Genetic Diversity and Population Structure of the Rice False Smut Pathogen Ustilaginoidea virens in the Sichuan-Chongqing Region

Understanding the Genetic Diversity and Population Structure of Indian Isolates of Ustilaginoidea virens

False smut caused by Ustilaginoidea virens is an emerging disease of rice in India. The disease is causing economic loss to farmers through the reduction of yield and quality of rice. To devise a suitable approach to manage the disease effectively, an understanding of the genetic diversity and population structure of the pathogen is essential. Hence, a total of 34 isolates of U. virens obtained from different locations in India were characterized using 25 genomes-specific SSR markers showing higher polymorphic information content (PIC) that produced 203 alleles with a mean of 8.12 per marker. The genetic diversity varied from 0.00 to 0.885 with an average of 0.673. Based on the phylogenetic tree, the 34 isolates of U. virens were grouped into two major clusters (Cluster I and Cluster II). Cluster I included isolates from Andhra Pradesh, Bihar, Kerala, Manipur, Mizoram, Punjab, and West Bengal, while Cluster II included isolates from Assam, Manipur, Meghalaya, and Odisha. The isolates from the same/nearby locations were partially assembled into the same cluster. The analysis of molecular variance (AMOVA) showed the highest variation of 86% found among the individuals while the least variation of 14% was observed between the populations. The population structures of 34 isolates of U. virens evaluated using STRUCTURE and Principal coordinates analysis (PCoA) separated the 34 isolates into two distinct subpopulations. The high genetic variation in the isolates indicated their substantial potential to evolve and mutate, potentially causing damage to rice crops in future.

Biology, Pathogenicity, and Genetic Diversity of the Rice Pathogen Ustilaginoidea virens in Heilongjiang Province, China

Rice false smut (RFS) is pervasive and has emerged as the primary disease affecting rice productivity. Due to the lack of effective chemical control, disease-resistant varieties are the primary method of managing the disease. This study aimed to investigate the influence of biological characteristics such as hyphal growth rate, spore production and germination ability on the pathogenicity of Ustilaginoidea virens. The genetic diversity of 86 U. virens isolates was analyzed, and the tolerant varieties were identified using Rep-PCR molecular markers. The results indicated that among the U. virens isolates analyzed, about 31, 27 and 28 strains exhibited fast, medium and slow mycelium growth rates, respectively. Among the U. virens isolates analyzed, about 33, 27 and 26 strains exhibited strong, medium and weak sporulation abilities, respectively. In addition, among the U. virens isolates analyzed, about 29, 30 and 27 strains exhibited strong, medium and weak spore germination, respectively. No significant correlation was noted between mycelium growth rate and pathogenicity, but sporulation ability, spore germination ability and liquid culture were positively correlated (p < 0.05). Moreover, the genetic structure of U. virens was diverse and complex. There was a significant correlation between the genetic differentiation and pathogenicity of U. virens in Heilongjiang Province, China, with a maximum coefficient of 0.1786 and a minimum coefficient of 0.0129 between Harbin and Suihua, but no significant correlation was found with gene groups or geographical regions. The study found that genes and geographical population variation were primarily within the population, with 95.63% and 4.37% variation (p > 0.05), respectively, while pathogenicity population variation was mainly within the population, with 86.08% and 13.92% variation (p > 0.05), respectively. Pathogenicity had a significant effect on the differentiation of U. virens. Most rice varieties were susceptible, with 3 resistant, 8 moderately resistant, 9 moderately susceptible, 8 susceptible and 12 highly susceptible to RFS disease. Collectively, these results indicate that the tolerance of rice against U. virens is poor, which merits further investigation.

Sensitivity Baselines, Resistance Monitoring, and Molecular Mechanisms of the Rice False Smut Pathogen Ustilaginoidea virens to Prochloraz and Azoxystrobin in Four Regions of Southern China

Rice false smut caused by Ustilaginoidea virens is one of the most devastating fungal diseases of rice (Oryza sativa) worldwide. Prochloraz and azoxystrobin belong to the groups of demethylation inhibitors and quinone outside inhibitors, respectively, and are commonly used for controlling this disease. In this study, we analyzed the sensitivities of 100 U. virens isolates from Yunnan, Sichuan, Chongqing, and Zhejiang in Southern China to prochloraz and azoxystrobin. The ranges of EC50 for prochloraz and azoxystrobin were 0.004-0.536 and 0.020-0.510 μg/mL, with means and standard errors of 0.062 ± 0.008 and 0.120 ± 0.007 μg/mL, respectively. However, the sensitivity frequency distributions of U. virens to prochloraz and azoxystrobin indicated the emergence of subpopulations with decreased sensitivity. Therefore, the mean EC50 values of 74% and 68% of the isolates at the main peak, 0.031 ± 0.001 and 0.078 ± 0.004 μg/mL, were used as the sensitivity baselines of U. virens to prochloraz and azoxystrobin, respectively. We found significant sensitivity differences to azoxystrobin among different geographical populations and no correlation between the sensitivities of U. virens to prochloraz and azoxystrobin. Among 887 U. virens isolates, the isolate 5-3-1 from Zhejiang showed moderate resistance to prochloraz, with a resistance factor of 22.45, while no nucleotide variation in the 1986-bp upstream or 1827-bp gene regions of CYP51 from 5-3-1 was detected. Overexpression of CYP51 is probably responsible for its resistance to prochloraz. Finally, artificial inoculation showed that 5-3-1 was highly pathogenic to rice, suggesting that the resistance of U. virens to prochloraz must be monitored and managed in Zhejiang.

Genetic Diversity and Pathogenic Variation of the Rice False Smut Pathogen Ustilaginoidea virens from Different Rice Cultivars

Rice false smut, caused by Ustilaginoidea virens, has become one of the most devastating grain diseases of rice worldwide. Understanding the genetic diversity of U. virens is essential for efficient disease control and breeding for disease resistance. However, little is known about the genetic variation of U. virens from different rice cultivars. We investigated the genetic diversity and pathogenic variation of U. virens isolates from 10 rice cultivars in Zhejiang, China. A total of 260 polymorphic loci and 27 haplotypes were identified based on the 2,137-bp combined DNA fragments of all individuals; hap_4 was the most common haplotype, represented by 41 isolates. Phylogeny indicated that all isolates were divided into four genetic groups. Group I was the largest, with 98 isolates, distributed mainly in eight cultivar populations, whereas 90% of the isolates collected from a Changxiang cultivar were clustered in Group IV. Furthermore, the pairwise F_ST values exhibited significant genetic differentiation in 27 of the pairwise comparisons between populations, accounting for 23.21% of the total genetic variation. The genetic composition of the isolates of the CX population was distinguishable from that of the other nine populations, and genetic recombination was found in a few isolates. Finally, 27 haplotype representative isolates showed high variation in pathogenicity, and the isolates from the genetic subpopulation I were likely to be more virulent than those from genetic subpopulations II and III. Collectively, these findings suggest that differences in rice cultivars play an important role in the genetic variation of U. virens.

Diversity Analysis of the Rice False Smut Pathogen Ustilaginoidea virens in Southwest China

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.

Characterization of Genetic Diversity and Variation in Pathogenicity of the Rice False Smut Pathogen Ustilaginoidea virens from a Single Source

Rice false smut, caused by Ustilaginoidea virens, is one of the most destructive fungal diseases in rice-growing countries. Studies of the genetic diversity, evolution, and pathogenicity of U. virens can provide more information for disease control and cultivar breeding. Contrary to previous studies on the genetic diversity of different geographical populations of U. virens, this study analyzed the genetic variation of U. virens from different panicles of the same rice cultivar in a field in Yunnan Province using single nucleotide polymorphism molecular markers. A total of 183 polymorphic loci and five haplotypes, hap_1 to hap_5, were identified based on the 1,350-bp combined DNA fragment of 127 isolates, showing some genetic diversity. Hap_1 and hap_3 had the highest occurrence, indicating they were the dominant haplotypes in the field. Further analysis showed that most rice panicles could be coinfected by different haplotypes, and even a few spikelets could be coinfected by multiple haplotypes. The phylogeny indicated that all isolates were divided into five genetic groups. Groups I, II, and III clustered together and were distinguished from Groups IV and V. Significant genetic variations in five pairwise comparisons of panicle populations, accounting for 72.45% of the total variation, were found according to F_ST values. This variation might be caused by different field microenvironments and the uneven distribution of inoculum sources. An unweighted pair-group method with arithmetic means dendrogram and the population structure revealed that the genetic composition of the isolates collected from YN1, YN2, and YN4, which were dominated by the same genetic subgroup, was different from that collected from YN3. Finally, genetic recombination was found in 11 isolates; hap_2 and hap_5, probably as genetic recombination progenies produced by sexual hybridization between hap_1 and hap_3, acquired a greater virulence than their ancestors according to population structure and pathogenicity analyses. These results will help us understand the genetic diversity, evolution, and infection process of U. virens and aid in the development of more effective management strategies for rice false smut, including new cultivars with improved resistance.