Genetic diversity and population structure analysis of isolates of the rice false smut pathogen Ustilaginoidea virens in India

Abstract

Genetic diversity assessment and population structure analysis are essential for characterization of pathogens and their isolates. Markers are essential tools for exploring genetic variation among the isolates. False smut of rice caused by Ustilaginoidea virens, formerly Villosiclava virens, is a major emerging disease of rice in India. A high level of variability is observed at the field level, but no information is available from India on genetic diversity and population structure. This is the first report of genetic diversity and population structure of U. virens from India that included 63 isolates distributed across the vast geographical area of eastern and north‐eastern India (18.9 to 26.7°N and 82.6 to 94.2°E). Seventeen RAPDs and 14 SSRs were identified as polymorphic and a total of 140 alleles were detected across the populations. The average number of alleles per locus for each primer was 4.5. All the isolates were grouped into two major clusters, with partial geographical segregation that was supported by principal coordinate analysis. Mantel test suggested genetic distance within the isolates increased with increasing geographical distance. Analysis of molecular variation showed more genetic variation within populations and less among populations. This outcome will help in understanding genetic diversity of U. virens from eastern and north‐eastern India and in planning effective management strategies.

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

“…Only two sub‐populations, that is the maximum value of ∆K = 2 was found on analysis of RAPD and SSR obtained data. Bag, Ray, et al (2021), Bag, Basak, et al (2021) also observed two sub‐populations during the analysis of U . virens isolates collected from eastern and north‐eastern India.…”

“…Recently, in one study on U . virens populations from eastern and north‐eastern India have also shown 60% similarities (Bag et al, 2021; Bag, Ray, et al, 2021). Jia et al, 2015, also used 19 SSR markers for diversity analysis of 87 U .…”

“…Isolation and purification of each isolate of U . virens was done following the modified method developed by Bag, Ray, et al (2021), Bag, Basak, et al (2021). False smut balls were first surface sterilized in the 4% sodium hypochlorite (NaOCl) for 3 min followed by washing with sterile double‐distilled water three times.…”

Alterations to the Physico-Chemical Properties of Rice Grain upon Infection by False Smut Disease and Challenge Inoculation by the Native Bioagents

“…RFS was initially identified by Cooke in 1878 in Tirunelveli, Tamil Nadu, India, and was considered a minor and sporadic disease limited to a few areas [2]. Interestingly, RFS was commonly referred to as the "Laxmi-buti" disease, symbolizing a bountiful harvest and prosperity associated with the goddess of wealth and prosperity [3].…”

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 (Cooke) Takah (teleomorph Villosiclava virens ) infecting rice spikelets, is currently a devastating fungal disease [ 1 , 2 , 3 , 4 ]. In recent years, the disease has occurred all over the world, and the outbreak has been more frequent and increasing year by year in rice-producing areas in China [ 5 , 6 , 7 , 8 ]. According to statistics, from 2008 to 2016, the annual average area of false smut in China reached 3.062 million hectares, resulting in an average annual yield loss of 158.6 million kilograms [ 8 ].…”