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Fu R, Chen C, Wang J, Liu Y, Zhao L, Lu D. Diversity Analysis of the Rice False Smut Pathogen Ustilaginoidea virens in Southwest China. J Fungi (Basel) 2022; 8:1204. [PMID: 36422026 PMCID: PMC9694781 DOI: 10.3390/jof8111204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 04/10/2024] Open
Abstract
Rice false smut caused by Ustilaginoidea virens is a destructive disease in rice cropping areas of the world. The present study is focused on the morphology, pathogenicity, mating-type loci distribution, and genetic characterization of different isolates of U. virens. A total of 221 strains of U. virens were collected from 13 rice-growing regions in southwest China. The morphological features of these strains exhibited high diversity, and the pathogenicity of the smut fungus showed significant differentiation. There was no correlation between pathogenicity and sporulation. Mating-type locus (MAT) analysis revealed that all 221 isolates comprised heterothallic and homothallic forms, wherein 204 (92.31%) and 17 (7.69%) isolates belonged to heterothallic and homothallic mating types, respectively. Among 204 strains of heterothallic mating types, 62 (28.05%) contained MAT1-1-1 idiomorphs, and 142 isolates (64.25%) had the MAT1-2-1 idiomorph. Interestingly, strains isolated from the same fungus ball had different mating types. The genetic structure of the isolates was analyzed using simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNPs). All isolates were clustered into five genetic groups. The values of Nei's gene diversity (H) and Shannon's information index (I) indicated that all strains as a group had higher genetic diversity than strains from a single geographical population. The pairwise population fixation index (FST) values also indicated significant genetic differentiation among all compared geographical populations. The analysis of molecular variation (AMOVA) indicated greater genetic variation within individual populations and less genetic variation among populations. The results showed that most of the strains were not clustered according to their geographical origin, showing the rich genetic diversity and the complex and diverse genetic background of U. virens in southwest China. These results should help to better understand the biological and genetic diversity of U. virens in southwest China and provide a theoretical basis for building effective management strategies.
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Affiliation(s)
- Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, 20# Jingjusi Rd., Chengdu 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, 20# Jingjusi Rd., Chengdu 610066, China
- 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, 20# Jingjusi Rd., Chengdu 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Yao Liu
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China
| | - Liyu Zhao
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, 20# Jingjusi Rd., Chengdu 610066, China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, 20# Jingjusi Rd., Chengdu 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
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Fang A, Fu Z, Wang Z, Fu Y, Qin Y, Bai Z, Tan Z, Cai J, Yang Y, Yu Y, Sun W, Bi C. Genetic Diversity and Population Structure of the Rice False Smut Pathogen Ustilaginoidea virens in the Sichuan-Chongqing Region. PLANT DISEASE 2022; 106:93-100. [PMID: 34340563 DOI: 10.1094/pdis-04-21-0750-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rice false smut caused by Ustilaginoidea virens is one of the most devastating fungal diseases of rice panicles worldwide. In this study, two novel molecular markers derived from single nucleotide polymorphism-rich genomic DNA fragments and a previously reported molecular marker were used for analyzing the genetic diversity and population structure of 167 U. virens isolates collected from nine areas in the Sichuan-Chongqing region, China. A total of 62 haplotypes were identified, and a few haplotypes with high frequency were found and distributed in two to three areas, suggesting gene flow among different geographical populations. All isolates were divided into six genetic groups. Groups I and VI were the largest, with 61 and 48 isolates, respectively. The pairwise FST values showed significant genetic differentiation among all compared geographical populations. Analysis of molecular variance showed that intergroup genetic variation accounted for 40.17% of the total genetic variation, while 59.83% of genetic variation came from intragroup genetic variation. The unweighted pair-group method with arithmetic means dendrogram and population structure revealed that the genetic composition of isolates collected from Santai, Nanchong, Yongchuan, and Wansheng dominated by the same genetic subgroup was different from those collected from other areas. In addition, genetic recombination was found in a few isolates. These findings will help to improve the strategies for rice false smut management and resistance breeding, such as evaluating breeding lines with different isolates or haplotypes at different elevations and landforms.
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Affiliation(s)
- Anfei Fang
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Zhuangyuan Fu
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Zexiong Wang
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Yuhang Fu
- Sericulture Station of Chongqing, Chongqing 400020, China
| | - Yubao Qin
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Zhenxu Bai
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Ze Tan
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Junsong Cai
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Yuheng Yang
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Yang Yu
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Wenxian Sun
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Chaowei Bi
- College of Plant Protection, Southwest University, Chongqing 400715, China
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