The expression pattern of a rice disease resistance gene xa3/xa26 is differentially regulated by the genetic backgrounds and developmental stages that influence its function

Small RNAs and Gene Network in a Durable Disease Resistance Gene--Mediated Defense Responses in Rice

Accumulating data have suggested that small RNAs (sRNAs) have important functions in plant responses to pathogen invasion. However, it is largely unknown whether and how sRNAs are involved in the regulation of rice responses to the invasion of Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight, the most devastating bacterial disease of rice worldwide. We performed simultaneous genome-wide analyses of the expression of sRNAs and genes during early defense responses of rice to Xoo mediated by a major disease resistance gene, Xa3/Xa26, which confers durable and race-specific qualitative resistance. A large number of sRNAs and genes showed differential expression in Xa3/Xa26-mediated resistance. These differentially expressed sRNAs include known microRNAs (miRNAs), unreported miRNAs, and small interfering RNAs. The candidate genes, with expression that was negatively correlated with the expression of sRNAs, were identified, indicating that these genes may be regulated by sRNAs in disease resistance in rice. These results provide a new perspective regarding the putative roles of sRNA candidates and their putative target genes in durable disease resistance in rice.

Map-based cloning and characterization of BPH29, a B3 domain-containing recessive gene conferring brown planthopper resistance in rice

Rice (Oryza sativa L.) production, essential for global food security, is threatened by the brown planthopper (BPH). The breeding of host-resistant crops is an economical and environmentally friendly strategy for pest control, but few resistance gene resources have thus far been cloned. An indica rice introgression line RBPH54, derived from wild rice Oryza rufipogon, has been identified with sustainable resistance to BPH, which is governed by recessive alleles at two loci. In this study, a map-based cloning approach was used to fine-map one resistance gene locus to a 24kb region on the short arm of chromosome 6. Through genetic analysis and transgenic experiments, BPH29, a resistance gene containing a B3 DNA-binding domain, was cloned. The tissue specificity of BPH29 is restricted to vascular tissue, the location of BPH attack. In response to BPH infestation, RBPH54 activates the salicylic acid signalling pathway and suppresses the jasmonic acid/ethylene-dependent pathway, similar to plant defence responses to biotrophic pathogens. The cloning and characterization of BPH29 provides insights into molecular mechanisms of plant-insect interactions and should facilitate the breeding of rice host-resistant varieties.

Disease resistance in rice and the role of molecular breeding in protecting rice crops against diseases

Rice diseases (bacterial, fungal, or viral) threaten food productivity. Host resistance is the most efficient, environmentally friendly method to cope with such diverse pathogens. Quantitative resistance conferred by quantitative trait loci (QTLs) is a valuable resource for rice disease resistance improvement. Although QTLs confer partial but durable resistance to many pathogen species in different crop plants, the molecular mechanisms of quantitative disease resistance remain mostly unknown. Quantitative resistance and non-host resistance are types of broad-spectrum resistance, which are mediated by resistance (R) genes. Because R genes activate different resistance pathways, investigating the genetic spectrum of resistance may lead to minimal losses from harmful diseases. Genome studies can reveal interactions between different genes and their pathways and provide insight into gene functions. Protein–protein interaction (proteomics) studies using molecular and bioinformatics tools may further enlighten our understanding of resistance phenomena.

Enhancement of innate immune system in monocot rice by transferring the dicotyledonous elongation factor Tu receptor EFR

The elongation factor Tu (EF-Tu) receptor (EFR) in cruciferous plants specifically recognizes the N-terminal acetylated elf18 region of bacterial EF-Tu and thereby activates plant immunity. It has been demonstrated that Arabidopsis EFR confers broad-spectrum bacterial resistance in the EFR transgenic solanaceous plants. Here, the transgenic rice plants (Oryza sativa L. ssp. japonica cv. Zhonghua 17) and cell cultures with constitutive expression of AtEFR were developed to investigate whether AtEFR senses EF-Tu and thus enhances bacterial resistance in the monocot plants. We demonstrated that the Xanthomonas oryzae-derived elf18 peptide induced oxidative burst and mitogen-activated protein kinase activation in the AtEFR transgenic rice cells and plants, respectively. Pathogenesis-related genes, such as OsPBZ1, were upregulated dramatically in transgenic rice plant and cell lines in response to elf18 stimulation. Importantly, pretreatment with elf18 triggered strong resistance to X. oryzae pv. oryzae in the transgenic plants, which was largely dependent on the AtEFR expression level. These plants also exhibited enhanced resistance to rice bacterial brown stripe, but not to rice fungal blast. Collectively, the results indicate that the rice plants with heterologous expression of AtEFR recognize bacterial EF-Tu and exhibit enhanced broad-spectrum bacterial disease resistance and that pattern recognition receptor-mediated immunity may be manipulated across the two plant classes, dicots and monocots.

The WRKY45-2 WRKY13 WRKY42 transcriptional regulatory cascade is required for rice resistance to fungal pathogen

Blast caused by fungal Magnaporthe oryzae is a devastating disease of rice (Oryza sativa) worldwide, and this fungus also infects barley (Hordeum vulgare). At least 11 rice WRKY transcription factors have been reported to regulate rice response to M. oryzae either positively or negatively. However, the relationships of these WRKYs in the rice defense signaling pathway against M. oryzae are unknown. Previous studies have revealed that rice WRKY13 (as a transcriptional repressor) and WRKY45-2 enhance resistance to M. oryzae. Here, we show that rice WRKY42, functioning as a transcriptional repressor, suppresses resistance to M. oryzae. WRKY42-RNA interference (RNAi) and WRKY42-overexpressing (oe) plants showed increased resistance and susceptibility to M. oryzae, accompanied by increased or reduced jasmonic acid (JA) content, respectively, compared with wild-type plants. JA pretreatment enhanced the resistance of WRKY42-oe plants to M. oryzae. WRKY13 directly suppressed WRKY42. WRKY45-2, functioning as a transcriptional activator, directly activated WRKY13. In addition, WRKY13 directly suppressed WRKY45-2 by feedback regulation. The WRKY13-RNAi WRKY45-2-oe and WRKY13-oe WRKY42-oe double transgenic lines showed increased susceptibility to M. oryzae compared with WRKY45-2-oe and WRKY13-oe plants, respectively. These results suggest that the three WRKYs form a sequential transcriptional regulatory cascade. WRKY42 may negatively regulate rice response to M. oryzae by suppressing JA signaling-related genes, and WRKY45-2 transcriptionally activates WRKY13, whose encoding protein in turn transcriptionally suppresses WRKY42 to regulate rice resistance to M. oryzae.

Marker-assisted breeding of Indonesia local rice variety Siputeh for semi-dwarf phonetype, good grain quality and disease resistance to bacterial blight

BACKGROUND

Rice is one of the most important staple food crops in Asia. Since the first green revolution beginning in 1960s, high-yield semidwarf modern rice varieties have been widely planted; however, traditional rice varieties with tall plant type are still grown in many countries due to their good grain quality and adaptation to local climate and environment. Siputeh, a local rice variety mainly planted in Java and Sumatra islands of Indonesia, produces long grain rice with good cooking and eating quality. However, the variety has low yield with tall plant type and long growth duration and is highly susceptible to biotic and abiotic stress.

RESULTS

Siputeh as the recurrent female was crossed with the donor line WH421, an elite paternal line of hybrid rice containing the sd1, Wx (b), Xa4 and Xa21 genes, followed by backcrossing and self-pollination. TS4, a BC3F4 line derived from the breeding program, was obtained through marker-assisted selection for the sd1, Wx (b), Xa4 and Xa21 loci. TS4 has semi-dwarf phenotype and short growth duration. TS4 conferred disease resistance to multiple Xanthomonas oryzae pv. oryzae (Xoo) strains collected from different countries around the world. TS4 achieved higher grain yield than Siputeh in two field trials conducted in Banda Aceh, Indonesia and Lingshui, China, respectively. Finally, TS4 has better grain quality than Siputeh in terms of degree of chalkiness and amylose content.

CONCLUSION

An improved rice line, designed as TS4, has been developed to contain semi-dwarf gene sd1, low amylase content gene Wx (b) and bacterial light resistance genes Xa4 and Xa21 through marker-assisted selection. TS4 has semi-dwarf phenotype with reduced growth duration, produces high yield with good grain quality and provides broad-spectrum resistance to Xoo strains. The development of TS4 enriches the diversity of local rice varieties with high yield potential and good grain quality.

The environment exerts a greater influence than the transgene on the transcriptome of field-grown wheat expressing the Pm3b allele

Wheat provides 20 % of the calories consumed worldwide. Powdery mildew infections of wheat can result in more than 30 % yield loss but it has been demonstrated that wheat overexpressing Pm3b, an allele of the R gene Pm3, has enhanced resistance against powdery mildew under field conditions. A gene expression profile study using GeneChip Wheat Genome Array and Fluidigm 96.96 Dynamic Arrays was performed to obtain insights into the mode of action of Pm3b and to elucidate the molecular basis of pleiotropic effects observed in three out of four independent transgenic events under field conditions. A cluster analysis of the microarray data and a principal component analysis of the Fluidigm 96.96 Dynamic Arrays data showed that transgenic lines and null segregants grouped together. The microarray analysis of samples from fungicide-treated plants revealed that significantly fewer genes were differentially expressed in Pm3b#1 than in Pm3b#2, which had a pleiotropic phenotype in the field, compared to their null segregants. Together, our data provide evidence that the environment influenced gene expression in the Pm3b lines more than the transgene itself.

Role of intron-mediated enhancement on accumulation of an Arabidopsis NB-LRR class R-protein that confers resistance to Cucumber mosaic virus

The accumulation of RCY1 protein, which is encoded by RESISTANCE TO CMV(Y) (RCY1), a CC-NB-LRR class R-gene, is tightly correlated with the strength of the resistance to a yellow strain of Cucumber mosaic virus [CMV(Y)] in Arabidopsis thaliana. In order to enhance resistance to CMV by overexpression of RCY1, A. thaliana was transformed with intron-less RCY1 cDNA construct under the control of strong CaMV35S promoter. Remarkably, a relative amount of RCY1 protein accumulation in the transformants was much lower than that in plants expressing genomic RCY1 under the control of its native promoter. To identify a regulatory element of RCY1 that could cause such differential levels of RCY1 accumulation, a series of RCY1 cDNA and genomic RCY1 constructs were transiently expressed in Nicotiana benthamiana leaves by the Agrobacterium-mediated infiltration method. Comparative analysis of the level of RCY1 accumulation in the leaf tissues transiently expressing each construct indicated that the intron located in the RCY1-coding region of genomic RCY1, but not the native RCY1 genomic promoter or the 5'-and 3'-untranslated regions of RCY1, was indispensable for high level RCY1 accumulation. The increased levels of RCY1 accelerated plant disease defense reactions. Interestingly, such intron-mediated enhancement of RCY1 accumulation depended neither on the abundance of the RCY1 transcript nor on the RCY1 specific-intron sequence. Taken together, intron-mediated RCY1 expression seems to play a key role in the expression of complete resistance to CMV(Y) by maintaining RCY1 accumulation at high levels.

Rice OsPAD4 functions differently from Arabidopsis AtPAD4 in host-pathogen interactions

The extensively studied Arabidopsis phytoalexin deficient 4 (AtPAD4) gene plays an important role in Arabidopsis disease resistance; however, the function of its sequence ortholog in rice is unknown. Here, we show that rice OsPAD4 appears not to be the functional ortholog of AtPAD4 in host-pathogen interactions, and that the OsPAD4 encodes a plasma membrane protein but that AtPAD4 encodes a cytoplasmic and nuclear protein. Suppression of OsPAD4 by RNA interference (RNAi) increased rice susceptibility to the biotrophic pathogen Xanthomonas oryzae pv. oryzae (Xoo), which causes bacteria blight disease in local tissue. OsPAD4-RNAi plants also show compromised wound-induced systemic resistance to Xoo. The increased susceptibility to Xoo was associated with reduced accumulation of jasmonic acid (JA) and phytoalexin momilactone A (MOA). Exogenous application of JA complemented the phenotype of OsPAD4-RNAi plants in response to Xoo. The following results suggest that OsPAD4 functions differently than AtPAD4 in response to pathogen infection. First, OsPAD4 plays an important role in wound-induced systemic resistance, whereas AtPAD4 mediates systemic acquired resistance. Second, OsPAD4-involved defense signaling against Xoo is JA-dependent, but AtPAD4-involved defense signaling against biotrophic pathogens is salicylic acid-dependent. Finally, OsPAD4 is required for the accumulation of terpenoid-type phytoalexin MOA in rice-bacterium interactions, but AtPAD4-mediated resistance is associated with the accumulation of indole-type phytoalexin camalexin.

Rice BiP3 regulates immunity mediated by the PRRs XA3 and XA21 but not immunity mediated by the NB-LRR protein, Pi5

Plant innate immunity is mediated by pattern recognition receptors (PRRs) and intracellular NB-LRR (nucleotide-binding domain and leucine-rich repeat) proteins. Overexpression of the endoplasmic reticulum (ER) chaperone, luminal-binding protein 3 (BiP3) compromises resistance to Xanthomonas oryzae pv. oryzae (Xoo) mediated by the rice PRR XA21 [12]. Here we show that BiP3 overexpression also compromises resistance mediated by rice XA3, a PRR that provides broad-spectrum resistance to Xoo. In contrast, BiP3 overexpression has no effect on resistance mediated by rice Pi5, an NB-LRR protein that confers resistance to the fungal pathogen Magnaporthe oryzae (M. oryzae). Our results suggest that rice BiP3 regulates membrane-resident PRR-mediated immunity.

Rice WRKY13 regulates cross talk between abiotic and biotic stress signaling pathways by selective binding to different cis-elements

Plants use a complex signal transduction network to regulate their adaptation to the ever-changing environment. Rice (Oryza sativa) WRKY13 plays a vital role in the cross talk between abiotic and biotic stress signaling pathways by suppressing abiotic stress resistance and activating disease resistance. However, it is not clear how WRKY13 directly regulates this cross talk. Here, we show that WRKY13 is a transcriptional repressor. During the rice responses to drought stress and bacterial infection, WRKY13 selectively bound to certain site- and sequence-specific cis-elements on the promoters of SNAC1 (for STRESS RESPONSIVE NO APICAL MERISTEM, ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR1/2, CUP-SHAPED COTYLEDON), the overexpression of which increases drought resistance, and WRKY45-1, the knockout of which increases both bacterial disease and drought resistance. WRKY13 also bound to two cis-elements of its native promoter to autoregulate the balance of its gene expression in different physiological activities. WRKY13 was induced in leaf vascular tissue, where bacteria proliferate, during infection, and in guard cells, where the transcriptional factor SNAC1 enhances drought resistance, during both bacterial infection and drought stress. These results suggest that WRKY13 regulates the antagonistic cross talk between drought and disease resistance pathways by directly suppressing SNAC1 and WRKY45-1 and autoregulating its own expression via site- and sequence-specific cis-elements on the promoters of these genes in vascular tissue where bacteria proliferate and guard cells where the transcriptional factor SNAC1 mediates drought resistance by promoting stomatal closure.

Insights into organ-specific pathogen defense responses in plants: RNA-seq analysis of potato tuber-Phytophthora infestans interactions

Background

The late blight pathogen Phytophthora infestans can attack both potato foliage and tubers. Although interaction transcriptome dynamics between potato foliage and various pathogens have been reported, no transcriptome study has focused specifically upon how potato tubers respond to pathogen infection. When inoculated with P. infestans, tubers of nontransformed ‘Russet Burbank’ (WT) potato develop late blight disease while those of transgenic ‘Russet Burbank’ line SP2211 (+RB), which expresses the potato late blight resistance gene RB (Rpi-blb1), do not. We compared transcriptome responses to P. infestans inoculation in tubers of these two lines.

Results

We demonstrated the practicality of RNA-seq to study tetraploid potato and present the first RNA-seq study of potato tuber diseases. A total of 483 million paired end Illumina RNA-seq reads were generated, representing the transcription of around 30,000 potato genes. Differentially expressed genes, gene groups and ontology bins that exhibited differences between the WT and +RB lines were identified. P. infestans transcripts, including those of known effectors, were also identified.

Conclusion

Faster and stronger activation of defense related genes, gene groups and ontology bins correlate with successful tuber resistance against P. infestans. Our results suggest that the hypersensitive response is likely a general form of resistance against the hemibiotrophic P. infestans—even in potato tubers, organs that develop below ground.

Rice versus Xanthomonas oryzae pv. oryzae: a unique pathosystem

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating disease of rice worldwide. The qualitative or pathogen race-specific resistance to this pathogen conferred by major disease resistance (MR) genes has been widely used in rice improvement. Accumulating genetic and molecular data have revealed that the molecular mechanisms of rice qualitative resistance to Xoo are largely different from those of qualitative resistance in other plant-pathogen pathosystems. In this review, we focus on the unique features of rice qualitative resistance to Xoo based on MR genes that have been identified and characterized. The distinctiveness of the rice-Xoo interaction provides a unique pathosystem to elucidate the diverse molecular mechanisms in plant qualitative resistance.

Molecular strategies to improve rice disease resistance

Rice diseases such as blast (Magnaporthe oryzae), sheath blight (Rhizoctonia solani) and bacterial blight (Xanthomonas oryzae pv oryzae) are a major obstacle to achieving optimal yields. To complement conventional breeding method, molecular and transgenic method represents an increasingly important approach for genetic improvement of disease resistance and reduction of pesticide usage. During the past two decades, a wide variety of genes and mechanisms involved in rice defense response have been identified and elucidated. These include components of pathogen recognition, signal transduction, downstream defense-related proteins, and crosstalk among different signaling pathways. In addition, various molecular strategies including use of specialized promoters, modification of target protein structures have been studied and proposed to improve the effectiveness of transgenes. While genetically improving rice for enhanced disease resistance, it is important to consider potential effects of the transgene on rice yield, tolerance to abiotic stresses, and defense against other pathogens.

Does your gene need a background check? How genetic background impacts the analysis of mutations, genes, and evolution

The premise of genetic analysis is that a causal link exists between phenotypic and allelic variation. However, it has long been documented that mutant phenotypes are not a simple result of a single DNA lesion, but are instead due to interactions of the focal allele with other genes and the environment. Although an experimentally rigorous approach focused on individual mutations and isogenic control strains has facilitated amazing progress within genetics and related fields, a glimpse back suggests that a vast complexity has been omitted from our current understanding of allelic effects. Armed with traditional genetic analyses and the foundational knowledge they have provided, we argue that the time and tools are ripe to return to the underexplored aspects of gene function and embrace the context-dependent nature of genetic effects. We assert that a broad understanding of genetic effects and the evolutionary dynamics of alleles requires identifying how mutational outcomes depend upon the 'wild type' genetic background. Furthermore, we discuss how best to exploit genetic background effects to broaden genetic research programs.

RNAi phenotypes are influenced by the genetic background of the injected strain

Background

RNA interference (RNAi) is a powerful tool to study gene function in organisms that are not amenable to classical forward genetics. Hence, together with the ease of comprehensively identifying genes by new generation sequencing, RNAi is expanding the scope of animal species and questions that can be addressed in terms of gene function. In the case of genetic mutants, the genetic background of the strains used is known to influence the phenotype while this has not been described for RNAi experiments.

Results

Here we show in the red flour beetle Tribolium castaneum that RNAi against Tc-importin α1 leads to different phenotypes depending on the injected strain. We rule out off target effects and show that sequence divergence does not account for this difference. By quantitatively comparing phenotypes elicited by RNAi knockdown of four different genes we show that there is no general difference in RNAi sensitivity between these strains. Finally, we show that in case of Tc-importin α1 the difference depends on the maternal genotype.

Conclusions

These results show that in RNAi experiments strain specific differences have to be considered and that a proper documentation of the injected strain is required. This is especially important for the increasing number of emerging model organisms that are being functionally investigated using RNAi. In addition, our work shows that RNAi is suitable to systematically identify the differences in the gene regulatory networks present in populations of the same species, which will allow novel insights into the evolution of animal diversity.

Molecular characterization and comparative sequence analysis of defense-related gene, Oryza rufipogon receptor-like protein kinase 1

Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within yield QTL yld1.1 from the wild rice Oryza rufipogon (accession IRGC105491). A 2055 bp coding region and two exons were identified. Southern blotting determined OrufRPK1 to be a single copy gene. Sequence comparison with cultivated rice orthologs (OsI219RPK1, OsI9311RPK1 and OsJNipponRPK1, respectively derived from O. sativa ssp. indica cv. MR219, O. sativa ssp. indica cv. 9311 and O. sativa ssp. japonica cv. Nipponbare) revealed the presence of 12 single nucleotide polymorphisms (SNPs) with five non-synonymous substitutions, and 23 insertion/deletion sites. The biological role of the OrufRPK1 as a defense related LRR-RLK is proposed on the basis of cDNA sequence characterization, domain subfamily classification, structural prediction of extra cellular domains, cluster analysis and comparative gene expression.

A CCCH-type zinc finger nucleic acid-binding protein quantitatively confers resistance against rice bacterial blight disease

Bacterial blight is a devastating disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv oryzae (Xoo). Zinc finger proteins harboring the motif with three conserved cysteine residues and one histidine residue (CCCH) belong to a large family. Although at least 67 CCCH-type zinc finger protein genes have been identified in the rice genome, their functions are poorly understood. Here, we report that one of the rice CCCH-type zinc finger proteins, C3H12, containing five typical CX(8)-CX(5)-CX(3)-H zinc finger motifs, is involved in the rice-Xoo interaction. Activation of C3H12 partially enhanced resistance to Xoo, accompanied by the accumulation of jasmonic acid (JA) and induced expression of JA signaling genes in rice. In contrast, knockout or suppression of C3H12 resulted in partially increased susceptibility to Xoo, accompanied by decreased levels of JA and expression of JA signaling genes in rice. C3H12 colocalized with a minor disease resistance quantitative trait locus to Xoo, and the enhanced resistance of randomly chosen plants in the quantitative trait locus mapping population correlated with an increased expression level of C3H12. The C3H12 protein localized in the nucleus and possessed nucleic acid-binding activity in vitro. These results suggest that C3H12, as a nucleic acid-binding protein, positively and quantitatively regulates rice resistance to Xoo and that its function is likely associated with the JA-dependent pathway.

Ortholog alleles at Xa3/Xa26 locus confer conserved race-specific resistance against Xanthomonas oryzae in rice

The rice disease resistance (R) gene Xa3/Xa26 (having also been named Xa3 and Xa26) against Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight disease, belongs to a multiple gene family clustered in chromosome 11 and is from an AA genome rice cultivar (Oryza sativa L.). This family encodes leucine-rich repeat (LRR) receptor kinase-type proteins. Here, we show that the orthologs (alleles) of Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3, from wild Oryza species O. officinalis (CC genome) and O. minuta (BBCC genome), respectively, were also R genes against Xoo. Xa3/Xa26-2 and Xa3/Xa26-3 conferred resistance to 16 of the 18 Xoo strains examined. Comparative sequence analysis of the Xa3/Xa26 families in the two wild Oryza species showed that Xa3/Xa26-3 appeared to have originated from the CC genome of O. minuta. The predicted proteins encoded by Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3 share 91-99% sequence identity and 94-99% sequence similarity. Transgenic plants carrying a single copy of Xa3/Xa26, Xa3/Xa26-2, or Xa3/Xa26-3, in the same genetic background, showed a similar resistance spectrum to a set of Xoo strains, although plants carrying Xa3/Xa26-2 or Xa3/Xa26-3 showed lower resistance levels than the plants carrying Xa3/Xa26. These results suggest that the Xa3/Xa26 locus predates the speciation of A and C genome, which is approximately 7.5 million years ago. Thus, the resistance specificity of this locus has been conserved for a long time.

A pair of orthologs of a leucine-rich repeat receptor kinase-like disease resistance gene family regulates rice response to raised temperature

BACKGROUND

Rice Xa3/Xa26 disease-resistance gene encodes a leucine-rich repeat (LRR) receptor kinase-type protein against Xanthomonas oryzae pv. oryzae (Xoo) and belongs to a multigene family. However, the functions of most genes in this family are unknown.

RESULTS

Here we report that two orthologs of this family, the NRKe from rice variety Nipponbare and 9RKe from variety 93-11 at the RKe locus, have similar functions although they encode different proteins. This pair of orthologs could not mediate resistance to Xoo, but they were transcriptionally induced by raised temperature. Transcriptional activation of NRKe or 9RKe resulted in the formation of temperature-sensitive lesion mimics, which were spots of dead cells associated with accumulation of superoxides, in different organs of the transgenic plants. These plants were more sensitive to high temperature shock than wild-type controls. Transgenic plants carrying a chimeric protein consisting of the LRR domain of NRKe and the kinase domain of Xa3/Xa26 developed the same lesion mimics as the NRKe-transgenic plants, whereas transgenic plants carrying another chimeric protein consisting of the LRR domain of Xa3/Xa26 and the kinase domain of NRKe were free of lesion mimic. All the transgenic plants carrying a chimeric protein were susceptible to Xoo.

CONCLUSION

These results suggest that the RKe locus is involved in rice response to raised temperature. The LRR domain of RKe protein appears to be important to sense increased temperature. The RKe-involved temperature-related pathway and Xa3/Xa26-mediated disease-resistance pathway may partially overlap.

A paralog of the MtN3/saliva family recessively confers race-specific resistance to Xanthomonas oryzae in rice

Approximately one third of the identified 34 rice major disease resistance (R) genes conferring race-specific resistance to different strains of Xanthomonas oryzae pv. oryzae (Xoo), which causes rice bacterial blight disease, are recessive genes. However, only two of the recessive resistance genes have been characterized thus far. Here we report the characterization of another recessive resistance gene, xa25, for Xoo resistance. The xa25, localized in the centromeric region of chromosome 12, mediates race-specific resistance to Xoo strain PXO339 at both seedling and adult stages by inhibiting Xoo growth. It encodes a protein of the MtN3/saliva family, which is prevalent in eukaryotes, including mammals. Transformation of the dominant Xa25 into a resistant rice line carrying the recessive xa25 abolished its resistance to PXO339. The encoding proteins of recessive xa25 and its dominant allele Xa25 have eight amino acid differences. The expression of dominant Xa25 but not recessive xa25 was rapidly induced by PXO339 but not other Xoo strain infections. The nature of xa25-encoding protein and its expression pattern in comparison with its susceptible allele in rice-Xoo interaction indicate that the mechanism of xa25-mediated resistance appears to be different from that conferred by most of the characterized R proteins.

Transgenic Pm3b wheat lines show resistance to powdery mildew in the field

Plant resistance (R) genes are highly effective in protecting plants against diseases, but pathogens can overcome such genes relatively easily by adaptation. Consequently, in many cases R genes do not confer durable resistance in agricultural environments. One possible strategy to make the use of R genes more sustainable depends on the modification of R genes followed by transformation. To test a possible transgenic use of R genes, we overexpressed in wheat the Pm3b resistance gene against powdery mildew under control of the maize ubiquitin promoter. Four independent transgenic lines were tested in the greenhouse and the field during 3 years. The four lines showed a five- to 600-fold transgene overexpression compared with the expression of the endogenous Pm3b gene in the landrace 'Chul'. Powdery mildew resistance was significantly improved in all lines in the greenhouse and the field, both with naturally occurring infection or after artificial inoculation. Under controlled environmental conditions, the line with the strongest overexpression of the Pm3b gene showed a dramatic increase in resistance to powdery mildew isolates that are virulent on the endogenous Pm3b. Under a variety of field conditions, but never in the greenhouse, three of the four transgenic lines showed pleiotropic effects on spike and leaf morphology. The highest overexpressing line had the strongest side effects, suggesting a correlation between expression level and phenotypic changes. These results demonstrate that the successful transgenic use of R genes critically depends on achieving an optimal level of their expression, possibly in a tissue-specific way.

Controlling rice bacterial blight in Africa: needs and prospects

Rice cultivation has drastically increased in Africa over the last decade. During this time, the region has also seen a rise in the incidence of rice bacterial blight caused by the pathogen Xanthomonas oryzae pv. oryzae. The disease is expanding to new rice production areas and threatens food security in the region. Yield losses caused by X. oryzae pv. oryzae range from 20 to 30% and can be as high as 50% in some areas. Employing resistant cultivars is the most economical and effective way to control this disease. To facilitate development and strategic deployment of rice cultivars with resistance to bacterial blight, biotechnology tools and approaches, including marker-assisted breeding, gene combinations for disease control, and multiplex-PCR for pathogen diagnosis, have been developed. Although these technologies are routinely used elsewhere, their application in Africa remains limited, usually due to high cost and advanced technical skills required. To combat this problem, developers of the technologies at research institutions need to work with farmers from an early stage to create and promote the integration of successful, low cost applications of research biotech products. Here, we review the current knowledge and biotechnologies available to improve bacterial blight control. We will also discuss how to facilitate their application in Africa and delivery to the field.

Genomic organization, induced expression and promoter activity of a resistance gene analog (PmTNL1) in western white pine (Pinus monticola)

Cronartium ribicola causes white pine blister rust (WPBR) in subgenus Strobus. Various genetic and molecular approaches were used to detect white pine genes contributing to host resistance. The molecular role of the NBS-LRR family is highly related to plant immuno-activity against various pathogens and pests. In the present study, genomic organization of a resistance gene analog (RGA), designated as PmTNL1, and its allelic variants were characterized in Pinus monticola. PmTNL1 showed high identity with TIR-NBS-LRR proteins from other plants. qRT-PCR revealed that the PmTNL1 transcript was expressed at low basal levels in different tissues and exhibited similar patterns during compatible and incompatible interactions of P. monticola with C. ribicola at early stages post inoculation. In comparison, PmTNL1 was up-regulated significantly in diseased P. monticola tissues with WPBR symptoms. Expression of the PmTNL1 promoter::GUS fusion gene in transgenic Arabidopsis demonstrated that GUS signal appeared only inside phloem tissues of young seedlings and at hydathodes and branching and organ-connecting points in mature Arabidopsis plants. Similar to the endogenous expression pattern for this gene in pine, GUS activity was up-regulated significantly around vascular tissues locally at pathogen infection sites, but little or no induction was observed in response to abiotic stresses. A DNA marker was developed based on variation of the LRR-coding region, and PmTNL1 was mapped to one genetic linkage group using a pedigree with major dominant gene (Cr2) conferring HR resistance to C. ribicola. These results suggest that PmTNL1 may play an important role in white pine partial resistance against C. ribicola.

OsEDR1 negatively regulates rice bacterial resistance via activation of ethylene biosynthesis

Rice OsEDR1 is a sequence ortholog of Arabidopsis EDR1. However, its molecular function is unknown. We show here that OsEDR1-suppressing/knockout (KO) plants, which developed spontaneous lesions on the leaves, have enhanced resistance to Xanthomonas oryzae pv. oryzae (Xoo) causing bacterial blight disease. This resistance was associated with increased accumulation of salicylic acid (SA) and jasmonic acid (JA), induced expression of SA- and JA-related genes and suppressed accumulation of 1-aminocyclopropane-1-carboxylic acid (ACC), the direct precursor of ethylene, and expression of ethylene-related genes. OsEDR1-KO plants also showed suppressed production of ethylene. Knockout of OsEDR1 suppressed the ACC synthase (ACS) gene family, which encodes the rate-limiting enzymes of ethylene biosynthesis by catalysing the formation of ACC. The lesion phenotype and enhanced bacterial resistance of the OsEDR1-KO plants was partly complemented by the treatment with ACC. ACC treatment was associated with decreased SA and JA biosynthesis in OsEDR1-KO plants. In contrast, aminoethoxyvinylglycine, the inhibitor of ethylene biosynthesis, promoted expression of SA and JA synthesis-related genes in OsEDR1-KO plants. These results suggest that ethylene is a negative signalling molecule in rice bacterial resistance. In the rice-Xoo interaction, OsEDR1 transcriptionally promotes the synthesis of ethylene that, in turn, suppresses SA- and JA-associated defence signalling.

Manipulating broad-spectrum disease resistance by suppressing pathogen-induced auxin accumulation in rice

Breeding crops with the quality of broad-spectrum disease resistance using genetic resources is one of the principal goals of crop improvement. However, the molecular mechanism of broad-spectrum resistance remains largely unknown. Here, we show that GH3-2, encoding an indole-3-acetic acid (IAA)-amido synthetase, mediates a broad-spectrum resistance to bacterial Xanthomonas oryzae pv oryzae and Xanthomonas oryzae pv oryzicola and fungal Magnaporthe grisea in rice (Oryza sativa). IAA, the major form of auxin in rice, results in rice more vulnerable to the invasion of different types of pathogens, which is at least partly due to IAA-induced loosening of the cell wall, the natural protective barrier of plant cells to invaders. X. oryzae pv oryzae, X. oryzae pv oryzicola, and M. grisea secrete IAA, which, in turn, may induce rice to synthesize its own IAA at the infection site. IAA induces the production of expansins, the cell wall-loosening proteins, and makes rice vulnerable to pathogens. GH3-2 is likely contributing to a minor quantitative trait locus for broad-spectrum resistance. Activation of GH3-2 inactivates IAA by catalyzing the formation of an IAA-amino acid conjugate, which results in the suppression of expansin genes. Thus, GH3-2 mediates basal resistance by suppressing pathogen-induced IAA accumulation. It is expected that, regulated by a pathogen-induced strong promoter, GH3-2 alone may be used for breeding rice with a broad-spectrum disease resistance.

Ectopic expression of rice Xa21 overcomes developmentally controlled resistance to Xanthomonas oryzae pv. oryzae

Recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs) activates the innate immune response. The rice PRR, XA21, confers robust resistance at adult stages to most strains of the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo). Seedlings are still easily infected by Xoo, causing severe yield losses. Here we report that Xa21 is induced by Xoo infection and that ectopic expression of Xa21 confers resistance at three leaf stage (three-week-old), overcoming the developmental limitation of XA21-mediated resistance. Ectopic expression of Xa21 also up-regulates a larger set of defense-related genes as compared to Xa21 driven by the native promoter. These results indicate that altered regulation of Xa21 expression is useful for developing enhanced resistance to Xoo at multiple developmental stages.

High-resolution mapping of the brown planthopper resistance gene Bph6 in rice and characterizing its resistance in the 9311 and Nipponbare near isogenic backgrounds

Brown planthopper (Nilaparvata lugens Stål, BPH) is one of the most destructive insect pests of rice. Exploring resistance genes from diverse germplasms and incorporating them into cultivated varieties are critical for controlling this insect. The rice variety Swarnalata was reported to carry a resistance gene (designated Bph6), which has not yet been assigned to a chromosome location and the resistance mechanism is still unknown. In this study, we identified and mapped this gene using the F(2) and backcrossing populations and characterized its resistance in indica 9311 and japonica Nipponbare using near isogenic lines (NILs). In analysis of 9311/Swarnalata F(2) population, the Bph6 gene was located on the long arm of chromosome 4 between the SSR markers RM6997 and RM5742. The gene was further mapped precisely to a 25-kb region delimited between the STS markers Y19 and Y9; and the distance between these markers is 25-kb in Nipponbare genome. The Bph6 explained 77.5% of the phenotypic variance of BPH resistance in F(2) population and 84.9% in BC(2)F(2) population. Allele from Swarnalata significantly increased resistance to the BPH, resulted in a reduced damage score. In characterization of Bph6-mediated resistance, the BPH insects showed significant preference between NIL-9311 and 9311 in 3 h and between NIL-NIP and Nipponbare in 120 h after release. BPH growth and development were inhibited, and the insect's survival rates were lower on Bph6-NIL plants, compared with the parents 9311 and Nipponbare. The results indicate that the Bph6 exerted prolonged antixenotic and antibiotic effects in Bph6-NIL plants, and NIL-9311 plants showed a quicker and stronger effect toward BPH than NIL-NIP plants.

Opposite functions of a rice mitogen-activated protein kinase during the process of resistance against Xanthomonas oryzae

The pathogen-induced plant defense signaling network consists of multiple components, although only some of them are characterized. Most of the known components function either as activators or repressors in host-pathogen interactions. Here we report that a mitogen-activated protein kinase, OsMPK6, functions both as an activator and a repressor in rice resistance against Xanthomonas oryzae pv. oryzae (Xoo), the causal organism of bacterial blight disease. Activation of OsMPK6 resulted in the formation of lesion mimics and local resistance to Xoo, accompanied by the accumulation of salicylic acid (SA) and jasmonic acid (JA), and the induced expression of SA- and JA-signaling genes. Nuclear localization of OsMPK6 was essential for local resistance, suggesting that modulating the expression of defense-responsive genes through transcription regulators may be the primary mechanism of OsMPK6-mediated local resistance. The knock-out of OsMPK6 resulted in enhanced Xoo resistance, increased accumulation of SA and enhanced resistance to X. oryzae pv. oryzicola, the causal organism of bacterial streak disease, in systemic tissues. Xoo infection induced the expression of PR1a, the marker gene of systemic acquired resistance (SAR), in systemic health tissues of OsMPK6-knock-out plants. These results suggest that OsMPK6 negatively regulates SAR. Thus OsMPK6 is a two-faced player in the rice-Xoo interaction.

The Arabidopsis downy mildew resistance gene RPP8 is induced by pathogens and salicylic acid and is regulated by W box cis elements

Plants disease resistance (R) genes encode specialized receptors that are quantitative, rate-limiting defense regulators. R genes must be expressed at optimum levels to function properly. If expression is too low, downstream defense responses are not activated efficiently. Conversely, overexpression of R genes can trigger autoactivation of defenses with deleterious consequences for the plant. Little is known about R gene regulation, particularly under defense-inducing conditions. We examined regulation of the Arabidopsis thaliana gene RPP8 (resistance to Hyaloperonospora arabidopsidis, isolate Emco5). RPP8 was induced in response to challenge with H. arabidopsidis or application of salicylic acid, as shown with RPP8-Luciferase transgenic plants and quantitative reverse-transcription polymerase chain reaction of endogenous alleles. The RPP1 and RPP4 genes were also induced by H. arabidopsidis and salicylic acid, suggesting that some RPP genes are subject to feedback amplification. The RPP8 promoter contains three W box cis elements. Site-directed mutagenesis of all three W boxes greatly diminished RPP8 basal expression, inducibility, and resistance in transgenic plants. Motif searches indicated that the W box is the only known cis element that is statistically overrepresented in Arabidopsis nucleotide-binding leucine-rich repeat promoters. These results indicate that WRKY transcription factors can regulate expression of surveillance genes at the top of the defense-signaling cascade.

The CC-NB-LRR-type Rdg2a resistance gene confers immunity to the seed-borne barley leaf stripe pathogen in the absence of hypersensitive cell death

Background

Leaf stripe disease on barley (Hordeum vulgare) is caused by the seed-transmitted hemi-biotrophic fungus Pyrenophora graminea. Race-specific resistance to leaf stripe is controlled by two known Rdg (Resistance to Drechslera graminea) genes: the H. spontaneum-derived Rdg1a and Rdg2a, identified in H. vulgare. The aim of the present work was to isolate the Rdg2a leaf stripe resistance gene, to characterize the Rdg2a locus organization and evolution and to elucidate the histological bases of Rdg2a-based leaf stripe resistance.

Principal Findings

We describe here the positional cloning and functional characterization of the leaf stripe resistance gene Rdg2a. At the Rdg2a locus, three sequence-related coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NB-LRR) encoding genes were identified. Sequence comparisons suggested that paralogs of this resistance locus evolved through recent gene duplication, and were subjected to frequent sequence exchange. Transformation of the leaf stripe susceptible cv. Golden Promise with two Rdg2a-candidates under the control of their native 5′ regulatory sequences identified a member of the CC-NB-LRR gene family that conferred resistance against the Dg2 leaf stripe isolate, against which the Rdg2a-gene is effective. Histological analysis demonstrated that Rdg2a-mediated leaf stripe resistance involves autofluorescing cells and prevents pathogen colonization in the embryos without any detectable hypersensitive cell death response, supporting a cell wall reinforcement-based resistance mechanism.

Conclusions

This work reports about the cloning of a resistance gene effective against a seed borne disease. We observed that Rdg2a was subjected to diversifying selection which is consistent with a model in which the R gene co-evolves with a pathogen effector(s) gene. We propose that inducible responses giving rise to physical and chemical barriers to infection in the cell walls and intercellular spaces of the barley embryo tissues represent mechanisms by which the CC-NB-LRR-encoding Rdg2a gene mediates resistance to leaf stripe in the absence of hypersensitive cell death.

Regulation of the expression of plant resistance gene SNC1 by a protein with a conserved BAT2 domain

Plant Resistance (R) genes encode immune receptors that recognize pathogens and activate defense responses. Because of fitness costs associated with maintaining R protein-mediated resistance, expression levels of R genes have to be tightly regulated. However, mechanisms on how R-gene expression is regulated are poorly understood. Here we show that MODIFIER OF snc1, 1 (MOS1) regulates the expression of SUPPRESSOR OF npr1-1, CONSTITUTIVE1 (SNC1), which encodes a Toll/interleukin receptor-nucleotide binding site-leucine-rich repeat type of R protein in Arabidopsis (Arabidopsis thaliana). In the mos1 loss-of-function mutant plants, snc1 expression is repressed and constitutive resistance responses mediated by snc1 are lost. The repression of snc1 expression in mos1 is released by knocking out DECREASE IN DNA METHYLATION1. In mos1 mutants, DNA methylation in a region upstream of SNC1 is altered. Furthermore, expression of snc1 transgenes using the native promoter does not require MOS1, indicating that regulation of SNC1 expression by MOS1 is at the chromatin level. Map-based cloning of MOS1 revealed that it encodes a novel protein with a HLA-B ASSOCIATED TRANSCRIPT2 (BAT2) domain that is conserved in plants and animals. Our study on MOS1 suggests that BAT2 domain-containing proteins may function in regulation of gene expression at chromatin level.

A benefit of high temperature: increased effectiveness of a rice bacterial blight disease resistance gene

*Continuous planting of crops containing single disease resistance (R) genes imposes a strong selection for virulence in pathogen populations, often rendering the R gene ineffective. Increasing environmental temperatures may complicate R-gene-mediated disease control because high temperatures often promote disease development and reduce R gene effectiveness. Here, performance of one rice bacterial blight disease R gene was assessed in field and growth chamber studies to determine the influence of temperature on R gene effectiveness and durability. *Disease severity and virulence of Xanthomonas oryzae pv. oryzae (Xoo) populations were monitored in field plots planted to rice with and without the bacterial blight R gene Xa7 over 11 yr. The performance of Xa7 was determined in high- and low-temperature regimes in growth chambers. *Rice with Xa7 exhibited less disease than lines without Xa7 over 11 yr, even though virulence of Xoo field populations increased. Xa7 restricted disease more effectively at high than at low temperatures. Other R genes were less effective at high temperatures. *We propose that Xa7 restricts disease and Xoo population size more efficiently in high temperature cropping seasons compared with cool seasons creating fluctuating selection, thereby positively impacting durability of Xa7.

Multiple gene loci affecting genetic background-controlled disease resistance conferred by R gene Xa3/Xa26 in rice

The function of bacterial-blight resistance gene Xa3/Xa26 in rice is influenced by genetic background; the Oryza sativa L. ssp. japonica background can increase Xa3/Xa26 expression, resulting in an enhanced resistance. To identify whether Xa3/Xa26 transcript level is the only factor contributing to genetic background-controlled resistance, we screened an F(2) population that was developed from a cross between Oryza sativa L. ssp. indica and japonica rice lines and was segregating for Xa3/Xa26, and compared the expression profiles of a pair of indica and japonica rice lines that both carried Xa3/Xa26. Eight quantitative trait loci (QTLs), in addition to Xa3/Xa26, were identified as contributing to the bacterial resistance of this population. Four of the eight QTLs were contributed to the japonica line. The resistance of this population was also affected by epistatic effects. Some F(2) individuals showed significantly increased Xa3/Xa26 transcripts, but the increased transcripts did not completely correlate with the reduced disease in this population. The analysis of the expression profile of Xa3/Xa26-mediated resistance using a microarray containing approximate 7,990 rice genes identified 44 differentially expressed genes. Thirty-five genes were rapidly activated in the japonica background, but not in the indica background, during disease resistance. These results suggest that multiple factors, including the one resulting in increased Xa3/Xa26 expression, may contribute to the enhanced resistance in the japonica background. These factors can cause a variation in gene expression profile that differs from that in the indica background during disease resistance.

A pair of allelic WRKY genes play opposite roles in rice-bacteria interactions

Although allelic diversity of genes has been reported to play important roles in different physiological processes, information on allelic diversity of defense-responsive genes in host-pathogen interactions is limited. Here, we report that a pair of allelic genes, OsWRKY45-1 and OsWRKY45-2, which encode proteins with a 10-amino acid difference, play opposite roles in rice (Oryza sativa) resistance against bacterial pathogens. Bacterial blight caused by Xanthomonas oryzae pv oryzae (Xoo), bacterial streak caused by Xanthomonas oryzae pv oryzicola (Xoc), and fungal blast caused by Magnaporthe grisea are devastating diseases of rice worldwide. OsWRKY45-1-overexpressing plants showed increased susceptibility and OsWRKY45-1-knockout plants showed enhanced resistance to Xoo and Xoc. In contrast, OsWRKY45-2-overexpressing plants showed enhanced resistance and OsWRKY45-2-suppressing plants showed increased susceptibility to Xoo and Xoc. Interestingly, both OsWRKY45-1- and OsWRKY45-2-overexpressing plants showed enhanced resistance to M. grisea. OsWRKY45-1-regulated Xoo resistance was accompanied by increased accumulation of salicylic acid and jasmonic acid and induced expression of a subset of defense-responsive genes, while OsWRKY45-2-regulated Xoo resistance was accompanied by increased accumulation of jasmonic acid but not salicylic acid and induced expression of another subset of defense-responsive genes. These results suggest that both OsWRKY45-1 and OsWRKY45-2 are positive regulators in rice resistance against M. grisea, but the former is a negative regulator and the latter is a positive regulator in rice resistance against Xoo and Xoc. The opposite roles of the two allelic genes in rice-Xoo interaction appear to be due to their mediation of different defense signaling pathways.

Dissection of the factors affecting development-controlled and race-specific disease resistance conferred by leucine-rich repeat receptor kinase-type R genes in rice

Development-controlled resistance and resistance specificity frequently restrict the application of a disease resistance (R) gene in crop breeding programs. Xa3/Xa26 and Xa21, encoding leucine-rich repeat (LRR)-kinase type plasma membrane proteins, mediate race-specific resistance to Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight, one of the most devastating rice diseases. Plants carrying Xa3/Xa26 and plants carrying Xa21 have different resistance spectra and the functions of the two R genes are regulated by developmental stage. Four chimeric genes encoding proteins consisting of different parts of XA3/XA26 and XA21 were constructed by domain swapping and transformed into a susceptible rice variety. The resistance spectra and development-regulated resistance of the transgenic plants carrying Xa3/Xa26, Xa21, or chimeric gene to different Xoo strains were analyzed in the same genetic background. The results suggest that the gradually increased expression of Xa3/Xa26 and Xa21 plays an important role in the progressively enhanced Xoo resistance during rice development. In addition, the LRR domains of XA3/XA26 and XA21 are important determinants of race-specific recognition during rice-Xoo interaction, but juxtamembrane regions of the two R proteins also appear to contribute to resistance specificity.

Pathogen-induced expressional loss of function is the key factor in race-specific bacterial resistance conferred by a recessive R gene xa13 in rice

The fully recessive disease resistance (R) gene xa13, which mediates race-specific resistance to Xanthomonas oryzae pv. oryzae (Xoo), encodes a plasma membrane protein that differs by one amino acid from that encoded by its dominant (susceptible) allele Xa13. The molecular mechanism of xa13-mediated resistance is largely unknown. Here we show that, compared with its dominant allele, expressional non-reaction of xa13 to Xoo infection, not its protein composition, is the key factor for xa13-mediated resistance. We used the promoter (P(Xa13)) of the dominant Xa13, which was induced by only the incompatible Xoo strain for xa13, to regulate xa13 and xa13(Leu49) (a natural recessive allele of xa13) in the rice line IRBB13 carrying xa13. The transgenic plants showed the same level of susceptibility and bacterial growth rate as those of the rice line carrying dominant Xa13, accompanied by the induced accumulation of xa13 or xa13(Leu49) proteins. Constitutive expression of dominant XA13 or different xa13 proteins (xa13, xa13(Leu49), xa13(Ala85) or xa13(Val184)) in IRBB13 had no effect on Xoo infection in the transgenic plants. These results suggest that race-specific pathogen-induced Xa13 expression is critical for infection. Thus, xa13 stands out from other R genes in that its functions in disease resistance are due to only the loss of pathogen-induced transcriptional motivation caused by natural selection.

Higher copy numbers of the potato RB transgene correspond to enhanced transcript and late blight resistance levels

Late blight of potato ranks among the costliest of crop diseases worldwide. Host resistance offers the best means for controlling late blight, but previously deployed single resistance genes have been short-lived in their effectiveness. The foliar blight resistance gene RB, previously cloned from the wild potato Solanum bulbocastanum, has proven effective in greenhouse tests of transgenic cultivated potato. In this study, we examined the effects of the RB transgene on foliar late blight resistance in transgenic cultivated potato under field production conditions. In a two-year replicated trial, the RB transgene, under the control of its endogenous promoter, provided effective disease resistance in various genetic backgrounds, including commercially prominent potato cultivars, without fungicides. RB copy numbers and transcript levels were estimated with transgene-specific assays. Disease resistance was enhanced as copy numbers and transcript levels increased. The RB gene, like many other disease resistance genes, is constitutively transcribed at low levels. Transgenic potato lines with an estimated 15 copies of the RB transgene maintain high RB transcript levels and were ranked among the most resistant of 57 lines tested. We conclude that even in these ultra-high copy number lines, innate RNA silencing mechanisms have not been fully activated. Our findings suggest resistance-gene transcript levels may have to surpass a threshold before triggering RNA silencing. Strategies for the deployment of RB are discussed in light of the current research.

Correlation between transcript abundance of the RB gene and the level of the RB-mediated late blight resistance in potato

Numerous disease-resistance genes have been cloned and characterized in various plant species. Only a few of these reported genes were transcriptionally induced or had enhanced transcription upon pathogen infection. Here, we report that transcription of the RB gene, which was cloned from the wild potato species Solanum bulbocastanum and confers resistance to potato late blight, was significantly increased after inoculation with the late blight pathogen Phytophthora infestans. Different RB transgenic lines showed different levels of resistance, which were correlated with the amounts of RB transcript in the transgenic plants. Different transgenic lines also showed different patterns of RB transcription 1, 3, and 5 days after P. infestans inoculation. Interestingly, the RB gene showed a higher basal level of transcription and a more dramatic transcriptional increase upon inoculation in S. bulbocastanum than in all potato transgenic lines. Our results revealed a predictive correlation between transcript abundance of the RB gene and the level of the RB-mediated late blight resistance. High level of resistance was associated with a combination of rapid RB transcript induction immediately after pathogen infection followed by the steady production of RB transcript. Thus, the transcription level of the RB gene provides a valuable marker for selecting and deploying RB-containing potato lines for late blight control.

A rice gene of de novo origin negatively regulates pathogen-induced defense response

How defense genes originated with the evolution of their specific pathogen-responsive traits remains an important problem. It is generally known that a form of duplication can generate new genes, suggesting that a new gene usually evolves from an ancestral gene. However, we show that a new defense gene in plants may evolve by de novo origination, resulting in sophisticated disease-resistant functions in rice. Analyses of gene evolution showed that this new gene, OsDR10, had homologs only in the closest relative, Leersia genus, but not other subfamilies of the grass family; therefore, it is a rice tribe-specific gene that may have originated de novo in the tribe. We further show that this gene may evolve a highly conservative rice-specific function that contributes to the regulation difference between rice and other plant species in response to pathogen infections. Biologic analyses including gene silencing, pathologic analysis, and mutant characterization by transformation showed that the OsDR10-suppressed plants enhanced resistance to a broad spectrum of Xanthomonas oryzae pv. oryzae strains, which cause bacterial blight disease. This enhanced disease resistance was accompanied by increased accumulation of endogenous salicylic acid (SA) and suppressed accumulation of endogenous jasmonic acid (JA) as well as modified expression of a subset of defense-responsive genes functioning both upstream and downstream of SA and JA. These data and analyses provide fresh insights into the new biologic and evolutionary processes of a de novo gene recruited rapidly.

Strategies for developing Green Super Rice

From a global viewpoint, a number of challenges need to be met for sustainable rice production: (i) increasingly severe occurrence of insects and diseases and indiscriminate pesticide applications; (ii) high pressure for yield increase and overuse of fertilizers; (iii) water shortage and increasingly frequent occurrence of drought; and (iv) extensive cultivation in marginal lands. A combination of approaches based on the recent advances in genomic research has been formulated to address these challenges, with the long-term goal to develop rice cultivars referred to as Green Super Rice. On the premise of continued yield increase and quality improvement, Green Super Rice should possess resistances to multiple insects and diseases, high nutrient efficiency, and drought resistance, promising to greatly reduce the consumption of pesticides, chemical fertilizers, and water. Large efforts have been focused on identifying germplasms and discovering genes for resistance to diseases and insects, N- and P-use efficiency, drought resistance, grain quality, and yield. The approaches adopted include screening of germplasm collections and mutant libraries, gene discovery and identification, microarray analysis of differentially regulated genes under stressed conditions, and functional test of candidate genes by transgenic analysis. Genes for almost all of the traits have now been isolated in a global perspective and are gradually incorporated into genetic backgrounds of elite cultivars by molecular marker-assisted selection or transformation. It is anticipated that such strategies and efforts would eventually lead to the development of Green Super Rice.