Cultural Characteristics, Genetic Diversity and Population Structure Analysis of an Emerging False Smut Pathogen Ustilaginoidea Virens Collected from Different Agro Climatic Zones of India

Abstract

Abstract Rice false smut (RFS) instigated by the fungus Ustilaginoidea virens, has emerged as one of the most devastating grain diseases in the mainstream of rice-planting regions worldwide. A total of fifty six distinct isolates of Ustilaginoidea virens collected from different states of India were characterized morphologically and also at molecular level. Isolates showed variation in the size of the spore, color of mycelium and shape of the hyphae. The spores were globose, irregularly round to elliptical and warty on the surface with diameters ranging from 4.12 to 6.34 µm. The maximum colony diameter was found in Telangana isolate Uv305 (66.00 mm) and minimum was in Uttar Pradesh isolate Uv214 (17.50 mm). Genetic Diversity was analyzed by using 12 SSR primers out of which 7 were found to be polymorphic The number of alleles per locus vary from 5 to10. The maximum number of polymorphism was shown by UvSSR97 followed by UVSSR79, UvSSR226 and Uv SSR276 while least polymorphism was observed in UvSSR107, and Uv163 primer. The Dendrogram generated based on polymorphic data revealed a considerable amount of diversity by grouping the isolates in five clusters. The PIC ranged from 0.079 to 0.900. The value of Shannon information index ranged from 2.99 to 4.52. The pairwise population fixation index (FST) value also indicated significant genetic variation among all compared geographical populations. All the isolates could be grouped into three groups according to their genetic structure confirmed through model based cluster algorithm using STRUCTURE v2.3.4. This in-depth understanding of U. virens population structure and diversity holds valuable implications for effectively managing rice false smut disease on a comprehensive scale.