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Oreiro EG, Grimares EK, Atienza-Grande G, Quibod IL, Roman-Reyna V, Oliva R. Genome-Wide Associations and Transcriptional Profiling Reveal ROS Regulation as One Underlying Mechanism of Sheath Blight Resistance in Rice. Mol Plant Microbe Interact 2020; 33:212-222. [PMID: 31634039 DOI: 10.1094/mpmi-05-19-0141-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Rice sheath blight, caused by the necrotrophic fungus Rhizoctonia solani Kühn, continues to be an important and challenging rice disease worldwide. Here, we used genome-wide association studies over a high-density rice array to facilitate the identification of potential novel genes and quantitative trait loci related to sheath blight resistance. We identified multiple regions that significantly associated with independent disease components in chromosomes 1, 4, and 11 under controlled condition. In particular, we investigated qLN1128, a quantitative trait locus enriched with defense-related genes that reduce disease lesions in a near-isogenic line. RNA profiling of the line carrying qLN1128 showed a number of differentially expressed genes related to the reactive oxygen species (ROS)-redox pathway. Histochemical staining revealed less ROS accumulation on the resistant line, suggesting efficient ROS deregulation that delays pathogen colonization. The detection of genomic regions controlling multiple mechanisms of resistance to sheath blight will provide tools to design effective breeding interventions in rice.
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Affiliation(s)
- Eula Gems Oreiro
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Earlyn Kate Grimares
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Institute of Weed Science, Entomology and Plant Pathology, College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Genelou Atienza-Grande
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Institute of Weed Science, Entomology and Plant Pathology, College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Ian Lorenzo Quibod
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Veronica Roman-Reyna
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Ricardo Oliva
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Quibod IL, Grande G, Oreiro EG, Borja FN, Dossa GS, Mauleon R, Cruz CV, Oliva R. Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot. PLoS One 2015; 10:e0139256. [PMID: 26422147 PMCID: PMC4589537 DOI: 10.1371/journal.pone.0139256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/09/2015] [Indexed: 12/26/2022] Open
Abstract
Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.
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Affiliation(s)
- Ian Lorenzo Quibod
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Genelou Grande
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Eula Gems Oreiro
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Frances Nikki Borja
- T.T. Chang- Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines
| | - Gerbert Sylvestre Dossa
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
- Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany
| | - Ramil Mauleon
- T.T. Chang- Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines
| | - Casiana Vera Cruz
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Ricardo Oliva
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
- * E-mail:
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