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Koyama T, Tezuka T, Nagano AJ, Murakami J, Yoshikawa T. Differential Stress Responses to Rice Blast Fungal Infection Associated with the Vegetative Growth Phase in Rice. PLANTS (BASEL, SWITZERLAND) 2025; 14:241. [PMID: 39861594 PMCID: PMC11769066 DOI: 10.3390/plants14020241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 01/10/2025] [Accepted: 01/13/2025] [Indexed: 01/27/2025]
Abstract
During vegetative growth, plants undergo various morphological and physiological changes in the transition from the juvenile phase to the adult phase. In terms of stress resistance, it has been suggested that plants gain or reinforce disease resistance during the process of maturation, which is recognized as adult plant resistance or age-related resistance. While much knowledge has been obtained about changes in disease resistance as growth stages progress, knowledge about changes in plant responses to pathogens with progressing age in plants is limited. In this study, we experimentally compared rice blast resistance in rice leaves sampled from plants at different growth phases. The results indicate differential infection progression and fungal status depending on growth stage. Transcriptome analysis following blast fungus infection revealed that several genes involved in the defense response were upregulated in both the juvenile and intermediate stage, but the expression changes of many genes were growth phase-specific. These findings highlight differences in rice leaf stress responses to blast infection at different growth stages.
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Affiliation(s)
- Takuma Koyama
- Department of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takumi Tezuka
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima 411-8540, Japan
| | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku University, Otsu 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan
| | - Jiro Murakami
- Faculty of Agriculture, Kibi International University, Minami-Awaji 656-0484, Japan
| | - Takanori Yoshikawa
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima 411-8540, Japan
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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Franco Ortega S, Ferrocino I, Adams I, Silvestri S, Spadaro D, Gullino ML, Boonham N. Monitoring and Surveillance of Aerial Mycobiota of Rice Paddy through DNA Metabarcoding and qPCR. J Fungi (Basel) 2020; 6:jof6040372. [PMID: 33348656 PMCID: PMC7766667 DOI: 10.3390/jof6040372] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 01/16/2023] Open
Abstract
The airborne mycobiota has been understudied in comparison with the mycobiota present in other agricultural environments. Traditional, culture-based methods allow the study of a small fraction of the organisms present in the atmosphere, thus missing important information. In this study, the aerial mycobiota in a rice paddy has been examined during the cropping season (from June to September 2016) using qPCRs for two important rice pathogens (Pyricularia oryzae and Bipolaris oryzae) and by using DNA metabarcoding of the fungal ITS region. The metabarcoding results demonstrated a higher alpha diversity (Shannon–Wiener diversity index H′ and total number of observed species) at the beginning of the trial (June), suggesting a higher level of community complexity, compared with the end of the season. The main taxa identified by HTS analysis showed a shift in their relative abundance that drove the cluster separation as a function of time and temperature. The most abundant OTUs corresponded to genera such as Cladosporium, Alternaria, Myrothecium, or Pyricularia. Changes in the mycobiota composition were clearly dependent on the average air temperature with a potential impact on disease development in rice. In parallel, oligotyping analysis was performed to obtain a sub-OTU identification which revealed the presence of several oligotypes of Pyricularia and Bipolaris with relative abundance changing during monitoring.
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Affiliation(s)
- Sara Franco Ortega
- Centre of Competence for the Innovation in the Agro-Environmental Sector—AGROINNOVA, University of Turin, Via Paolo Braccini 2, I-10095 Grugliasco (TO), Italy; (S.F.O.); (M.L.G.)
| | - Ilario Ferrocino
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Via Paolo Braccini 2, I-10095 Grugliasco (TO), Italy;
| | - Ian Adams
- FERA, National Agri-Food Innovation Campus, Sand Hutton, York YO41 1LZ, UK;
| | - Simone Silvestri
- Ente Nazionale per la Risicultura (ENTERISI), Strada per Ceretto 4, 27030 Castello d’Agogna (PV), Italy;
| | - Davide Spadaro
- Centre of Competence for the Innovation in the Agro-Environmental Sector—AGROINNOVA, University of Turin, Via Paolo Braccini 2, I-10095 Grugliasco (TO), Italy; (S.F.O.); (M.L.G.)
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Via Paolo Braccini 2, I-10095 Grugliasco (TO), Italy;
- Correspondence:
| | - Maria Lodovica Gullino
- Centre of Competence for the Innovation in the Agro-Environmental Sector—AGROINNOVA, University of Turin, Via Paolo Braccini 2, I-10095 Grugliasco (TO), Italy; (S.F.O.); (M.L.G.)
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Via Paolo Braccini 2, I-10095 Grugliasco (TO), Italy;
| | - Neil Boonham
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK;
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Fan X, Matsumoto H, Wang Y, Hu Y, Liu Y, Fang H, Nitkiewicz B, Lau SYL, Wang Q, Fang H, Wang M. Microenvironmental Interplay Predominated by Beneficial Aspergillus Abates Fungal Pathogen Incidence in Paddy Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:13042-13052. [PMID: 31631659 DOI: 10.1021/acs.est.9b04616] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rice fungal pathogens, responsible for severe rice yield loss and biotoxin contamination, cause increasing concerns on environmental safety and public health. In the paddy environment, we observed that the asymptomatic rice phyllosphere microenvironment was dominated by an indigenous fungus, Aspergillus cvjetkovicii, which positively correlated with alleviated incidence of Magnaporthe oryzae, one of the most aggressive plant pathogens. Through the comparative metabolic profiling for the rice phyllosphere microenvironment, two metabolites were assigned as exclusively enriched metabolic markers in the asymptomatic phyllosphere and increased remarkably in a population-dependent manner with A. cvjetkovicii. These two metabolites evidenced to be produced by A. cvjetkovicii in either a phyllosphere microenvironment or artificial media were purified and identified as 2(3H)-benzofuranone and azulene, respectively, by gas chromatography coupled to triple quadrupole mass spectrometry and nuclear magnetic resonance analyses. Combining with bioassay analysis in vivo and in vitro, we found that 2(3H)-benzofuranone and azulene exerted dissimilar actions at the stage of infection-related development of M. oryzae. A. cvjetkovicii produced 2(3H)-benzofuranone at the early stage to suppress MoPer1 gene expression, leading to inhibited mycelial growth, while azulene produced lately was involved in blocking of appressorium formation by downregulation of MgRac1. More profoundly, the microenvironmental interplay dominated by A. cvjetkovicii significantly blocked M. oryzae epidemics in the paddy environment from 54.7 to 68.5% (p < 0.05). Our study first demonstrated implication of the microenvironmental interplay dominated by indigenous and beneficial fungus to ecological balance and safety of the paddy environment.
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Affiliation(s)
| | | | | | - Yang Hu
- Zhejiang Provincial Key Laboratory of Biological and Chemical Utilization of Forest Resources , Zhejiang Academy of Forestry , Hangzhou 310058 , Zhejiang , China
| | | | - Hongda Fang
- College of Plant Protection , Hunan Agricultural University , Changsha 410128 , China
| | - Bartosz Nitkiewicz
- Department of Biochemistry, Faculty of Biology and Biotechnology , University of Warmia and Mazury , Oczapowskiego 1A , 10-719 Olsztyn , Poland
| | - Sharon Yu Ling Lau
- Sarawak Tropical Peat Research Institute , 94300 Kota Samarahan , Sarawak , Malaysia
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Ortega SF, Tomlinson J, Hodgetts J, Spadaro D, Gullino ML, Boonham N. Development of Loop-Mediated Isothermal Amplification Assays for the Detection of Seedborne Fungal Pathogens Fusarium fujikuroi and Magnaporthe oryzae in Rice Seed. PLANT DISEASE 2018; 102:1549-1558. [PMID: 30673431 DOI: 10.1094/pdis-08-17-1307-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bakanae disease (caused by Fusarium fujikuroi) and rice blast (caused by Magnaporthe oryzae) are two of the most important seedborne pathogens of rice. The detection of both pathogens in rice seed is necessary to maintain high quality standards and avoid production losses. Currently, blotter tests are used followed by morphological identification of the developing pathogens to provide an incidence of infection in seed lots. Two loop-mediated isothermal amplification assays were developed with primers designed to target the elongation factor 1-α sequence of F. fujikuroi and the calmodulin sequence of M. oryzae. The specificity, sensitivity, selectivity, repeatability, and reproducibility for each assay was assessed in line with the international validation standard published by the European and Mediterranean Plant Protection Organization (PM7/98). The results showed a limit of detection of 100 to 999 fg of DNA of F. fujikuroi and 10 to 99 pg of M. oryzae DNA. When combined with a commercial DNA extraction kit, the assays were demonstrated to be effective for use in detection of the pathogens in commercial batches of infected rice seed of different cultivars, giving results equivalent to the blotter method, thus demonstrating the reliability of the method for the surveillance of F. fujikuroi and M. oryzae in seed-testing laboratories.
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Affiliation(s)
- Sara Franco Ortega
- Centre of Competence for the Innovation in the Agro-Environmental Sector-Agroinnova, and Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Turin, I-10095 Grugliasco, TO, Italy
| | | | | | - Davide Spadaro
- Centre of Competence for the Innovation in the Agro-environmental Sector-Agroinnova, and DiSAFA, University of Turin
| | - Maria Lodovica Gullino
- Centre of Competence for the Innovation in the Agro-environmental Sector-Agroinnova, and DiSAFA, University of Turin
| | - Neil Boonham
- FERA, and IAFRI, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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Real-time PCR quantification of the plant growth promoting bacteria Herbaspirillum seropedicae strain SmR1 in maize roots. Mol Biotechnol 2015; 56:660-70. [PMID: 24563376 DOI: 10.1007/s12033-014-9742-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The plant growth promoting bacteria Herbaspirillum seropedicae SmR1 is an endophytic diazotroph found in several economically important crops. Considering that methods to monitor the plant-bacteria interaction are required, our objective was to develop a real-time PCR method for quantification of PGPB H. seropedicae in the rhizosphere of maize seedlings. Primer pairs were designed, and their specificity was verified using DNA from 12 different bacterial species. Ten standard curves of qPCR assay using HERBAS1 primers and tenfold serial dilutions of H. seropedicae SmR1 DNA were performed, and PCR efficiency of 91 % and correlation coefficient of 0.99 were obtained. H. seropedicae SmR1 limit of detection was 10(1) copies (corresponding to 60.3 fg of bacterial DNA). qPCR assay using HERBAS1 was used to detect and quantify H. seropedicae strain SmR1 in inoculated maize roots, cultivated in vitro and in pots, harvested 1, 4, 7, and 10 days after inoculation. The estimated bacterial DNA copy number per gram of root was in the range 10(7)-10(9) for plants grown in vitro and it was around 10(6) for plants grown in pots. Primer pair HERBAS1 was able to quantify H. seropedicae SmR1, and this assay can be useful for monitoring plant-bacteria interaction.
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Sun G, Liu J, Li G, Zhang X, Chen T, Chen J, Zhang H, Wang D, Sun F, Pan H. Quick and Accurate Detection and Quantification of Magnaporthe oryzae in Rice Using Real-Time Quantitative Polymerase Chain Reaction. PLANT DISEASE 2015; 99:219-224. [PMID: 30699568 DOI: 10.1094/pdis-05-14-0485-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rice blast, caused by Magnaporthe oryzae, is one of the most severe fungal diseases in rice worldwide. In this study, we developed methods to quickly and accurately detect and quantify M. oryzae in the pure cultures of the fungus, rice plants, and rice seed by using SYBR Green I of the real-time quantitative polymerase chain reaction (qPCR). Results of absolute qPCR show that Magnaporthe oryzae can be detected at as low as 6.9 × 10-5 ng of genomic DNA. Results also show that all 10 varieties of rice seed examined in this study contain this fungus, indicating that M. oryzae is generally widespread in rice seed. We report the quantification of DNA of M. oryzae in rice leaves collected in the field, instead of in the lab, using relative qPCR by using rice actin gene as a housekeeping gene. Our results show great practical significance because we would know the potential fungal infection even before planting.
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Affiliation(s)
- Geng Sun
- College of Plant Sciences, Jilin University, Jilin, Changchun 130062, China, and State Key Laboratory of the Discovery and Development of Novel Pesticide, Shenyang Research Institute of Chemical Industry Co., Ltd., Shenyang 110021, China
| | | | - Guihua Li
- College of Plant Sciences, Jilin University
| | | | | | | | - Hao Zhang
- College of Resource and Environment, Jilin Agricultural University
| | - Dongping Wang
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544
| | - Fengjie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043
| | - Hongyu Pan
- College of Plant Sciences, Jilin University
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Yang W, Zhang H, Li M, Wang Z, Zhou J, Wang S, Lu G, Fu F. Early diagnosis of blast fungus, Magnaporthe oryzae, in rice plant by using an ultra-sensitive electrically magnetic-controllable electrochemical biosensor. Anal Chim Acta 2014; 850:85-91. [DOI: 10.1016/j.aca.2014.08.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/31/2014] [Accepted: 08/14/2014] [Indexed: 02/04/2023]
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