1
|
Zhou L, Mubeen M, Iftikhar Y, Zheng H, Zhang Z, Wen J, Khan RAA, Sajid A, Solanki MK, Sohail MA, Kumar A, Massoud EES, Chen L. Rice false smut pathogen: implications for mycotoxin contamination, current status, and future perspectives. Front Microbiol 2024; 15:1344831. [PMID: 38585697 PMCID: PMC10996400 DOI: 10.3389/fmicb.2024.1344831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/06/2024] [Indexed: 04/09/2024] Open
Abstract
Rice serves as a staple food across various continents worldwide. The rice plant faces significant threats from a range of fungal, bacterial, and viral pathogens. Among these, rice false smut disease (RFS) caused by Villosiclava virens is one of the devastating diseases in rice fields. This disease is widespread in major rice-growing regions such as China, Pakistan, Bangladesh, India, and others, leading to significant losses in rice plantations. Various toxins are produced during the infection of this disease in rice plants, impacting the fertilization process as well. This review paper lightens the disease cycle, plant immunity, and infection process during RFS. Mycotoxin production in RFS affects rice plants in multiple ways, although the exact phenomena are still unknown.
Collapse
Affiliation(s)
- Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Mustansar Mubeen
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Yasir Iftikhar
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Hongxia Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenhao Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junli Wen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | | | - Ashara Sajid
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Muhammad Aamir Sohail
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ajay Kumar
- Amity University of Biotechnology, Amity University, Noida, India
| | - Ehab El Sayed Massoud
- Biology Department, Faculty of Science and Arts in Dahran Aljnoub, King Khalid University, Abha, Saudi Arabia
| | - Liezhong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
2
|
Fu R, Zhao L, Chen C, Wang J, Lu D. Conjunctive Analysis of BSA-Seq and SSR Markers Unveil the Candidate Genes for Resistance to Rice False Smut. Biomolecules 2024; 14:79. [PMID: 38254679 PMCID: PMC10813778 DOI: 10.3390/biom14010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Rice false smut (RFS) caused by the fungus Ustilaginoidea virens (Cook) leads to serious yield losses in rice. Identification of the gene or quantitative trait loci (QTLs) is crucial to resistance breeding and mitigation of RFS damage. In this study, we crossed a resistant variety, IR77298-14-1-2::IRGC117374-1, with a susceptible indica cultivar, 9311, and evaluated recombinant inbred lines in a greenhouse. The genetic analysis showed that the RFS resistance of IR77298-14-1-2::IRGC117374-1 was controlled by multiple recessive loci. We identified a novel QTL, qRFS12.01, for RFS resistance in IR77298-14-1-2::IRGC117374-1 by combining bulked segregant analysis with whole genome resequencing (BSA-seq) and simple sequence repeat (SSR) marker mapping approaches. The phenotypic effect of qRFS12.01 on RFS resistance reached 28.74%, suggesting that SSR markers linked to qRFS12.01 are valuable for marker-assisted breeding of RFS resistance in rice. The prediction of putative candidate genes within qRFS12.01 revealed five disease resistance proteins containing NB-ARC domains. In conclusion, our findings provide a new rice chromosome region carrying genes/QTLs for resistance to RFS.
Collapse
Affiliation(s)
- Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Liyu Zhao
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
| | - Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Jian Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu 610066, China; (R.F.)
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| |
Collapse
|
3
|
Simon EV, Hechanova SL, Hernandez JE, Li CP, Tülek A, Ahn EK, Jairin J, Choi IR, Sundaram RM, Jena KK, Kim SR. Available cloned genes and markers for genetic improvement of biotic stress resistance in rice. Front Plant Sci 2023; 14:1247014. [PMID: 37731986 PMCID: PMC10507716 DOI: 10.3389/fpls.2023.1247014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023]
Abstract
Biotic stress is one of the major threats to stable rice production. Climate change affects the shifting of pest outbreaks in time and space. Genetic improvement of biotic stress resistance in rice is a cost-effective and environment-friendly way to control diseases and pests compared to other methods such as chemical spraying. Fast deployment of the available and suitable genes/alleles in local elite varieties through marker-assisted selection (MAS) is crucial for stable high-yield rice production. In this review, we focused on consolidating all the available cloned genes/alleles conferring resistance against rice pathogens (virus, bacteria, and fungus) and insect pests, the corresponding donor materials, and the DNA markers linked to the identified genes. To date, 48 genes (independent loci) have been cloned for only major biotic stresses: seven genes for brown planthopper (BPH), 23 for blast, 13 for bacterial blight, and five for viruses. Physical locations of the 48 genes were graphically mapped on the 12 rice chromosomes so that breeders can easily find the locations of the target genes and distances among all the biotic stress resistance genes and any other target trait genes. For efficient use of the cloned genes, we collected all the publically available DNA markers (~500 markers) linked to the identified genes. In case of no available cloned genes yet for the other biotic stresses, we provided brief information such as donor germplasm, quantitative trait loci (QTLs), and the related papers. All the information described in this review can contribute to the fast genetic improvement of biotic stress resistance in rice for stable high-yield rice production.
Collapse
Affiliation(s)
- Eliza Vie Simon
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
- Institute of Crop Science (ICropS), University of the Philippines Los Baños, Laguna, Philippines
| | - Sherry Lou Hechanova
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
| | - Jose E. Hernandez
- Institute of Crop Science (ICropS), University of the Philippines Los Baños, Laguna, Philippines
| | - Charng-Pei Li
- Taiwan Agricultural Research Institute (TARI), Council of Agriculture, Taiwan
| | - Adnan Tülek
- Trakya Agricultural Research Institute, Edirne, Türkiye
| | - Eok-Keun Ahn
- National Institute of Crop Science, Rural Development Administration (RDA), Republic of Korea
| | - Jirapong Jairin
- Division of Rice Research and Development, Rice Department, Bangkok, Thailand
| | - Il-Ryong Choi
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
- National Institute of Crop Science, Rural Development Administration (RDA), Republic of Korea
| | - Raman M. Sundaram
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - Kshirod K. Jena
- School of Biotechnology, KIIT Deemed University, Bhubaneswar, Odisha, India
| | - Sung-Ryul Kim
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
| |
Collapse
|
4
|
Yang D, He N, Huang F, Jin Y, Li S. The Genetic Mechanism of the Immune Response to the Rice False Smut (RFS) Fungus Ustilaginoidea virens. Plants (Basel) 2023; 12:741. [PMID: 36840089 PMCID: PMC9961370 DOI: 10.3390/plants12040741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Rice false smut (RFS), which is caused by Ustilaginoidea virens (U. virens), has become one of the most devastating diseases in rice-growing regions worldwide. The disease results in a significant yield loss and poses health threats to humans and animals due to producing mycotoxins. In this review, we update the understanding of the symptoms and resistance genes of RFS, as well as the genomics and effectors in U. virens. We also highlight the genetic mechanism of the immune response to RFS. Finally, we analyse and explore the identification method for RFS, breeding for resistance against the disease, and interactions between the effector proteins and resistance (R) proteins, which would be involved in the development of rice disease resistance materials for breeding programmes.
Collapse
Affiliation(s)
- Dewei Yang
- Institute of Rice, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Niqing He
- Institute of Rice, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Fenghuang Huang
- Institute of Rice, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Yidan Jin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shengping Li
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
5
|
Huang Y, Cui K, Zhang Z, Chai R, Xie H, Shou J, Fu J, Li G, Liu J, Wu S, Sun G, Zhang J, Deng Y, He Z. Identification and fine-mapping of quantitative trait loci (QTL) conferring rice false smut resistance in rice. J Genet Genomics 2022; 50:276-279. [PMID: 36496169 DOI: 10.1016/j.jgg.2022.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Yifeng Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Kaixuan Cui
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Rongyao Chai
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Hongguang Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, China
| | - Jianyao Shou
- Shaoxing Agricultural Technology Promotion Center, Shaoxing, Zhejiang 311800, China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Guolin Li
- Pingxiang Academy of Agricultural Sciences, Pingxiang, Jiangxi 337099, China
| | - Jiyun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shuangqing Wu
- Enshi Academy of Agricultural Sciences, Enshi, Hubei 445002, China
| | - Guochang Sun
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China.
| | - Jianfu Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, China.
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| |
Collapse
|
6
|
Wang Y, Yang L, Yang Q, Dong J, Wang Y, Duan Y, Yin W, Zheng L, Sun W, Fan J, Luo CX, Li G. Gap-Free Nuclear and Mitochondrial Genomes of Ustilaginoidea virens JS60-2, a Fungal Pathogen Causing Rice False Smut. Mol Plant Microbe Interact 2022; 35:1120-1123. [PMID: 36510363 DOI: 10.1094/mpmi-07-22-0158-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Rice false smut (RFS), caused by Ustilaginoidea virens, has become a major disease in recent years, and mycotoxins produced by U. virens often threaten food safety. To study fungal pathogenesis and identify potential targets for developing new fungicides, gap-free nuclear and complete mitochondrial genomes of U. virens JS60-2 were sequenced and assembled. Using the second and third generation sequencing data, we assembled a 38.02-Mb genome that consists of seven contigs with the contig N50 being 6.32-Mb. In total, 8,486 protein-coding genes were annotated in the genome, including 21 secondary metabolism gene clusters. We also assembled the complete mitochondrial genome, which is 102,498 bp, with 28% GC content. The JS60-2 genomes assembled in this study will facilitate research on U. virens and contribute to RFS control. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Yin Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Yang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qun Yang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Dong
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yufu Wang
- Key Lab of Horticultural Plant Biology, Ministry of Education, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuhang Duan
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weixiao Yin
- Key Lab of Horticultural Plant Biology, Ministry of Education, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu Zheng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenxian Sun
- College of Plant Protection and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, 100193, China
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Chao-Xi Luo
- Key Lab of Horticultural Plant Biology, Ministry of Education, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guotian Li
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|