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Naqvi SAH, Abbas A, Farhan M, Kiran R, Hassan Z, Mehmood Y, Ali A, Ahmed N, Hassan MZ, Alrefaei AF, Ölmez F, Yang SH, Baloch FS. Unveiling the Genetic Tapestry: Exploring Rhizoctonia solani AG-3 Anastomosis Groups in Potato Crops across Borders. PLANTS (BASEL, SWITZERLAND) 2024; 13:715. [PMID: 38475561 DOI: 10.3390/plants13050715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
The current study was carried out to screen 10 isolates (ARS-01-ARS-10) of Rhizoctonia. solani from potato tubers cv. Kuroda, which were collected from various potato fields in Multan, Pakistan. The isolates were found to be morphologically identical, as the hyphae exhibit the production of branches at right angles and acute angles often accompanied by septum near the emerging branches. Anastomosis grouping showed that these isolates belonged to AG-3. A pathogenicity test was performed against the susceptible Kuroda variety and among the isolates, ARS-05 exhibited the highest mean severity score of approximately 5.43, followed by ARS-09, which showed a mean severity score of about 3.67, indicating a moderate level of severity. On the lower end of the severity scale, isolates ARS-06 and ARS-07 displayed mean severity scores of approximately 0.53 and 0.57, respectively, suggesting minimal symptom severity. These mean severity scores offer insights into the varying degrees of symptom expression among the different isolates of R. solani under examination. PCoA indicates that the severe isolate causing black scurf on the Kuroda variety was AG-3. A comprehensive analysis of the distribution, genetic variability, and phylogenetic relationships of R. solani anastomosis groups (AGs) related to potato crops across diverse geographic regions was also performed to examine AG prevalence in various countries. AG-3 was identified as the most widespread group, prevalent in Sweden, China, and the USA. AG-5 showed prominence in Sweden and the USA, while AG-2-1 exhibited prevalence in China and Japan. The phylogenetic analysis unveiled two different clades: Clade I comprising AG-3 and Clade II encompassing AG-2, AG-4, and AG-5, further subdivided into three subclades. Although AGs clustered together regardless of origin, their genetic diversity revealed complex evolutionary patterns. The findings pave the way for region-specific disease management strategies to combat R. solani's impact on potato crops.
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Affiliation(s)
- Syed Atif Hasan Naqvi
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Aqleem Abbas
- Department of Agriculture and Food Technology, Karakoram International University, Gilgit Baltistan, Gilgit 15100, Pakistan
| | - Muhammad Farhan
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Rafia Kiran
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Zeshan Hassan
- College of Agriculture, University of Layyah, Layyah 31200, Pakistan
| | - Yasir Mehmood
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Amjad Ali
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Niaz Ahmed
- Department of Soil Science, Bahauddin Zakariya University, Multan 60800, Pakistan
| | | | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Fatih Ölmez
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Seung-Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, Yenişehir, Mersin 33343, Türkiye
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Wang Y, Sun Q, Zhao J, Liu T, Du H, Shan W, Wu K, Xue X, Yang C, Liu J, Chen Z, Hu K, Feng Z, Zuo S. Fine mapping and candidate gene analysis of qSB12 YSB, a gene conferring major quantitative resistance to rice sheath blight. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:246. [PMID: 37973669 DOI: 10.1007/s00122-023-04482-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/07/2023] [Indexed: 11/19/2023]
Abstract
KEY MESSAGE qSB12YSB, a major quantitative sheath blight resistance gene originated from rice variety YSBR1 with good breeding potential, was mapped to a 289-Kb region on chromosome 12. Sheath blight (ShB), caused by Rhizoctonia solani kühn, is one of the most serious global rice diseases. Rice resistance to ShB is a typical of quantitative trait controlled by multiple quantitative trait loci (QTLs). Many QTLs for ShB resistance have been reported while only few of them were fine-mapped. In this study, we identified a QTL on chromosome 12, in which the qSB12YSB resistant allele shows significant ShB resistance, by using 150 BC4 backcross inbred lines employing the resistant rice variety YSBR1 as the donor and the susceptible variety Lemont (LE) as the recurrent parent. We further fine-mapped qSB12YSB to a 289-kb region by generating 34 chromosomal segment substitution lines and identified a total of 18 annotated genes as the most likely candidates for qSB12YSB after analyzing resequencing and transcriptomic data. KEGG analysis suggested that qSB12YSB might activate secondary metabolites biosynthesis and ROS scavenging system to improve ShB resistance. qSB12YSB conferred significantly stable resistance in three commercial rice cultivars (NJ9108, NJ5055 and NJ44) in field trials when introduced through marker assisted selection. Under severe ShB disease conditions, qSB12YSB significantly reduced yield losses by up to 13.5% in the LE background, indicating its great breeding potential. Our results will accelerate the isolation of qSB12YSB and its utilization in rice breeding programs against ShB.
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Affiliation(s)
- Yu Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Quanyi Sun
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Jianhua Zhao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Taixuan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Haibo Du
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Wenfeng Shan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Keting Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Xiang Xue
- Yangzhou Polytechnic College, Yangzhou, 225009, People's Republic of China
- Jiangsu Safety and Environment Technology and Equipment for Planting and Breeding Industry Engineering Research Center, Yangzhou Polytechnic College, Yangzhou, 225009, People's Republic of China
| | - Chao Yang
- MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jun Liu
- MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zongxiang Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Keming Hu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Zhiming Feng
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, 225009, People's Republic of China.
| | - Shimin Zuo
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009, People's Republic of China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, 225009, People's Republic of China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China/Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, People's Republic of China.
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Qi S, Wang J, Zhang Y, Naz M, Afzal MR, Du D, Dai Z. Omics Approaches in Invasion Biology: Understanding Mechanisms and Impacts on Ecological Health. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091860. [PMID: 37176919 PMCID: PMC10181282 DOI: 10.3390/plants12091860] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Invasive species and rapid climate change are affecting the control of new plant diseases and epidemics. To effectively manage these diseases under changing environmental conditions, a better understanding of pathophysiology with holistic approach is needed. Multiomics approaches can help us to understand the relationship between plants and microbes and construct predictive models for how they respond to environmental stresses. The application of omics methods enables the simultaneous analysis of plant hosts, soil, and microbiota, providing insights into their intricate relationships and the mechanisms underlying plant-microbe interactions. This can help in the development of novel strategies for enhancing plant health and improving soil ecosystem functions. The review proposes the use of omics methods to study the relationship between plant hosts, soil, and microbiota, with the aim of developing a new technique to regulate soil health. This approach can provide a comprehensive understanding of the mechanisms underlying plant-microbe interactions and contribute to the development of effective strategies for managing plant diseases and improving soil ecosystem functions. In conclusion, omics technologies offer an innovative and holistic approach to understanding plant-microbe interactions and their response to changing environmental conditions.
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Affiliation(s)
- Shanshan Qi
- School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jiahao Wang
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yi Zhang
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Misbah Naz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Muhammad Rahil Afzal
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Daolin Du
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Zhicong Dai
- School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
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Kaushik A, Roberts DP, Ramaprasad A, Mfarrej S, Nair M, Lakshman DK, Pain A. Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB. Front Microbiol 2022; 13:839524. [PMID: 35401459 PMCID: PMC8992008 DOI: 10.3389/fmicb.2022.839524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Rhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungi that damage economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host ranges. The genetic factors driving the unique features of R. solani pathology are not well characterized due to the limited availability of its annotated genomes. Therefore, we performed genome sequencing, assembly, annotation and functional analysis of 12 R. solani isolates covering 7 AGs and select subgroups (AG1-IA; AG1-IB; AG1-IC; AG2-2IIIB; AG3-PT, isolates Rhs 1AP and the hypovirulent Rhs1A1; AG3-TB; AG4-HG-I, isolates Rs23 and R118-11; AG5; AG6; and AG8), in which six genomes are reported for the first time. Using a pangenome comparative analysis of 12 R. solani isolates and 15 other Basidiomycetes, we defined the unique and shared secretomes, CAZymes, and effectors across the AGs. We have also elucidated the R. solani-derived factors potentially involved in determining AG-specific host preference, and the attributes distinguishing them from other Basidiomycetes. Finally, we present the largest repertoire of R. solani genomes and their annotated components as a comprehensive database, viz. RsolaniDB, with tools for large-scale data mining, functional enrichment and sequence analysis not available with other state-of-the-art platforms.
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Affiliation(s)
- Abhinav Kaushik
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniel P Roberts
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD, United States
| | - Abhinay Ramaprasad
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sara Mfarrej
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mridul Nair
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dilip K Lakshman
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD, United States
| | - Arnab Pain
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
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Comparative Proteomic Analysis of Rhizoctonia solani Isolates Identifies the Differentially Expressed Proteins with Roles in Virulence. J Fungi (Basel) 2022; 8:jof8040370. [PMID: 35448601 PMCID: PMC9029756 DOI: 10.3390/jof8040370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/25/2022] [Accepted: 04/01/2022] [Indexed: 11/28/2022] Open
Abstract
Sheath blight of rice is a destructive disease that could be calamitous to rice cultivation. The significant objective of this study is to contemplate the proteomic analysis of the high virulent and less virulent isolate of Rhizoctonia solani using a quantitative LC-MS/MS-based proteomic approach to identify the differentially expressed proteins promoting higher virulence. Across several rice-growing regions in Odisha, Eastern India, 58 Rhizoctonia isolates were obtained. All the isolates varied in their pathogenicity. The isolate RS15 was found to be the most virulent and RS22 was identified as the least virulent. The PCR amplification confirmed that the RS15 and RS22 belonged to the Rhizoctonia subgroup of AG1-IA with a specific primer. The proteomic information generated has been deposited in the PRIDE database with PXD023430. The virulent isolate consisted of 48 differentially abundant proteins, out of which 27 proteins had higher abundance, while 21 proteins had lower abundance. The analyzed proteins acquired functionality in fungal development, sporulation, morphology, pathogenicity, detoxification, antifungal activity, essential metabolism and transcriptional activities, protein biosynthesis, glycolysis, phosphorylation and catalytic activities in fungi. A Quantitative Real-Time PCR (qRT-PCR) was used to validate changes in differentially expressed proteins at the mRNA level for selected genes. The abundances of proteins and transcripts were positively correlated. This study provides the role of the proteome in the pathogenicity of R. solani AG1-IA in rice and underpins the mechanism behind the pathogen’s virulence in causing sheath blight disease.
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Zhao M, Wang C, Wan J, Li Z, Liu D, Yamamoto N, Zhou E, Shu C. Functional validation of pathogenicity genes in rice sheath blight pathogen Rhizoctonia solani by a novel host-induced gene silencing system. MOLECULAR PLANT PATHOLOGY 2021; 22:1587-1598. [PMID: 34453407 PMCID: PMC8578826 DOI: 10.1111/mpp.13130] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/28/2021] [Accepted: 08/04/2021] [Indexed: 05/10/2023]
Abstract
Rice sheath blight, caused by the soilborne fungus Rhizoctonia solani, causes severe yield losses worldwide. Elucidation of the pathogenic mechanism of R. solani is highly desired. However, the lack of a stable genetic transformation system has made it challenging to examine genes' functions in this fungus. Here, we present functional validation of pathogenicity genes in the rice sheath blight pathogen R. solani by a newly established tobacco rattle virus (TRV)-host-induced gene silencing (HIGS) system using the virulent R. solani AG-1 IA strain GD-118. RNA interference constructs of 33 candidate pathogenicity genes were infiltrated into Nicotiana benthamiana leaves with the TRV-HIGS system. Of these constructs, 29 resulted in a significant reduction in necrosis caused by GD-118 infection. For further validation of one of the positive genes, trehalose-6-phosphate phosphatase (Rstps2), stable rice transformants harbouring the double-stranded RNA (dsRNA) construct for Rstps2 were created. The transformants exhibited reduced gene expression of Rstps2, virulence, and trehalose accumulation in GD-118. We showed that the dsRNA for Rstps2 was taken up by GD-118 mycelia and sclerotial differentiation of GD-118 was inhibited. These findings offer gene identification opportunities for the rice sheath blight pathogen and a theoretical basis for controlling this disease by spray-induced gene silencing.
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Affiliation(s)
- Mei Zhao
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlDepartment of Plant PathologySouth China Agricultural UniversityGuangzhouChina
| | - Chenjiaozi Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlDepartment of Plant PathologySouth China Agricultural UniversityGuangzhouChina
| | - Jun Wan
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlDepartment of Plant PathologySouth China Agricultural UniversityGuangzhouChina
| | - Zanfeng Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlDepartment of Plant PathologySouth China Agricultural UniversityGuangzhouChina
| | - Dilin Liu
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangzhouChina
| | - Naoki Yamamoto
- College of AgronomySichuan Agricultural UniversityChengduChina
| | - Erxun Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlDepartment of Plant PathologySouth China Agricultural UniversityGuangzhouChina
| | - Canwei Shu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlDepartment of Plant PathologySouth China Agricultural UniversityGuangzhouChina
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Batnini M, Haddoudi I, Taamali W, Djebali N, Badri M, Mrabet M, Mhadhbi H. Medicago truncatula in Interaction with Fusarium and Rhizoctonia Phytopathogenic Fungi: Fungal Aggressiveness, Plant Response Biodiversity and Character Heritability Indices. THE PLANT PATHOLOGY JOURNAL 2021; 37:315-328. [PMID: 34365743 PMCID: PMC8357562 DOI: 10.5423/ppj.oa.01.2021.0010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/06/2021] [Accepted: 05/20/2021] [Indexed: 06/01/2023]
Abstract
Fusarium and Rhizoctonia genera are important pathogens of many field crops worldwide. They are constantly evolving and expanding their host range. Selecting resistant cultivars is an effective strategy to break their infection cycles. To this end, we screened a collection of Medicago truncatula accessions against Fusarium oxysporum, Fusarium solani, and Rhizoctonia solani strains isolated from different plant species. Despite the small collection, a biodiversity in the disease response of M. truncatula accessions ranging from resistant phenotypes to highly susceptible ones was observed. A17 showed relative resistance to all fungal strains with the lowest disease incidence and ratings while TN1.11 was among the susceptible accessions. As an initiation of the characterization of resistance mechanisms, the antioxidant enzymes' activities, at the early stages of infections, were compared between these contrasting accessions. Our results showed an increment of the antioxidant activities within A17 plants in leaves and roots. We also analyzed the responses of a population of recombinant inbred lines derived from the crossing of A17 and TN1.11 to the infection with the same fungal strains. The broad-sense heritability of measured traits ranged from 0.87 to 0.95, from 0.72 to 0.96, and from 0.14 to 0.85 under control, F. oxysporum, and R. solani conditions, respectively. This high estimated heritability underlines the importance of further molecular analysis of the observed resistance to identify selection markers that could be incorporated into a breeding program and thus improving soil-borne pathogens resistance in crops.
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Affiliation(s)
- Marwa Batnini
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, PB 2050, Tunisia
| | - Imen Haddoudi
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, PB 2050, Tunisia
- Department of Ecosystem Biology, University of South Bohemia in České Budějovice, České Budějovice, PB 37005, Czechia
| | - Wael Taamali
- Laboratory of Olive Biotechnology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, PB 2050, Tunisia
| | - Naceur Djebali
- Laboratory of Bioactive Substances, Center of Biotechnology of Borj-Cedria, Hammam-Lif, PB 2050, Tunisia
| | - Mounawer Badri
- Laboratory of Extremophile Plants, Center of Biotechnology of Borj-Cedria, Hammam-Lif, PB 2050, Tunisia
| | - Moncef Mrabet
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, PB 2050, Tunisia
| | - Haythem Mhadhbi
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, PB 2050, Tunisia
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Wang X, Wang A, Chen Z, Wei L. Phytotoxin of Rice Aggregate Sheath Spot Pathogen Rhizoctonia oryzae-sativae and Its Biological Activities. Can J Microbiol 2021; 67:827-834. [PMID: 34283923 DOI: 10.1139/cjm-2021-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rice aggregate sheath spot disease occurs in many countries, causing serious yield losses. In China, the disease-causing fungus Rhizoctonia oryzae-sativae was reported in 1985, and since then, it has rarely been reported in major rice-growing areas after almost 30 years. Compared with Rhizoctonia solani, R. oryzae-sativae has a significantly different physiological morphology and growth status, although both fungi affect rice leaves in very similar ways. The optimum temperature for the suitable growth of R. oryzae-sativae is 31 °C, which is consistent with previous reports. We extracted phytotoxins from R. oryzae-sativae and analyzed its biological activity via the detached leaf and radicle inhibition methods. Rhizoctonia solani and R. oryzae-sativae exhibit differences in terms of pathogenicity and toxins activity, which indicates that these fungi may produce different toxins components. Based on gas chromatography-mass spectrometry data, esters, phenols, and other components were present in the crude toxins extract of R. oryzae-sativae. Our research provides a new method for studying the phytotoxins of R. oryzae-sativae. However, further studies are needed to elucidate the pathogenic mechanisms responsible for the aggregate sheath spot disease on rice.
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Affiliation(s)
| | - Aimin Wang
- Institute of Agricultural Science in Jiangsu Coastal Areas, YanCheng, China;
| | - Zhiyi Chen
- Jiangsu Academy of Agricultural Sciences, 117941, Nanjing, China, 210014;
| | - Lihui Wei
- Jiangsu Academy of Agricultural Sciences, 117941, Nanjing, China, 210014;
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Lee DY, Jeon J, Kim KT, Cheong K, Song H, Choi G, Ko J, Opiyo SO, Correll JC, Zuo S, Madhav S, Wang GL, Lee YH. Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes. BMC Genomics 2021; 22:242. [PMID: 33827423 PMCID: PMC8028249 DOI: 10.1186/s12864-021-07549-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/23/2021] [Indexed: 11/24/2022] Open
Abstract
Background Plant pathogenic isolates of Rhizoctonia solani anastomosis group 1-intraspecific group IA (AG1-IA) infect a wide range of crops causing diseases such as rice sheath blight (ShB). ShB has become a serious disease in rice production worldwide. Additional genome sequences of the rice-infecting R. solani isolates from different geographical regions will facilitate the identification of important pathogenicity-related genes in the fungus. Results Rice-infecting R. solani isolates B2 (USA), ADB (India), WGL (India), and YN-7 (China) were selected for whole-genome sequencing. Single-Molecule Real-Time (SMRT) and Illumina sequencing were used for de novo sequencing of the B2 genome. The genomes of the other three isolates were then sequenced with Illumina technology and assembled using the B2 genome as a reference. The four genomes ranged from 38.9 to 45.0 Mbp in size, contained 9715 to 11,505 protein-coding genes, and shared 5812 conserved orthogroups. The proportion of transposable elements (TEs) and average length of TE sequences in the B2 genome was nearly 3 times and 2 times greater, respectively, than those of ADB, WGL and YN-7. Although 818 to 888 putative secreted proteins were identified in the four isolates, only 30% of them were predicted to be small secreted proteins, which is a smaller proportion than what is usually found in the genomes of cereal necrotrophic fungi. Despite a lack of putative secondary metabolite biosynthesis gene clusters, the rice-infecting R. solani genomes were predicted to contain the most carbohydrate-active enzyme (CAZyme) genes among all 27 fungal genomes used in the comparative analysis. Specifically, extensive enrichment of pectin/homogalacturonan modification genes were found in all four rice-infecting R. solani genomes. Conclusion Four R. solani genomes were sequenced, annotated, and compared to other fungal genomes to identify distinctive genomic features that may contribute to the pathogenicity of rice-infecting R. solani. Our analyses provided evidence that genomic conservation of R. solani genomes among neighboring AGs was more diversified than among AG1-IA isolates and the presence of numerous predicted pectin modification genes in the rice-infecting R. solani genomes that may contribute to the wide host range and virulence of this necrotrophic fungal pathogen. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07549-7.
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Affiliation(s)
- Da-Young Lee
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Jongbum Jeon
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon, 57922, South Korea
| | - Kyeongchae Cheong
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyeunjeong Song
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gobong Choi
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Jaeho Ko
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Stephen O Opiyo
- Ohio Agricultural Research and Development Center (OARDC) Molecular & Cellular Imaging Center (MCIC)-Columbus, The Ohio State University, Columbus, OH, 43210, USA
| | - James C Correll
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AK, 72701, USA
| | - Shimin Zuo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Sheshu Madhav
- Indian Council of Agricultural Research-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, 500030, Telangana, India
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Yong-Hwan Lee
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea. .,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea. .,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea. .,Center for Fungal Genetic Resources, Plant Immunity Research Center, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea.
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10
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Ghosh S, Kant R, Pradhan A, Jha G. RS_CRZ1, a C2H2-Type Transcription Factor Is Required for Pathogenesis of Rhizoctonia solani AG1-IA in Tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:26-38. [PMID: 33030394 DOI: 10.1094/mpmi-05-20-0121-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Rhizoctonia solani is a necrotrophic fungal pathogen that causes disease in diverse plant species. In recent years, the genomic and transcriptomic studies have identified several candidate pathogenicity determinants of R. solani; however, most of them remain to be validated. In this study, we report a viral vector-based host-induced gene silencing (HIGS) as well as a dsRNA (double-stranded RNA)-based approach to effectively downregulate genes of R. solani AG1-IA (BRS1 strain) during pathogenesis in tomato. We tested a few of the in-planta upregulated R. solani genes and observed that silencing of one of them, i.e., RS_CRZ1 (a C2H2 type zinc finger transcription factor) significantly compromises the pathogenesis of R. solani in tomato. The RS_CRZ1-silenced plants not only exhibited significant reduction in disease symptoms, but the depth of pathogen colonization was also compromised. Furthermore, we identified the R. solani genes that were coregulated with RS_CRZ1 during the pathogenicity process. The HIGS-mediated silencing of a few of them [CL1756Contig1; subtilisin-like protease and CL1817Contig2; 2OG-Fe(II) oxygenase] compromised the pathogenesis of R. solani in tomato. The ectopic expression of RS_CRZ1 complemented the crz1 mutant of yeast and restored tolerance against various metal ion stress. Overall, our study reveals the importance of RS_CRZ1 in managing the hostile environment encountered during host colonization. Also, it emphasizes the relevance of the HIGS and dsRNA-based gene silencing approach toward functional characterization of pathogenicity determinants of R. solani.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Srayan Ghosh
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Ravi Kant
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Amrita Pradhan
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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11
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Liang L, Cheng X, Dai T, Wang Z, Li J, Li X, Lei B, Liu P, Hao J, Liu X. Metabolic Fingerprinting for Identifying the Mode of Action of the Fungicide SYP-14288 on Rhizoctonia solani. Front Microbiol 2020; 11:574039. [PMID: 33362733 PMCID: PMC7755717 DOI: 10.3389/fmicb.2020.574039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/11/2020] [Indexed: 01/11/2023] Open
Abstract
The fungicide SYP-14288 has a high efficiency, low toxicity, and broad spectrum in inhibiting both fungi and oomycetes, but its mode of action (MoA) remains unclear on inhibiting fungi. In this study, the MoA was determined by analyzing the metabolism and respiratory activities of Rhizoctonia solani treated by SYP-14288. Wild-type strains and SYP-14288-resistant mutants of R. solani were incubated on potato dextrose agar amended with either SYP-14288 or one of select fungicides acting on fungal respiration, including complex I, II, and III inhibitors; uncouplers; and ATP synthase inhibitors. Mycelial growth was measured under fungicides treatments. ATP content was determined using an ATP assay kit, membrane potential of mitochondria was detected with the JC-1 kit, and respiratory rate was calculated based on the measurement of oxygen consumption of R. solani. A model of metabolic fingerprinting cluster was established to separate oxidation inhibitors and phosphorylation inhibitors. All the results together displayed a clear discrimination between oxidation inhibitors and phosphorylation inhibitors, and the latter inhibited ATP synthase production having or uncoupling activities. Based on the model, SYP-14288 was placed in phosphorylation inhibitor group, because it significantly reduced ATP content and membrane potential of mitochondria while increasing respiratory rate in R. solani. Therefore, the MoA of SYP-14288 on R. solani was confirmed to involve phosphorylation inhibition and possibly uncoupling activity.
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Affiliation(s)
- Li Liang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Xingkai Cheng
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Tan Dai
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zhiwen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Jin Li
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xueming Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Bin Lei
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Pengfei Liu
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Jianjun Hao
- School of Food and Agriculture, University of Maine, Orono, ME, United States
| | - Xili Liu
- Department of Plant Pathology, China Agricultural University, Beijing, China
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12
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Cheng X, Man X, Wang Z, Liang L, Zhang F, Wang Z, Liu P, Lei B, Hao J, Liu X. Fungicide SYP-14288 Inducing Multidrug Resistance in Rhizoctonia solani. PLANT DISEASE 2020; 104:2563-2570. [PMID: 32762501 DOI: 10.1094/pdis-01-20-0048-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Rhizoctonia solani is a widely distributed soilborne plant pathogen, and can cause significant economic losses to crop production. In chemical controls, SYP-14288 is highly effective against plant pathogens, including R. solani. To examine the sensitivity to SYP-14288, 112 R. solani isolates were collected from infected rice plants. An established baseline sensitivity showed that values of effective concentration for 50% growth inhibition (EC50) ranged from 0.0003 to 0.0138 μg/ml, with an average of 0.0055 ± 0.0030 μg/ml. The frequency distribution of the EC50 was unimodal and the range of variation factor (the ratio of maximal over minimal EC50) was 46.03, indicating that all wild-type strains were sensitive to SYP-14288. To examine the risk of fungicide resistance, 20 SYP-14288-resistant mutants were generated on agar plates amended with SYP-14288. Eighteen mutants remained resistant after 10 transfers, and their fitness was significantly different from the parental strain. All of the mutants grew more slowly but showed high virulence to rice plants, though lower than the parental strain. A cross-resistance assay demonstrated that there was a positive correlation between SYP-14288 and fungicides having or not having the same mode of action with SYP-14288, including fluazinam, fentin chloride, fludioxonil, difenoconazole, cyazofamid, chlorothalonil, and 2,4-dinitrophen. This result showed a multidrug resistance induced by SYP-14288, which could be a concern in increasing the spectrum of resistance in R. solani to commonly used fungicides.
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Affiliation(s)
- Xingkai Cheng
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Xuejing Man
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Zitong Wang
- College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Li Liang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Fan Zhang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Zhiwen Wang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Pengfei Liu
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Bin Lei
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, 403 Nanchang Road, Urumqi 830091, China
| | - Jianjun Hao
- School of Food and Agriculture, University of Maine, Orono, ME 04469, U.S.A
| | - Xili Liu
- College of Plant Protection, Northwest A&F University, Yangling 712100, China
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13
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Abdelsalam SSH, Kouzai Y, Watanabe M, Inoue K, Matsui H, Yamamoto M, Ichinose Y, Toyoda K, Tsuge S, Mochida K, Noutoshi Y. Identification of effector candidate genes of Rhizoctonia solani AG-1 IA expressed during infection in Brachypodium distachyon. Sci Rep 2020; 10:14889. [PMID: 32913311 PMCID: PMC7483729 DOI: 10.1038/s41598-020-71968-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/24/2020] [Indexed: 11/23/2022] Open
Abstract
Rhizoctonia solani is a necrotrophic phytopathogen belonging to basidiomycetes. It causes rice sheath blight which inflicts serious damage in rice production. The infection strategy of this pathogen remains unclear. We previously demonstrated that salicylic acid-induced immunity could block R. solani AG-1 IA infection in both rice and Brachypodium distachyon. R. solani may undergo biotrophic process using effector proteins to suppress host immunity before necrotrophic stage. To identify pathogen genes expressed at the early infection process, here we developed an inoculation method using B. distachyon which enables to sample an increased amount of semi-synchronous infection hyphae. Sixty-one R. solani secretory effector-like protein genes (RsSEPGs) were identified using in silico approach with the publicly available gene annotation of R. solani AG-1 IA genome and our RNA-sequencing results obtained from hyphae grown on agar medium. Expression of RsSEPGs was analyzed at 6, 10, 16, 24, and 32 h after inoculation by a quantitative reverse transcription-polymerase chain reaction and 52 genes could be detected at least on a single time point tested. Their expressions showed phase-specific patterns which were classified into 6 clusters. The 23 RsSEPGs in the cluster 1–3 and 29 RsSEPGs in the cluster 4–6 are expected to be involved in biotrophic and necrotrophic interactions, respectively.
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Affiliation(s)
- Sobhy S H Abdelsalam
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.,Plant Pathology Department, Faculty of Agriculture, Alexandria University, El-Shatby, Egypt
| | - Yusuke Kouzai
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Megumi Watanabe
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hidenori Matsui
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Mikihiro Yamamoto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yuki Ichinose
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Seiji Tsuge
- Graduate School of Agriculture, Kyoto Prefectural University, Kyoto, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.,Institute for Plant Science and Resources (IPSR), Okayama University, Okayama, Japan
| | - Yoshiteru Noutoshi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
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14
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Cereal Root Interactions with Soilborne Pathogens—From Trait to Gene and Back. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9040188] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Realizing the yield potential of crop plants in the presence of shifting pathogen populations, soil quality, rainfall, and other agro-environmental variables remains a challenge for growers and breeders worldwide. In this review, we discuss current approaches for combatting the soilborne phytopathogenic nematodes, Pratylenchus and Heterodera of wheat and barley, and Meloidogyne graminicola Golden and Birchfield, 1965 of rice. The necrotrophic fungal pathogens, Rhizoctonia solani Kühn 1858 AG-8 and Fusarium spp. of wheat and barley, also are discussed. These pathogens constitute major causes of yield loss in small-grain cereals of the Pacific Northwest, USA and throughout the world. Current topics include new sources of genetic resistance, molecular leads from whole genome sequencing and genome-wide patterns of hosts, nematode or fungal gene expression during root-pathogen interactions, host-induced gene silencing, and building a molecular toolbox of genes and regulatory sequences for deployment of resistance genes. In conclusion, improvement of wheat, barley, and rice will require multiple approaches.
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15
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Moffat CS, Stoll T, Moolhuijzen P. Proteomics of the wheat tan spot pathogen Pyrenophora tritici-repentis. BMC Res Notes 2018; 11:846. [PMID: 30497514 PMCID: PMC6267847 DOI: 10.1186/s13104-018-3936-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/21/2018] [Indexed: 11/10/2022] Open
Abstract
Objectives The fungus Pyrenophora tritici-repentis is a major pathogen of wheat worldwide, causing the leaf spotting disease tan spot. To best inform approaches for plant genetic resistance, an understanding of the biology and pathogenicity mechanisms of this fungal pathogen is essential. Here, intracellular and extracellular proteins of P. tritici-repentis were extracted, and peptides analysed via high-resolution mass spectrometry. Our objective was to generate a useful proteomics resource for P. tritici-repentis. A survey of proteins secreted by the pathogen into culture filtrate is especially useful, as these are likely to come in direct contact with the wheat host and may play important roles in infection/pathogenicity. The peptide data presented herein, has also been used to successfully verify and refine in silico predicted P. tritici-repentis gene annotations, through the validation of alternative splicing and reading frame shifts. Data description The data sets presented consist of peptide spectra of the extracellular and intracellular proteomes of three P. tritici-repentis isolates. Peptide matches to translated transcripts of the North American reference isolate Pt-1C-BFP are also provided.
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Affiliation(s)
- Caroline S Moffat
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.
| | - Thomas Stoll
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, QLD, Australia
| | - Paula Moolhuijzen
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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16
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Identification of fungi in shotgun metagenomics datasets. PLoS One 2018; 13:e0192898. [PMID: 29444186 PMCID: PMC5812651 DOI: 10.1371/journal.pone.0192898] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/31/2018] [Indexed: 01/22/2023] Open
Abstract
Metagenomics uses nucleic acid sequencing to characterize species diversity in different niches such as environmental biomes or the human microbiome. Most studies have used 16S rRNA amplicon sequencing to identify bacteria. However, the decreasing cost of sequencing has resulted in a gradual shift away from amplicon analyses and towards shotgun metagenomic sequencing. Shotgun metagenomic data can be used to identify a wide range of species, but have rarely been applied to fungal identification. Here, we develop a sequence classification pipeline, FindFungi, and use it to identify fungal sequences in public metagenome datasets. We focus primarily on animal metagenomes, especially those from pig and mouse microbiomes. We identified fungi in 39 of 70 datasets comprising 71 fungal species. At least 11 pathogenic species with zoonotic potential were identified, including Candida tropicalis. We identified Pseudogymnoascus species from 13 Antarctic soil samples initially analyzed for the presence of bacteria capable of degrading diesel oil. We also show that Candida tropicalis and Candida loboi are likely the same species. In addition, we identify several examples where contaminating DNA was erroneously included in fungal genome assemblies.
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17
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Kouzai Y, Kimura M, Watanabe M, Kusunoki K, Osaka D, Suzuki T, Matsui H, Yamamoto M, Ichinose Y, Toyoda K, Matsuura T, Mori IC, Hirayama T, Minami E, Nishizawa Y, Inoue K, Onda Y, Mochida K, Noutoshi Y. Salicylic acid-dependent immunity contributes to resistance against Rhizoctonia solani, a necrotrophic fungal agent of sheath blight, in rice and Brachypodium distachyon. THE NEW PHYTOLOGIST 2018; 217:771-783. [PMID: 29048113 PMCID: PMC5765516 DOI: 10.1111/nph.14849] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/13/2017] [Indexed: 05/20/2023]
Abstract
Rhizoctonia solani is a soil-borne fungus causing sheath blight. In consistent with its necrotrophic life style, no rice cultivars fully resistant to R. solani are known, and agrochemical plant defense activators used for rice blast, which upregulate a phytohormonal salicylic acid (SA)-dependent pathway, are ineffective towards this pathogen. As a result of the unavailability of genetics, the infection process of R. solani remains unclear. We used the model monocotyledonous plants Brachypodium distachyon and rice, and evaluated the effects of phytohormone-induced resistance to R. solani by pharmacological, genetic and microscopic approaches to understand fungal pathogenicity. Pretreatment with SA, but not with plant defense activators used in agriculture, can unexpectedly induce sheath blight resistance in plants. SA treatment inhibits the advancement of R. solani to the point in the infection process in which fungal biomass shows remarkable expansion and specific infection machinery is developed. The involvement of SA in R. solani resistance is demonstrated by SA-deficient NahG transgenic rice and the sheath blight-resistant B. distachyon accessions, Bd3-1 and Gaz-4, which activate SA-dependent signaling on inoculation. Our findings suggest a hemi-biotrophic nature of R. solani, which can be targeted by SA-dependent plant immunity. Furthermore, B. distachyon provides a genetic resource that can confer disease resistance against R. solani to plants.
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Affiliation(s)
- Yusuke Kouzai
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, 230-0045, Japan
| | - Mamiko Kimura
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Megumi Watanabe
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Kazuki Kusunoki
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Daiki Osaka
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Tomoko Suzuki
- Department of Science, Japan Women's University, Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Hidenori Matsui
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Mikihiro Yamamoto
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Yuki Ichinose
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
| | - Takakazu Matsuura
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
| | - Izumi C Mori
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
| | - Eiichi Minami
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8602, Japan
| | - Yoko Nishizawa
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8602, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, 230-0045, Japan
| | - Yoshihiko Onda
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, 230-0045, Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, 710-0046, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, 244-0813, Japan
| | - Yoshiteru Noutoshi
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, 700-8530, Japan
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18
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Copley TR, Duggavathi R, Jabaji S. The transcriptional landscape of Rhizoctonia solani AG1-IA during infection of soybean as defined by RNA-seq. PLoS One 2017; 12:e0184095. [PMID: 28877263 PMCID: PMC5587340 DOI: 10.1371/journal.pone.0184095] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/17/2017] [Indexed: 12/21/2022] Open
Abstract
Rhizoctonia solani Kühn infects most plant families and can cause significant agricultural yield losses worldwide; however, plant resistance to this disease is rare and short-lived, and therefore poorly understood, resulting in the use of chemical pesticides for its control. Understanding the functional responses of this pathogen during host infection can help elucidate the molecular mechanisms that are necessary for successful host invasion. Using the pathosystem model soybean-R. solani anastomosis group AG1-IA, we examined the global transcriptional responses of R. solani during early and late infection stages of soybean by applying an RNA-seq approach. Approximately, 148 million clean paired-end reads, representing 93% of R. solani AG1-IA genes, were obtained from the sequenced libraries. Analysis of R. solani AG1-IA transcripts during soybean invasion revealed that most genes were similarly expressed during early and late infection stages, and only 11% and 15% of the expressed genes were differentially expressed during early and late infection stages, respectively. Analyses of the differentially expressed genes (DEGs) revealed shifts in molecular pathways involved in antibiotics biosynthesis, amino acid and carbohydrate metabolism, as well as pathways involved in antioxidant production. Furthermore, several KEGG pathways were unique to each time point, particularly the up-regulation of genes related to toxin degradation (e.g., nicotinate and nicotinamid metabolism) at onset of necrosis, and those linked to synthesis of anti-microbial compounds and pyridoxine (vitamin B6) biosynthesis 24 h.p.o. of necrosis. These results suggest that particular genes or pathways are required for either invasion or disease development. Overall, this study provides the first insights into R. solani AG1-IA transcriptome responses to soybean invasion providing beneficial information for future targeted control methods of this successful pathogen.
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Affiliation(s)
- Tanya R. Copley
- Plant Science Department, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
| | - Raj Duggavathi
- Animal Science Department, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
| | - Suha Jabaji
- Plant Science Department, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
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19
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Anderson JP, Sperschneider J, Win J, Kidd B, Yoshida K, Hane J, Saunders DGO, Singh KB. Comparative secretome analysis of Rhizoctonia solani isolates with different host ranges reveals unique secretomes and cell death inducing effectors. Sci Rep 2017; 7:10410. [PMID: 28874693 PMCID: PMC5585356 DOI: 10.1038/s41598-017-10405-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/07/2017] [Indexed: 11/17/2022] Open
Abstract
Rhizoctonia solani is a fungal pathogen causing substantial damage to many of the worlds’ largest food crops including wheat, rice, maize and soybean. Despite impacting global food security, little is known about the pathogenicity mechanisms employed by R. solani. To enable prediction of effectors possessing either broad efficacy or host specificity, a combined secretome was constructed from a monocot specific isolate, a dicot specific isolate and broad host range isolate infecting both monocot and dicot hosts. Secretome analysis suggested R. solani employs largely different virulence mechanisms to well-studied pathogens, despite in many instances infecting the same host plants. Furthermore, the secretome of the broad host range AG8 isolate may be shaped by maintaining functions for saprophytic life stages while minimising opportunities for host plant recognition. Analysis of possible co-evolution with host plants and in-planta up-regulation in particular, aided identification of effectors including xylanase and inhibitor I9 domain containing proteins able to induce cell death in-planta. The inhibitor I9 domain was more abundant in the secretomes of a wide range of necrotising fungi relative to biotrophs. These findings provide novel targets for further dissection of the virulence mechanisms and potential avenues to control this under-characterised but important pathogen.
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Affiliation(s)
- Jonathan P Anderson
- CSIRO Agriculture and Food, Floreat, Western Australia, Australia. .,The UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia.
| | | | - Joe Win
- The Sainsbury Laboratory, Norwich, UK
| | - Brendan Kidd
- CSIRO Agriculture and Food, Floreat, Western Australia, Australia
| | | | - James Hane
- CSIRO Agriculture and Food, Floreat, Western Australia, Australia.,Curtin University, Bentley, Western Australia, Australia
| | - Diane G O Saunders
- The Sainsbury Laboratory, Norwich, UK.,The John Innes Centre, Norwich, UK
| | - Karam B Singh
- CSIRO Agriculture and Food, Floreat, Western Australia, Australia.,The UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
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20
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Liu Y, Hassan S, Kidd BN, Garg G, Mathesius U, Singh KB, Anderson JP. Ethylene Signaling Is Important for Isoflavonoid-Mediated Resistance to Rhizoctonia solani in Roots of Medicago truncatula. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:691-700. [PMID: 28510484 DOI: 10.1094/mpmi-03-17-0057-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The root-infecting necrotrophic fungal pathogen Rhizoctoniasolani causes significant disease to all the world's major food crops. As a model for pathogenesis of legumes, we have examined the interaction of R. solani AG8 with Medicago truncatula. RNAseq analysis of the moderately resistant M. truncatula accession A17 and highly susceptible sickle (skl) mutant (defective in ethylene sensing) identified major early transcriptional reprogramming in A17. Responses specific to A17 included components of ethylene signaling, reactive oxygen species metabolism, and consistent upregulation of the isoflavonoid biosynthesis pathway. Mass spectrometry revealed accumulation of the isoflavonoid-related compounds liquiritigenin, formononetin, medicarpin, and biochanin A in A17. Overexpression of an isoflavone synthase in M. truncatula roots increased isoflavonoid accumulation and resistance to R. solani. Addition of exogenous medicarpin suggested this phytoalexin may be one of several isoflavonoids required to contribute to resistance to R. solani. Together, these results provide evidence for the role of ethylene-mediated accumulation of isoflavonoids during defense against root pathogens in legumes. The involvement of ethylene signaling and isoflavonoids in the regulation of both symbiont-legume and pathogen-legume interactions in the same tissue may suggest tight regulation of these responses are required in the root tissue.
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Affiliation(s)
- Yao Liu
- 1 CSIRO Agriculture and Food, Floreat, Western Australia
- 2 Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Samira Hassan
- 3 Research School of Biology, Australian National University, Canberra, Australian Capital Territory; and
| | - Brendan N Kidd
- 1 CSIRO Agriculture and Food, Floreat, Western Australia
| | - Gagan Garg
- 1 CSIRO Agriculture and Food, Floreat, Western Australia
| | - Ulrike Mathesius
- 3 Research School of Biology, Australian National University, Canberra, Australian Capital Territory; and
| | - Karam B Singh
- 1 CSIRO Agriculture and Food, Floreat, Western Australia
- 4 The UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia
| | - Jonathan P Anderson
- 1 CSIRO Agriculture and Food, Floreat, Western Australia
- 4 The UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia
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21
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Xia Y, Fei B, He J, Zhou M, Zhang D, Pan L, Li S, Liang Y, Wang L, Zhu J, Li P, Zheng A. Transcriptome analysis reveals the host selection fitness mechanisms of the Rhizoctonia solani AG1IA pathogen. Sci Rep 2017; 7:10120. [PMID: 28860554 PMCID: PMC5579035 DOI: 10.1038/s41598-017-10804-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/15/2017] [Indexed: 11/12/2022] Open
Abstract
Rhizoctonia solani AG1IA is a major generalist pathogen that causes sheath blight. Its genome, which was the first to be sequenced from the Rhizoctonia genus, may serve as a model for studying pathogenic mechanisms. To explore the pathogen-host fitness mechanism of sheath-blight fungus, a comprehensive comparative transcriptome ecotype analysis of R. solani AG1IA isolated from rice, soybean and corn during infection was performed. Special characteristics in gene expression, gene ontology terms and expression of pathogenesis-associated genes, including genes encoding secreted proteins, candidate effectors, hydrolases, and proteins involved in secondary metabolite production and the MAPK pathway, were revealed. Furthermore, as an important means of pathogenic modulation, diverse alternative splicing of key pathogenic genes in Rhizoctonia solani AG1IA during infections of the abovementioned hosts was uncovered for the first time. These important findings of key factors in the pathogenicity of R. solani AG1IA ecotypes during infection of various hosts explain host preference and provide novel insights into the pathogenic mechanisms and host-pathogen selection. Furthermore, they provide information on the fitness of Rhizoctonia, a severe pathogen with a wide host range.
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Affiliation(s)
- Yuan Xia
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Binghong Fei
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiayu He
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Menglin Zhou
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Danhua Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linxiu Pan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuangcheng Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Southwest Corp Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an, 625014, China
| | - Yueyang Liang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Southwest Corp Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an, 625014, China
| | - Lingxia Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Southwest Corp Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an, 625014, China
| | - Jianqing Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Southwest Corp Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an, 625014, China
| | - Ping Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Southwest Corp Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an, 625014, China
| | - Aiping Zheng
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- Key Laboratory of Sichuan Crop Major Diseases, Sichuan Agricultural University, Chengdu, 611130, China.
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22
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Hu W, Pan X, Abbas HMK, Li F, Dong W. Metabolites contributing to Rhizoctonia solani AG-1-IA maturation and sclerotial differentiation revealed by UPLC-QTOF-MS metabolomics. PLoS One 2017; 12:e0177464. [PMID: 28489938 PMCID: PMC5425210 DOI: 10.1371/journal.pone.0177464] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/27/2017] [Indexed: 01/26/2023] Open
Abstract
Rhizoctonia solani is a causative agent of sheath blight, which results in huge economic losses every year. During its life cycle, the formation of sclerotia helps Rhizoctonia solani withstand a variety of unfavorable factors. Oxidative stress is a key factor that induces sclerotium formation. The differentiated and undifferentiated phenotypes of R. solani AG-1-IA were obtained by controlling aerial conditions. Metabolomics based on the mass spectrometry technique combined with multivariate and univariate analyses was used to investigate the metabolic variation in vegetative, differentiated and undifferentiated mycelia. Our results revealed that during maturation, the metabolic levels of N2-acetyl-L-ornithine, 3,1'-(OH)2-Gamma-carotene, (5Z,7E)-(1S,3R)-24,24-difluoro-24a-homo-9,10-seco-5,7,10(19)-cholestatrien-1,3,25-triol, stoloniferone O, PA(O-18:0/12:0), PA(P-16:0/14:0), PA(P-16:0/16:(19Z)) and PA(P-16:0/17:2(9Z,12Z)) were suppressed in both differentiated and undifferentiated mycelia. The concentrations of PE(20:1(11Z)/14:1(9Z)), PE(P-16:0/20:4(5Z,8Z,11Z,13E)(15OH[S])) and PS(12:0/18:1(9Z)) were increased in the differentiated group, while increased levels of N(gamma)-nitro-L-arginine, tenuazonic acid and 9S,10S,11R-trihydroxy-12Z,15Z-octadecadienoic acid were found in the undifferentiated group. Our results suggest that different levels of these metabolites may act as biomarkers for the developmental stages of R. solani AG-1-IA. Moreover, the mechanisms of sclerotium formation and mycelium differentiation were elucidated at the metabolic level.
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Affiliation(s)
- Wenjin Hu
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Xinli Pan
- Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Dortmund, Germany
| | - Hafiz Muhammad Khalid Abbas
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Fengfeng Li
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Wubei Dong
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, Hubei Province, China
- * E-mail:
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23
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Microevolutionary analyses of Pythium insidiosum isolates of Brazil and Thailand based on exo-1,3-β-glucanase gene. INFECTION GENETICS AND EVOLUTION 2017; 48:58-63. [DOI: 10.1016/j.meegid.2016.11.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 10/20/2016] [Accepted: 11/20/2016] [Indexed: 11/20/2022]
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24
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Zhang M, Cheng ST, Wang HY, Wu JH, Luo YM, Wang Q, Wang FX, Xia GX. iTRAQ-based proteomic analysis of defence responses triggered by the necrotrophic pathogen Rhizoctonia solani in cotton. J Proteomics 2016; 152:226-235. [PMID: 27871873 DOI: 10.1016/j.jprot.2016.11.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/12/2016] [Accepted: 11/14/2016] [Indexed: 01/11/2023]
Abstract
The soil-borne necrotrophic pathogen fungus Rhizoctonia solani is destructive, causing disease in various important crops. To date, little is known about the host defence mechanism in response to invasion of R. solani. Here, an iTRAQ-based proteomic analysis was employed to investigate pathogen-responsive proteins in the disease tolerant/resistant cotton cultivar CRI35. A total of 174 differentially accumulated proteins (DAPs) were identified after inoculation of cotton plants with R. solani. Functional categorization analysis indicated that these DAPs can be divided into 12 subclasses. Notably, a large portion of DAPs are known to function in reactive oxygen species (ROS) metabolism and the expression of several histone-modifying and DNA methylating proteins were significantly induced upon challenge with the fungus, indicating that the redox homeostasis and epigenetic regulation are important for cotton defence against the pathogen. Additionally, the expression of proteins involved in phenylpropanoid biosynthesis was markedly changed in response to pathogen invasion, which may reflect a particular contribution of secondary metabolism in protection against the fungal attack in cotton. Together, our results indicate that the defence response of cotton plants to R. solani infection is active and multifaceted and involves the induction of proteins from various innate immunity-related pathways. SIGNIFICANCE Cotton damping-off is a destructive disease caused by the necrotrophic fungus Rhizoctonia solani. To date, the host defence mechanism involved in the disease protection remains largely unknown. Here, we reported the first proteomic analysis on cotton immune responses against R. solani infection. Employing iTRAQ technique, we obtained a total of 174 differentially accumulated proteins (DAPs) that can be classified into 12 functional groups. Further analysis indicated that ROS homeostasis, epigenetic regulation and phenylpropanoid biosynthesis were tightly associated with the innate immune responses against R. solani infection in cotton. The obtained data provide not only important information for understanding the molecular mechanism involved in plant-R. solani interaction but also application clues for genetic breeding of crops with improved R. solani resistance.
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Affiliation(s)
- Min Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Plant Genomics, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shou-Ting Cheng
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Plant Genomics, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hai-Yun Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Plant Genomics, Beijing 100101, China
| | - Jia-He Wu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Plant Genomics, Beijing 100101, China
| | - Yuan-Ming Luo
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Microbial Resources, Beijing 100101, China
| | - Qian Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Microbial Resources, Beijing 100101, China
| | - Fu-Xin Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Plant Genomics, Beijing 100101, China.
| | - Gui-Xian Xia
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Plant Genomics, Beijing 100101, China.
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25
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Anderson JP, Hane JK, Stoll T, Pain N, Hastie ML, Kaur P, Hoogland C, Gorman JJ, Singh KB. Mass-spectrometry data for Rhizoctonia solani proteins produced during infection of wheat and vegetative growth. Data Brief 2016; 8:267-71. [PMID: 27331100 PMCID: PMC4906030 DOI: 10.1016/j.dib.2016.05.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/11/2016] [Accepted: 05/19/2016] [Indexed: 11/02/2022] Open
Abstract
Rhizoctonia solani is an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato, legumes and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about how R. solani causes disease. The data described in this article is derived from applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Comparisons of the data for sample types in this set will be useful to identify metabolic pathway changes as the fungus switches from saprophytic to a pathogenic lifestyle or pathogenicity related proteins contributing to the ability to cause disease on wheat. The data set is deposited in the PRIDE archive under identifier PRIDE: PXD002806.
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Affiliation(s)
- Jonathan P Anderson
- CSIRO Agriculture, Floreat, Western Australia; The University of Western Australia Institute of Agriculture, Crawley, Western Australia
| | | | - Thomas Stoll
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Marcus L Hastie
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Christine Hoogland
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Jeffrey J Gorman
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Karam B Singh
- CSIRO Agriculture, Floreat, Western Australia; The University of Western Australia Institute of Agriculture, Crawley, Western Australia
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