showed that KLP bound directly to the promoter region of PIN1a but not of PIN3b. Transient expression assays confirmed that LPA1 and KLP transcriptionally activate PIN1a, and that coexpression of KLP and LPA1 had an additive effect on the activation of PIN1a, suggesting that KLP enhances LPA1 transcriptional activation activity.

CONCLUSIONS

Taken together, our results show that KLP is a novel LPA1 interactor that promotes resistance of rice to ShB.

Strategies to Manage Rice Sheath Blight: Lessons from Interactions between Rice and Rhizoctonia solani

Rhizoctonia solani is an important phytopathogenic fungus with a wide host range and worldwide distribution. The anastomosis group AG1 IA of R. solani has been identified as the predominant causal agent of rice sheath blight, one of the most devastating diseases of crop plants. As a necrotrophic pathogen, R. solani exhibits many characteristics different from biotrophic and hemi-biotrophic pathogens during co-evolutionary interaction with host plants. Various types of secondary metabolites, carbohydrate-active enzymes, secreted proteins and effectors have been revealed to be essential pathogenicity factors in R. solani. Meanwhile, reactive oxygen species, phytohormone signaling, transcription factors and many other defense-associated genes have been identified to contribute to sheath blight resistance in rice. Here, we summarize the recent advances in studies on molecular interactions between rice and R. solani. Based on knowledge of rice-R. solani interactions and sheath blight resistance QTLs, multiple effective strategies have been developed to generate rice cultivars with enhanced sheath blight resistance.

Indeterminate domain 3 negatively regulates plant erectness and the resistance of rice to sheath blight by controlling PIN-FORMED gene expressions

Plant architecture and disease resistance are the key factors that control the production of yield. However, the mechanism behind these factors is largely unknown. In this study, we identified that indeterminate domain 3 (IDD3) was obviously induced by inoculation of Rhizoctonia solani AG1-IA. Plants that overexpressed IDD3 (IDD3 OX) were more susceptible, while idd3 mutants showed a similar response to sheath blight disease compared with wild-type plants. Interestingly, IDD3 OX plants developed a wider tiller angle and exhibited altered shoot gravitropism, while idd3 knock-out mutants showed no visible morphological differences compared with the wild-type plants. IDD3 is ubiquitously expressed in different tissues and stages, and the IDD3 transcript was induced by exogenously applied auxin. Expression of the PIN-FORMED (PIN) and Aux/IAA genes was altered in IDD3 OX compared with wild-type plants. Furthermore, IDD3 OX plants are sensitive to auxin and the polar auxin transporter inhibitor N-1-naphthylphalamic acid (NPA). Further yeast-one hybrid, chromatin immunoprecipitation (ChIP) and transient assays revealed that IDD3 directly represses PIN1b via promoter binding. Inoculation with R. solani indicated that PIN1b RNAi plants are more susceptible to sheath blight disease (ShB) compared with the wild-type. Taken together, our analyses suggest that IDD3 controls plant architecture and the resistance of rice to ShB via the regulation of PIN auxin transporter genes.

New insight into comprehensive analysis of INDETERMINATE DOMAIN (IDD) gene family in rice

The INDETERMINATE DOMAIN (IDD) transcription factor (TF), as a family of plant-specific zinc-finger proteins, regulates a variety of development processes and abiotic stresses in plants. IDD genes have been identified and characterized in other plants, however, the rice IDD family genes have not been investigated at genome-wide. In this study, 15 OsIDD genes were identified in rice genome and phylogenetically classified into two groups. Conserved motifs and potential interaction protein analysis about OsIDD proteins were carried out. Exon-intron structures, cis-acting elements and expression profiles of OsIDD genes were also examined. Exon-intron structures analysis revealed that overall structures of OsIDD genes were relatively conserved although they contained different numbers of introns. Cis-acting elements analysis suggested that most OsIDD gene transcripts could be induced by various abiotic stresses and phytohormones. The expression patterns of OsIDD genes were detected by qRT-PCR under cold and drought conditions, and by exogenous auxin (2,4-D), gibberellin (GA₃), and abscisic acid (ABA) treatments, respectively. The results showed that the OsIDDs might play essential roles under abiotic stresses and hormone responses. Distinct expression profiles in tissues/organs suggested that OsIDDs might be involved in different development processes in rice. More interestingly, the prediction of protein-protein interactions (PPIs) revealed OsIDDs could cooperate with some histone modifiers. Yeast two-hybrid assays were performed and confirmed it. Collectively, these results provide a foundation for further elucidation on the molecular mechanisms of OsIDD genes and advance our understanding of their biological function in rice.