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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). [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Nowadays, false smut of rice, caused by Ustilaginoidea virens, is a disease of interest in the world. Presently, its traditional status as 'minor disease' has changed with widespread reports of severity from all the rice growing countries of the world. While many reports are available on the yield loss from the disease, little is known of its effect on grain quality. The present study is planned mainly to evaluate the effect of false smut disease on grain quality of different rice varieties from India. False smut had significant effect on yield (loss of 0.7–8.6%), cooking and nutritional qualities of many popular Indian varieties. Significant changes (p < 0.05) in qualitative characters like hulling, milling, head rice recovery, kernel length after cooking, alkali spreading value, water uptake capacity and gel consistency were observed. Nutritional qualities like total protein content were variable within the 'healthy' varieties as well as within the 'diseased' varieties but the reduction of protein content in diseased grains over healthy was not significant. Amylose content and total phenol were found to be significantly high (p < 0.01) whereas antioxidant activities were significantly low (p < 0.01) in 'diseased' grains. All these changes in different quality parameters are emphasizing the impact of the disease on nutritional properties. This report is first of its kind from India and provides a template for further in-depth study to combat the disease so as to restrict yield loss and maintenance of rice grain quality. [Display omitted] • Yield loss due to False Smut (FS) disease of rice ranges 0.01–8.6%. • Yield loss% due to FS was higher in susceptible whereas lower in resistant rice varieties. • Hulling%, KLAC, ER, WU were significantly reduced in diseased rice grain (p < 0.05). • Antioxidant and protein were significantly low in diseased rice grain (p < 0.05). • Amylose and phenol were significantly high in diseased rice grains (p < 0.05). [ABSTRACT FROM AUTHOR]