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Xanthomonas oryzae pv. oryzae (Xoo) is a destructive pathogen that causes bacterial blight disease of rice worldwide. Xoo uses T3SS (type III secretion system) effectors to subvert rice innate immunity. However, the comprehensive knowledge of rice genes involved in T3SS effectors-mediated interaction remains unclear. In this study, the transcriptome profiles of rice infected with a virulent Xoo strain from North-eastern region of India relatives to its avirulent strain (that lacks functional T3SS) were analyzed at early (2–6 hpi) and late (16–24 hpi) hours of infection. Out of total 255 differentially expressed genes (DEGs), during early infection, 62 and 70 genes were upregulated and downregulated, respectively. At late infection, 70 and 53 genes were upregulated and downregulated, respectively. The transcriptomic data identified many differentially expressed resistant genes, transposons, transcription factors, serine/threonine protein kinase, cytochrome P450 and peroxidase genes that are involved in plant defense. Pathway analysis revealed that these DEGs are involved in hormone signaling, plant defense, cellular metabolism, growth and development processes. DEGs associated with plant defense were also validated through quantitative real-time PCR. Our study brings a comprehensive picture of the rice genes that are being differentially expressed during bacterial blight infection. Nevertheless, the DEG-associated pathways would provide sensible targets for developing resistance to bacterial blight. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-022-03193-4.

Made available in DSpace on 2020-12-11T12:42:34Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-03-16 National Natural Science Foundation of China CAS President's International Fellowship Initiative (PIFI) China Postdoctoral Science Foundation SERB-Start-Up Research Grant (Young Scientist) Scheme, Department of Science and Technology, Government of India, New Delhi Antimicrobial activity of silver nanoparticles (AgNPs) has been well documented in earlier studies. As their efficient role in combating phytopathogens has begun recently, there is a huge scope to explore their effectiveness in agriculture. Considering the strong antifungal activity of biosynthesized AgNPs (as reported in our previous study), our main aim is to elucidate their antibacterial activity against bacterial plant pathogens to authenticate their wide range of agricultural applications. The present manuscript highlights the potential role of biosynthesized AgNPs against Xanthomonas oryzae pv. oryzae (Xoo) causing disastrous sheath blight disease of rice worldwide. We observed strong antibacterial activity of biosynthesized AgNPs (size similar to 12 nm) against Xoo at 20, 30 and 50 mu g/mL concentrations. The significant inhibitory impact of AgNPs on biofilm formation by Xoo was noted even at the lower dose of 5 mu g/mL (p = 0.001). Maximum biofilm inhibition (p = 0.000) was caused at 50 mu g/mL concentration of AgNPs in comparison to control. Furthermore, disease suppression by biosynthesized AgNPs was authenticated under greenhouse conditions. Foliar spray of AgNPs significantly reduced the blight symptoms in rice sheaths as shown by 9.25% DLA (% Diseased leaf area) as compared to 33.91% DLA in Xoo inoculated rice plants. Altogether, our data suggest that biosynthesized AgNPs based nanoformulation can be applied for successful management of blight disease of rice. In addition, the antibiofilm strategies instigated by AgNPs can be exploited against a wide range of bacterial phytopathogens. In light of rapidly emerging antibiotic-resistant microbial strains, the current work provides an alternate effective platform for the application of nanoformulation for augmenting sustainability in the agriculture. Chinese Acad Sci, Xishuangbanna Trop Bot Garden, CAS Key Lab Trop Forest Ecol, Menglun 666303, Yunnan, Peoples R China Banaras Hindu Univ, Dept Mycol & Plant Pathol, Inst Agr Sci, Varanasi 221005, Uttar Pradesh, India Sao Paulo State Univ, Lab Environm Nanotechnol, Inst Sci & Technol Sorocaba, Sao Paulo, Brazil Somvanshi Res Fdn, 13-21 Vikas Nagar, Lucknow 226022, Uttar Pradesh, India Sao Paulo State Univ, Lab Environm Nanotechnol, Inst Sci & Technol Sorocaba, Sao Paulo, Brazil National Natural Science Foundation of China: 31700457 CAS President's International Fellowship Initiative (PIFI): 2019PC0095 China Postdoctoral Science Foundation: 2018M631112 SERB-Start-Up Research Grant (Young Scientist) Scheme, Department of Science and Technology, Government of India, New Delhi: YSS/2015/000082

The rice XA21 and XA3 pattern receptor kinases, derived from Oryza longistaminata and an Oryza. sativa japonica cultivar Wase Aikoku 3, respectively, confer resistance to strains of the Gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight disease. Previously, we showed that transfer of Xa21 to the model rice cultivar Kitaake enhances resistance to Xoo. In this manuscript we demonstrate that Kitaake expressing Xa3 confers resistance to Xoo strain PXO79 and that the stress-related marker genes PR10b and KO5 are upregulated in Xoo-infected Xa3 rice leaves. We also show that rice somatic embryogenesis receptor kinase 2 (OsSERK2) positively regulates XA3-mediated immunity in Kitaake. We found that overexpression of XA21 binding protein 15 (XB15) and XB24, two negative regulators of XA21-mediated immunity, do not affect XA3-mediated immunity in the Kitaake genetic background. Our results indicate that the rice immune receptors XA21 and XA3 employ both shared and distinct signaling components in their response to Xoo. The results are important to further understand pathogen-associated molecular pattern (PAMP)-triggered immunity in rice. Furthermore, the presence of Kitaake rice carrying Xa3 will facilitate genetic research to study the XA3-mediated immunity.

Genome sequence comparisons to infer likely gene functions require accurate ortholog assignments. In Pseudomonas spp., the sensor-regulator ColS-ColR two-component regulatory system responds to zinc and other metals to control certain membrane-related functions, including lipid A remodeling. In Xanthomonas spp., three different two-component regulatory systems, RaxH-RaxR, VgrS-VgrR, and DetS-DetR, have been denoted as ColS-ColR in several different genome annotations and publications. To clarify these assignments, we compared the sensor periplasmic domain sequences and found that those from Pseudomonas ColS and Xanthomonas RaxH share a similar size as well as the location of a Glu-X-X-Glu metal ion-binding motif. Furthermore, we determined that three genes adjacent to raxRH are predicted to encode enzymes that remodel the lipid A component of lipopolysaccharide. The modifications catalyzed by lipid A phosphoethanolamine transferase (EptA) and lipid A 1-phosphatase (LpxE) previously were detected in lipid A from multiple Xanthomonas spp. The third gene encodes a predicted lipid A glycosyl transferase (ArnT). Together, these results indicate that the Xanthomonas RaxH-RaxR system is orthologous to the Pseudomonas ColS-ColR system that regulates lipid A remodeling. To avoid future confusion, we recommend that the terms ColS and ColR no longer be applied to Xanthomonas spp., and that the Vgr, Rax, and Det designations be used instead.

Background Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of Bacterial Leaf Blight (BB), an emerging disease in rice in West-Africa which can induce up to 50 % of yield losses. So far, no specific resistance gene or QTL to African Xoo were mapped. The objectives of this study were to identify and map novels and specific resistance QTLs to African Xoo strains. Results The reference recombinant inbred lines (RIL) mapping population derived from the cross between IR64 and Azucena was used to investigate Xoo resistance. Resistance to African and Philippine Xoo strains representing different races was assessed on the RIL population under greenhouse conditions. Five major quantitative trait loci (QTL) for resistance against African Xoo were located on different chromosomes. Loci on chromosomes 1, 7, 9, 10 and 11 explained as much as 13 %, 37 %, 13 %, 11 % and 15 % of resistance variation, respectively. A major novel QTL located on chromosome 7 explained 37 % of the phenotypic variance to the African Xoo corresponding to race A3 whereas that on chromosome 11 is effective to all African races tested. Together with genes and QTLs for resistance to bacterial blight previously described, the QTLs described here were mapped onto the reference O. sativa subs japonica (var. Nipponbare) physical map. Conclusion We characterized new resistance QTLs. While some co-localize with known resistance genes/QTLs to Asian strains, others are specific to African strains. We result with new information on genes and QTLs for resistance to bacterial blight that will be useful for controlling the disease.

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight (BB) in rice (Oryza sativa L.). In this study, we investigated the genome-wide transcription patterns of two Xoo strains (KACC10331 and HB1009), which showed different virulence patterns against eight rice cultivars, including IRBB21 (carrying Xa21). In total, 743 genes showed a significant change (p-value < 0.001 in t-tests) in their mRNA expression levels in the HB1009 (K3a race) strain compared with the Xoo KACC10331 strain (K1 race). Among them, four remarkably enriched GO terms, DNA binding, transposition, cellular nitrogen compound metabolic process, and cellular macromolecule metabolic process, were identified in the upregulated genes. In addition, the expression of 44 genes was considerably higher (log2 fold changes > 2) in the HB1009 (K3a race) strain than in the Xoo KACC10331 (K1 race) strain. Furthermore, 13 and 12 genes involved in hypersensitive response and pathogenicity (hrp) and two-component regulatory systems (TCSs), respectively, were upregulated in the HB1009 (K3a race) strain compared with the Xoo KACC10331 (K1 race) strain, which we determined using either quantitative real-time PCR analysis or next-generation RNA sequencing. These results will be helpful to improve our understanding of Xoo and to gain a better insight into the Xoo–rice interactions.

SUMMARY We show that OsSERK2 is a regulator of innate immune signaling mediated by multiple non-RD receptor kinases (RKs) including XA21, XA3, and OsFLS2. OsSerk2-silenced rice lines are impaired in XA21-mediated immunity to Xoo PXO99, XA3-mediated immunity to Xoo PXO86, and OsFLS2-mediated defense responses. Thus, OsSERK2 is broadly involved in PRR-mediated immunity in rice., The rice XA21 immune receptor kinase and the structurally related XA3 receptor confer immunity to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight. Here we report the isolation of OsSERK2 (rice somatic embryogenesis receptor kinase 2) and demonstrate that OsSERK2 positively regulates immunity mediated by XA21 and XA3 as well as the rice immune receptor FLS2 (OsFLS2). Rice plants silenced for OsSerk2 display altered morphology and reduced sensitivity to the hormone brassinolide. OsSERK2 interacts with the intracellular domains of each immune receptor in the yeast two-hybrid system in a kinase activity-dependent manner. OsSERK2 undergoes bidirectional transphosphorylation with XA21 in vitro and forms a constitutive complex with XA21 in vivo. These results demonstrate an essential role for OsSERK2 in the function of three rice immune receptors and suggest that direct interaction with the rice immune receptors is critical for their function. Taken together, our findings suggest that the mechanism of OsSERK2-meditated regulation of rice XA21, XA3, and FLS2 differs from that of AtSERK3/BAK1-mediated regulation of Arabidopsis FLS2 and EFR.

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This article 'Improvement of conjugation methods for Xanthomonas oryzae pv. oryzae strain DY89031 to identify avrXa21 clones' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported.

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This article 'New rice breeding lines with multiple pest resistance' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported.

This article 'DNA fingerprinting of bacterial blight pathogen directly from infected leaves' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported.

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This article 'Repetitive Sequence-Based Polymerase Chain Reaction of Xanthomonas oryzae pv. oryzae and Pseudomonas species' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported.

This article 'Dna Fingerprinting of Xanthomonas oryzae pv. oryzae Using IS1112-Based Polymerase Chain Reaction' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported.

This article 'Genetic Diversity in Xanthomonas oryzae pv. oryzicola' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported.

This article 'Comparison of Xanthomonas oryzae pv. oryzae Strains From Africa, North America, and Asia By Restriction Fragment Length Polymorphism Analysis' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported.

This article 'DNA Fingerprinting of Xanthomonas oryzae pv. oryzae By Ligation-Mediated Polymerase Chain Reaction' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported., IRRI publication.

This article 'Genetic Manipulation of Xanthomonas oryzae pv. oryzae' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported.

This article 'Polymerase Chain Reaction Amplification of DNA From Bacterial Pathogens of Rice Using Specific Oligonucleotide Primers' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported., IRRI publication.

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This article 'New Races of Xanthomonas oryzae pv. oryzae (XOO) Among Strains Representing Major Rice-Growing Areas of India and Nepal' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported.

This article 'Effect of Plant Age on IR-BB21 Resistance to Xanthomonas oryzae pv. oryzae (XOO)' appeared in the International Rice Research Notes series, created by the International Rice Research Institute (IRRI) to expedite communication among scientists concerned with the development of improved technology for rice and rice-based systems. The series is a mechanism to help scientists keep each other informed of current rice research findings. The concise scientific notes are meant to encourage rice scientists to communicate with one another to obtain details on the research reported., IRRI publication.

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This article 'Differentiation Between the Bacteria Causing Bacterial Blight (BB), Bacterial Leaf Streak (BLS), and Bacterial Brown Blotch on Rice' appeared in the International Rice Research Newsletter series, created by the International Rice Research Institute (IRRI). The primary objective of this publication was to expedite communication among scientists concerned with the development of improved technology for rice and for rice based cropping systems. This publication will report what scientists are doing to increase the production of rice in as much as this crop feeds the most densely populated and land scarce nations in the world.