Genetic diversity and population structure analysis of rice false smut pathogen in North India using molecular markers

False smut, caused by Ustilaginoidea virens, is one of the emerging diseases of rice in the world. The fungi show a high degree of morphological and cultural variability and produce diverse symptoms. India is a vast country with 44-million-ha rice production area and has only one report on genetic diversity and population analysis of U. virens from the eastern and north-eastern region. Ten polymorphic RAPD and 21 SSR markers were used to analyse the genetic diversity and population structure of 81 isolates of U. virens from northern India, the second largest rice-growing region. In this study, higher Polymorphic Information Content (PIC) and Quality Nature of Data (QND) data in simple-sequence repeats (SSR) markers over random amplified polymorphic DNA (RAPD) revealed its higher efficacy; thus, SSR markers are highly informative and can help to dissect the genetic structures of U. virens. All markers yielded a total of 180 alleles with 1.0 effective alleles per loci. Genetic diversity ranged from 0.1 to 0.39. The principal coordinate analysis (PCoA), and structure analysis identified two genetic clusters of U. virens isolates with some degree of distinctness according to locations. But clusters, PCoA and structure analysis did not group the isolates according to their geographical origin and this may be due to high gene flow (Nm = 1.14).